%1 services

Through this project, we will continue building on the DOME recommendations, expanding them in scope, while also creating a concrete framework to increase adoption and overall impact of the DOME recommendations, looking both within ELIXIR and beyond.

The project will engage in the following three complementary activities:

1. Implement a framework around the DOME recommendations, including a registry to capture DOME-related information from existing and future literature, and a low-barrier software tool that will allow for the easy creation of DOME annotation by the wider community.
2. Review and connect the DOME recommendations in light of the particular needs, requirements and expectations of relevant ELIXIR communities, thus establishing a pathway towards adoption. 
3. Create a clear engagement plan to stakeholders beyond ELIXIR, linking to relevant global efforts and initiatives, including the RDA ML interest groups, the NIH AI activities and efforts in Industry (such as the Pistoia Alliance).

Through this project, we will continue building on the DOME recommendations, expanding them in scope, while also creating a concrete framework to increase adoption and overall impact of the DOME recommendations, looking both within ELIXIR and beyond.

The project will engage in the following three complementary activities:

1. Implement a framework around the DOME recommendations, including a registry to capture DOME-related information from existing and future literature, and a low-barrier software tool that will allow for the easy creation of DOME annotation by the wider community.
2. Review and connect the DOME recommendations in light of the particular needs, requirements and expectations of relevant ELIXIR communities, thus establishing a pathway towards adoption. 
3. Create a clear engagement plan to stakeholders beyond ELIXIR, linking to relevant global efforts and initiatives, including the RDA ML interest groups, the NIH AI activities and efforts in Industry (such as the Pistoia Alliance).

Through this project, we will continue building on the DOME recommendations, expanding them in scope, while also creating a concrete framework to increase adoption and overall impact of the DOME recommendations, looking both within ELIXIR and beyond.

The project will engage in the following three complementary activities:

1. Implement a framework around the DOME recommendations, including a registry to capture DOME-related information from existing and future literature, and a low-barrier software tool that will allow for the easy creation of DOME annotation by the wider community.
2. Review and connect the DOME recommendations in light of the particular needs, requirements and expectations of relevant ELIXIR communities, thus establishing a pathway towards adoption. 
3. Create a clear engagement plan to stakeholders beyond ELIXIR, linking to relevant global efforts and initiatives, including the RDA ML interest groups, the NIH AI activities and efforts in Industry (such as the Pistoia Alliance).

Through this project, we will continue building on the DOME recommendations, expanding them in scope, while also creating a concrete framework to increase adoption and overall impact of the DOME recommendations, looking both within ELIXIR and beyond.

The project will engage in the following three complementary activities:

1. Implement a framework around the DOME recommendations, including a registry to capture DOME-related information from existing and future literature, and a low-barrier software tool that will allow for the easy creation of DOME annotation by the wider community.
2. Review and connect the DOME recommendations in light of the particular needs, requirements and expectations of relevant ELIXIR communities, thus establishing a pathway towards adoption. 
3. Create a clear engagement plan to stakeholders beyond ELIXIR, linking to relevant global efforts and initiatives, including the RDA ML interest groups, the NIH AI activities and efforts in Industry (such as the Pistoia Alliance).

Through this project, we will continue building on the DOME recommendations, expanding them in scope, while also creating a concrete framework to increase adoption and overall impact of the DOME recommendations, looking both within ELIXIR and beyond.

The project will engage in the following three complementary activities:

1. Implement a framework around the DOME recommendations, including a registry to capture DOME-related information from existing and future literature, and a low-barrier software tool that will allow for the easy creation of DOME annotation by the wider community.
2. Review and connect the DOME recommendations in light of the particular needs, requirements and expectations of relevant ELIXIR communities, thus establishing a pathway towards adoption. 
3. Create a clear engagement plan to stakeholders beyond ELIXIR, linking to relevant global efforts and initiatives, including the RDA ML interest groups, the NIH AI activities and efforts in Industry (such as the Pistoia Alliance).

Through this project, we will continue building on the DOME recommendations, expanding them in scope, while also creating a concrete framework to increase adoption and overall impact of the DOME recommendations, looking both within ELIXIR and beyond.

The project will engage in the following three complementary activities:

1. Implement a framework around the DOME recommendations, including a registry to capture DOME-related information from existing and future literature, and a low-barrier software tool that will allow for the easy creation of DOME annotation by the wider community.
2. Review and connect the DOME recommendations in light of the particular needs, requirements and expectations of relevant ELIXIR communities, thus establishing a pathway towards adoption. 
3. Create a clear engagement plan to stakeholders beyond ELIXIR, linking to relevant global efforts and initiatives, including the RDA ML interest groups, the NIH AI activities and efforts in Industry (such as the Pistoia Alliance).

Through this project, we will continue building on the DOME recommendations, expanding them in scope, while also creating a concrete framework to increase adoption and overall impact of the DOME recommendations, looking both within ELIXIR and beyond.

The project will engage in the following three complementary activities:

1. Implement a framework around the DOME recommendations, including a registry to capture DOME-related information from existing and future literature, and a low-barrier software tool that will allow for the easy creation of DOME annotation by the wider community.
2. Review and connect the DOME recommendations in light of the particular needs, requirements and expectations of relevant ELIXIR communities, thus establishing a pathway towards adoption. 
3. Create a clear engagement plan to stakeholders beyond ELIXIR, linking to relevant global efforts and initiatives, including the RDA ML interest groups, the NIH AI activities and efforts in Industry (such as the Pistoia Alliance).

Through this project, we will continue building on the DOME recommendations, expanding them in scope, while also creating a concrete framework to increase adoption and overall impact of the DOME recommendations, looking both within ELIXIR and beyond.

The project will engage in the following three complementary activities:

1. Implement a framework around the DOME recommendations, including a registry to capture DOME-related information from existing and future literature, and a low-barrier software tool that will allow for the easy creation of DOME annotation by the wider community.
2. Review and connect the DOME recommendations in light of the particular needs, requirements and expectations of relevant ELIXIR communities, thus establishing a pathway towards adoption. 
3. Create a clear engagement plan to stakeholders beyond ELIXIR, linking to relevant global efforts and initiatives, including the RDA ML interest groups, the NIH AI activities and efforts in Industry (such as the Pistoia Alliance).

Through this project, we will continue building on the DOME recommendations, expanding them in scope, while also creating a concrete framework to increase adoption and overall impact of the DOME recommendations, looking both within ELIXIR and beyond.

The project will engage in the following three complementary activities:

1. Implement a framework around the DOME recommendations, including a registry to capture DOME-related information from existing and future literature, and a low-barrier software tool that will allow for the easy creation of DOME annotation by the wider community.
2. Review and connect the DOME recommendations in light of the particular needs, requirements and expectations of relevant ELIXIR communities, thus establishing a pathway towards adoption. 
3. Create a clear engagement plan to stakeholders beyond ELIXIR, linking to relevant global efforts and initiatives, including the RDA ML interest groups, the NIH AI activities and efforts in Industry (such as the Pistoia Alliance).

Through this project, we will continue building on the DOME recommendations, expanding them in scope, while also creating a concrete framework to increase adoption and overall impact of the DOME recommendations, looking both within ELIXIR and beyond.

The project will engage in the following three complementary activities:

1. Implement a framework around the DOME recommendations, including a registry to capture DOME-related information from existing and future literature, and a low-barrier software tool that will allow for the easy creation of DOME annotation by the wider community.
2. Review and connect the DOME recommendations in light of the particular needs, requirements and expectations of relevant ELIXIR communities, thus establishing a pathway towards adoption. 
3. Create a clear engagement plan to stakeholders beyond ELIXIR, linking to relevant global efforts and initiatives, including the RDA ML interest groups, the NIH AI activities and efforts in Industry (such as the Pistoia Alliance).

Through this project, we will continue building on the DOME recommendations, expanding them in scope, while also creating a concrete framework to increase adoption and overall impact of the DOME recommendations, looking both within ELIXIR and beyond.

The project will engage in the following three complementary activities:

1. Implement a framework around the DOME recommendations, including a registry to capture DOME-related information from existing and future literature, and a low-barrier software tool that will allow for the easy creation of DOME annotation by the wider community.
2. Review and connect the DOME recommendations in light of the particular needs, requirements and expectations of relevant ELIXIR communities, thus establishing a pathway towards adoption. 
3. Create a clear engagement plan to stakeholders beyond ELIXIR, linking to relevant global efforts and initiatives, including the RDA ML interest groups, the NIH AI activities and efforts in Industry (such as the Pistoia Alliance).

Through this project, we will continue building on the DOME recommendations, expanding them in scope, while also creating a concrete framework to increase adoption and overall impact of the DOME recommendations, looking both within ELIXIR and beyond.

The project will engage in the following three complementary activities:

1. Implement a framework around the DOME recommendations, including a registry to capture DOME-related information from existing and future literature, and a low-barrier software tool that will allow for the easy creation of DOME annotation by the wider community.
2. Review and connect the DOME recommendations in light of the particular needs, requirements and expectations of relevant ELIXIR communities, thus establishing a pathway towards adoption. 
3. Create a clear engagement plan to stakeholders beyond ELIXIR, linking to relevant global efforts and initiatives, including the RDA ML interest groups, the NIH AI activities and efforts in Industry (such as the Pistoia Alliance).

The provision of tools and services for the life sciences is highly distributed. There are very many providers ranging from large entities including service organizations well geared for software development, to individual scientists with limited technical expertise and resources.

There is often little coordination of the scientific scope, description, use or interoperability of the software. The picture is extremely fragmented and in many cases scientists must trawl the Web
in their search for adequate tools, or rely on the advice of colleagues to comprehend the diverse offerings.

Thus, the creation of a comprehensive, consistent and searchable registry should have a major positive effect on tool utilization by the life sciences community. The current work on creation of such a registry is the principal contribution of the Danish Node to ELIXIR as well as a contribution of ELIXIR as such to the BioMedBridges joint effort on the ESFRI roadmap.

The study is now complete, this work was picked up in a subsequent study. 

The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts.

The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.

The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts.

The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.

The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts.

The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.

The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts.

The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.

The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts.

The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.

The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts.

The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.

The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts.

The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.

This project will be led by the ELIXIR Proteomics Community in collaboration with members of the Metabolomics Community and three ELIXIR platforms. High-throughput proteomics has become a popular choice in biological, biomedical and clinical studies and led to the development of hundreds of bioinformatics tools and data analysis pipelines. Given their large diversity, there is a urgent need to compare and benchmark different software pipelines over a large data spectrum.

This study aims to create the framework to benchmark proteomics data analysis workflows, to be built upon and improve resources from ELIXIR Tool, Data and Compute platforms by creating an interface between them linked with public proteomics data and open source stand-alone software and pipelines.

The involved data will be annotated with at least EOSC minimum information according to ELIXIR metadata standards. Our benchmarking will identify robust workflows and therefore nurture the proteomics community with high quality standards required for reproducible research and clinical applications.

This project will be led by the ELIXIR Proteomics Community in collaboration with members of the Metabolomics Community and three ELIXIR platforms. High-throughput proteomics has become a popular choice in biological, biomedical and clinical studies and led to the development of hundreds of bioinformatics tools and data analysis pipelines. Given their large diversity, there is a urgent need to compare and benchmark different software pipelines over a large data spectrum.

This study aims to create the framework to benchmark proteomics data analysis workflows, to be built upon and improve resources from ELIXIR Tool, Data and Compute platforms by creating an interface between them linked with public proteomics data and open source stand-alone software and pipelines.

The involved data will be annotated with at least EOSC minimum information according to ELIXIR metadata standards. Our benchmarking will identify robust workflows and therefore nurture the proteomics community with high quality standards required for reproducible research and clinical applications.

This project will be led by the ELIXIR Proteomics Community in collaboration with members of the Metabolomics Community and three ELIXIR platforms. High-throughput proteomics has become a popular choice in biological, biomedical and clinical studies and led to the development of hundreds of bioinformatics tools and data analysis pipelines. Given their large diversity, there is a urgent need to compare and benchmark different software pipelines over a large data spectrum.

This study aims to create the framework to benchmark proteomics data analysis workflows, to be built upon and improve resources from ELIXIR Tool, Data and Compute platforms by creating an interface between them linked with public proteomics data and open source stand-alone software and pipelines.

The involved data will be annotated with at least EOSC minimum information according to ELIXIR metadata standards. Our benchmarking will identify robust workflows and therefore nurture the proteomics community with high quality standards required for reproducible research and clinical applications.

This project will be led by the ELIXIR Proteomics Community in collaboration with members of the Metabolomics Community and three ELIXIR platforms. High-throughput proteomics has become a popular choice in biological, biomedical and clinical studies and led to the development of hundreds of bioinformatics tools and data analysis pipelines. Given their large diversity, there is a urgent need to compare and benchmark different software pipelines over a large data spectrum.

This study aims to create the framework to benchmark proteomics data analysis workflows, to be built upon and improve resources from ELIXIR Tool, Data and Compute platforms by creating an interface between them linked with public proteomics data and open source stand-alone software and pipelines.

The involved data will be annotated with at least EOSC minimum information according to ELIXIR metadata standards. Our benchmarking will identify robust workflows and therefore nurture the proteomics community with high quality standards required for reproducible research and clinical applications.

This project will be led by the ELIXIR Proteomics Community in collaboration with members of the Metabolomics Community and three ELIXIR platforms. High-throughput proteomics has become a popular choice in biological, biomedical and clinical studies and led to the development of hundreds of bioinformatics tools and data analysis pipelines. Given their large diversity, there is a urgent need to compare and benchmark different software pipelines over a large data spectrum.

This study aims to create the framework to benchmark proteomics data analysis workflows, to be built upon and improve resources from ELIXIR Tool, Data and Compute platforms by creating an interface between them linked with public proteomics data and open source stand-alone software and pipelines.

The involved data will be annotated with at least EOSC minimum information according to ELIXIR metadata standards. Our benchmarking will identify robust workflows and therefore nurture the proteomics community with high quality standards required for reproducible research and clinical applications.

This project will be led by the ELIXIR Proteomics Community in collaboration with members of the Metabolomics Community and three ELIXIR platforms. High-throughput proteomics has become a popular choice in biological, biomedical and clinical studies and led to the development of hundreds of bioinformatics tools and data analysis pipelines. Given their large diversity, there is a urgent need to compare and benchmark different software pipelines over a large data spectrum.

This study aims to create the framework to benchmark proteomics data analysis workflows, to be built upon and improve resources from ELIXIR Tool, Data and Compute platforms by creating an interface between them linked with public proteomics data and open source stand-alone software and pipelines.

The involved data will be annotated with at least EOSC minimum information according to ELIXIR metadata standards. Our benchmarking will identify robust workflows and therefore nurture the proteomics community with high quality standards required for reproducible research and clinical applications.

This project will be led by the ELIXIR Proteomics Community in collaboration with members of the Metabolomics Community and three ELIXIR platforms. High-throughput proteomics has become a popular choice in biological, biomedical and clinical studies and led to the development of hundreds of bioinformatics tools and data analysis pipelines. Given their large diversity, there is a urgent need to compare and benchmark different software pipelines over a large data spectrum.

This study aims to create the framework to benchmark proteomics data analysis workflows, to be built upon and improve resources from ELIXIR Tool, Data and Compute platforms by creating an interface between them linked with public proteomics data and open source stand-alone software and pipelines.

The involved data will be annotated with at least EOSC minimum information according to ELIXIR metadata standards. Our benchmarking will identify robust workflows and therefore nurture the proteomics community with high quality standards required for reproducible research and clinical applications.

This project will be led by the ELIXIR Proteomics Community in collaboration with members of the Metabolomics Community and three ELIXIR platforms. High-throughput proteomics has become a popular choice in biological, biomedical and clinical studies and led to the development of hundreds of bioinformatics tools and data analysis pipelines. Given their large diversity, there is a urgent need to compare and benchmark different software pipelines over a large data spectrum.

This study aims to create the framework to benchmark proteomics data analysis workflows, to be built upon and improve resources from ELIXIR Tool, Data and Compute platforms by creating an interface between them linked with public proteomics data and open source stand-alone software and pipelines.

The involved data will be annotated with at least EOSC minimum information according to ELIXIR metadata standards. Our benchmarking will identify robust workflows and therefore nurture the proteomics community with high quality standards required for reproducible research and clinical applications.

This project will be led by the ELIXIR Proteomics Community in collaboration with members of the Metabolomics Community and three ELIXIR platforms. High-throughput proteomics has become a popular choice in biological, biomedical and clinical studies and led to the development of hundreds of bioinformatics tools and data analysis pipelines. Given their large diversity, there is a urgent need to compare and benchmark different software pipelines over a large data spectrum.

This study aims to create the framework to benchmark proteomics data analysis workflows, to be built upon and improve resources from ELIXIR Tool, Data and Compute platforms by creating an interface between them linked with public proteomics data and open source stand-alone software and pipelines.

The involved data will be annotated with at least EOSC minimum information according to ELIXIR metadata standards. Our benchmarking will identify robust workflows and therefore nurture the proteomics community with high quality standards required for reproducible research and clinical applications.

The study will convene and establish a consensus on high-level community-driven standards:

• Workflow / Task Orchestration Service: A minimal API specification that will support heterogenous containerised workflow (e.g. CWL, Galaxy, Nextflow, etc.) workloads for secured execution across the ELIXIR Federation of compute/cloud sites.
• Tool / Workflow Registry Service: A minimal API specification that will provide access to curated heterogeneous container formats (e.g. Docker, Singularity) and workflow specifications (e.g. CWL, Galaxy, Nextflow, etc.) to be used as part of the workflow orchestration service.
• Data Repository Service: A minimal API specification that will support the discovery and secured access to ELIXIR Core Data Resources and ELIXIR Node provided datasets as part of the workflow orchestration service.
• Data and Workflow Security Protocols: Embedding security relying on ELIXIR AAI across all ELIXIR APIs to ensure secure access to data, tools and workflows to allow analysis to be performed on sensitive data.

This will be achieved by coordinating the expertise in the ELIXIR Platforms (Compute & Tools) and work taking place within the Nodes and related projects (e.g. EOSC-Life, EOSC-Hub), and will be broken down into three work packages: 

1. Leveraging EOSC-Life workflows infrastructure
2. ELIXIR Infrastructure for Orchestrating Containers and Workflows
3. Coordinating ELIXIR Data Discovery and Transfer Services

and a number of Community Lead Use Cases: 

1. Human data requiring security protocols provided by AAI, and data transfer services
2. Single cell transcriptomics workflow that could be adapted for different organisms
3. Metabolomics workflow adopted by the PhenoMeNal project
4. Proteomics workflow aligning with the IS around benchmarking workflows to ensure reproducible research and potential clinical applications

The study will convene and establish a consensus on high-level community-driven standards:

• Workflow / Task Orchestration Service: A minimal API specification that will support heterogenous containerised workflow (e.g. CWL, Galaxy, Nextflow, etc.) workloads for secured execution across the ELIXIR Federation of compute/cloud sites.
• Tool / Workflow Registry Service: A minimal API specification that will provide access to curated heterogeneous container formats (e.g. Docker, Singularity) and workflow specifications (e.g. CWL, Galaxy, Nextflow, etc.) to be used as part of the workflow orchestration service.
• Data Repository Service: A minimal API specification that will support the discovery and secured access to ELIXIR Core Data Resources and ELIXIR Node provided datasets as part of the workflow orchestration service.
• Data and Workflow Security Protocols: Embedding security relying on ELIXIR AAI across all ELIXIR APIs to ensure secure access to data, tools and workflows to allow analysis to be performed on sensitive data.

This will be achieved by coordinating the expertise in the ELIXIR Platforms (Compute & Tools) and work taking place within the Nodes and related projects (e.g. EOSC-Life, EOSC-Hub), and will be broken down into three work packages: 

1. Leveraging EOSC-Life workflows infrastructure
2. ELIXIR Infrastructure for Orchestrating Containers and Workflows
3. Coordinating ELIXIR Data Discovery and Transfer Services

and a number of Community Lead Use Cases: 

1. Human data requiring security protocols provided by AAI, and data transfer services
2. Single cell transcriptomics workflow that could be adapted for different organisms
3. Metabolomics workflow adopted by the PhenoMeNal project
4. Proteomics workflow aligning with the IS around benchmarking workflows to ensure reproducible research and potential clinical applications

The study will convene and establish a consensus on high-level community-driven standards:

• Workflow / Task Orchestration Service: A minimal API specification that will support heterogenous containerised workflow (e.g. CWL, Galaxy, Nextflow, etc.) workloads for secured execution across the ELIXIR Federation of compute/cloud sites.
• Tool / Workflow Registry Service: A minimal API specification that will provide access to curated heterogeneous container formats (e.g. Docker, Singularity) and workflow specifications (e.g. CWL, Galaxy, Nextflow, etc.) to be used as part of the workflow orchestration service.
• Data Repository Service: A minimal API specification that will support the discovery and secured access to ELIXIR Core Data Resources and ELIXIR Node provided datasets as part of the workflow orchestration service.
• Data and Workflow Security Protocols: Embedding security relying on ELIXIR AAI across all ELIXIR APIs to ensure secure access to data, tools and workflows to allow analysis to be performed on sensitive data.

This will be achieved by coordinating the expertise in the ELIXIR Platforms (Compute & Tools) and work taking place within the Nodes and related projects (e.g. EOSC-Life, EOSC-Hub), and will be broken down into three work packages: 

1. Leveraging EOSC-Life workflows infrastructure
2. ELIXIR Infrastructure for Orchestrating Containers and Workflows
3. Coordinating ELIXIR Data Discovery and Transfer Services

and a number of Community Lead Use Cases: 

1. Human data requiring security protocols provided by AAI, and data transfer services
2. Single cell transcriptomics workflow that could be adapted for different organisms
3. Metabolomics workflow adopted by the PhenoMeNal project
4. Proteomics workflow aligning with the IS around benchmarking workflows to ensure reproducible research and potential clinical applications

The study will convene and establish a consensus on high-level community-driven standards:

• Workflow / Task Orchestration Service: A minimal API specification that will support heterogenous containerised workflow (e.g. CWL, Galaxy, Nextflow, etc.) workloads for secured execution across the ELIXIR Federation of compute/cloud sites.
• Tool / Workflow Registry Service: A minimal API specification that will provide access to curated heterogeneous container formats (e.g. Docker, Singularity) and workflow specifications (e.g. CWL, Galaxy, Nextflow, etc.) to be used as part of the workflow orchestration service.
• Data Repository Service: A minimal API specification that will support the discovery and secured access to ELIXIR Core Data Resources and ELIXIR Node provided datasets as part of the workflow orchestration service.
• Data and Workflow Security Protocols: Embedding security relying on ELIXIR AAI across all ELIXIR APIs to ensure secure access to data, tools and workflows to allow analysis to be performed on sensitive data.

This will be achieved by coordinating the expertise in the ELIXIR Platforms (Compute & Tools) and work taking place within the Nodes and related projects (e.g. EOSC-Life, EOSC-Hub), and will be broken down into three work packages: 

1. Leveraging EOSC-Life workflows infrastructure
2. ELIXIR Infrastructure for Orchestrating Containers and Workflows
3. Coordinating ELIXIR Data Discovery and Transfer Services

and a number of Community Lead Use Cases: 

1. Human data requiring security protocols provided by AAI, and data transfer services
2. Single cell transcriptomics workflow that could be adapted for different organisms
3. Metabolomics workflow adopted by the PhenoMeNal project
4. Proteomics workflow aligning with the IS around benchmarking workflows to ensure reproducible research and potential clinical applications

The study will convene and establish a consensus on high-level community-driven standards:

• Workflow / Task Orchestration Service: A minimal API specification that will support heterogenous containerised workflow (e.g. CWL, Galaxy, Nextflow, etc.) workloads for secured execution across the ELIXIR Federation of compute/cloud sites.
• Tool / Workflow Registry Service: A minimal API specification that will provide access to curated heterogeneous container formats (e.g. Docker, Singularity) and workflow specifications (e.g. CWL, Galaxy, Nextflow, etc.) to be used as part of the workflow orchestration service.
• Data Repository Service: A minimal API specification that will support the discovery and secured access to ELIXIR Core Data Resources and ELIXIR Node provided datasets as part of the workflow orchestration service.
• Data and Workflow Security Protocols: Embedding security relying on ELIXIR AAI across all ELIXIR APIs to ensure secure access to data, tools and workflows to allow analysis to be performed on sensitive data.

This will be achieved by coordinating the expertise in the ELIXIR Platforms (Compute & Tools) and work taking place within the Nodes and related projects (e.g. EOSC-Life, EOSC-Hub), and will be broken down into three work packages: 

1. Leveraging EOSC-Life workflows infrastructure
2. ELIXIR Infrastructure for Orchestrating Containers and Workflows
3. Coordinating ELIXIR Data Discovery and Transfer Services

and a number of Community Lead Use Cases: 

1. Human data requiring security protocols provided by AAI, and data transfer services
2. Single cell transcriptomics workflow that could be adapted for different organisms
3. Metabolomics workflow adopted by the PhenoMeNal project
4. Proteomics workflow aligning with the IS around benchmarking workflows to ensure reproducible research and potential clinical applications

The study will convene and establish a consensus on high-level community-driven standards:

• Workflow / Task Orchestration Service: A minimal API specification that will support heterogenous containerised workflow (e.g. CWL, Galaxy, Nextflow, etc.) workloads for secured execution across the ELIXIR Federation of compute/cloud sites.
• Tool / Workflow Registry Service: A minimal API specification that will provide access to curated heterogeneous container formats (e.g. Docker, Singularity) and workflow specifications (e.g. CWL, Galaxy, Nextflow, etc.) to be used as part of the workflow orchestration service.
• Data Repository Service: A minimal API specification that will support the discovery and secured access to ELIXIR Core Data Resources and ELIXIR Node provided datasets as part of the workflow orchestration service.
• Data and Workflow Security Protocols: Embedding security relying on ELIXIR AAI across all ELIXIR APIs to ensure secure access to data, tools and workflows to allow analysis to be performed on sensitive data.

This will be achieved by coordinating the expertise in the ELIXIR Platforms (Compute & Tools) and work taking place within the Nodes and related projects (e.g. EOSC-Life, EOSC-Hub), and will be broken down into three work packages: 

1. Leveraging EOSC-Life workflows infrastructure
2. ELIXIR Infrastructure for Orchestrating Containers and Workflows
3. Coordinating ELIXIR Data Discovery and Transfer Services

and a number of Community Lead Use Cases: 

1. Human data requiring security protocols provided by AAI, and data transfer services
2. Single cell transcriptomics workflow that could be adapted for different organisms
3. Metabolomics workflow adopted by the PhenoMeNal project
4. Proteomics workflow aligning with the IS around benchmarking workflows to ensure reproducible research and potential clinical applications

The study will convene and establish a consensus on high-level community-driven standards:

• Workflow / Task Orchestration Service: A minimal API specification that will support heterogenous containerised workflow (e.g. CWL, Galaxy, Nextflow, etc.) workloads for secured execution across the ELIXIR Federation of compute/cloud sites.
• Tool / Workflow Registry Service: A minimal API specification that will provide access to curated heterogeneous container formats (e.g. Docker, Singularity) and workflow specifications (e.g. CWL, Galaxy, Nextflow, etc.) to be used as part of the workflow orchestration service.
• Data Repository Service: A minimal API specification that will support the discovery and secured access to ELIXIR Core Data Resources and ELIXIR Node provided datasets as part of the workflow orchestration service.
• Data and Workflow Security Protocols: Embedding security relying on ELIXIR AAI across all ELIXIR APIs to ensure secure access to data, tools and workflows to allow analysis to be performed on sensitive data.

This will be achieved by coordinating the expertise in the ELIXIR Platforms (Compute & Tools) and work taking place within the Nodes and related projects (e.g. EOSC-Life, EOSC-Hub), and will be broken down into three work packages: 

1. Leveraging EOSC-Life workflows infrastructure
2. ELIXIR Infrastructure for Orchestrating Containers and Workflows
3. Coordinating ELIXIR Data Discovery and Transfer Services

and a number of Community Lead Use Cases: 

1. Human data requiring security protocols provided by AAI, and data transfer services
2. Single cell transcriptomics workflow that could be adapted for different organisms
3. Metabolomics workflow adopted by the PhenoMeNal project
4. Proteomics workflow aligning with the IS around benchmarking workflows to ensure reproducible research and potential clinical applications

The study will convene and establish a consensus on high-level community-driven standards:

• Workflow / Task Orchestration Service: A minimal API specification that will support heterogenous containerised workflow (e.g. CWL, Galaxy, Nextflow, etc.) workloads for secured execution across the ELIXIR Federation of compute/cloud sites.
• Tool / Workflow Registry Service: A minimal API specification that will provide access to curated heterogeneous container formats (e.g. Docker, Singularity) and workflow specifications (e.g. CWL, Galaxy, Nextflow, etc.) to be used as part of the workflow orchestration service.
• Data Repository Service: A minimal API specification that will support the discovery and secured access to ELIXIR Core Data Resources and ELIXIR Node provided datasets as part of the workflow orchestration service.
• Data and Workflow Security Protocols: Embedding security relying on ELIXIR AAI across all ELIXIR APIs to ensure secure access to data, tools and workflows to allow analysis to be performed on sensitive data.

This will be achieved by coordinating the expertise in the ELIXIR Platforms (Compute & Tools) and work taking place within the Nodes and related projects (e.g. EOSC-Life, EOSC-Hub), and will be broken down into three work packages: 

1. Leveraging EOSC-Life workflows infrastructure
2. ELIXIR Infrastructure for Orchestrating Containers and Workflows
3. Coordinating ELIXIR Data Discovery and Transfer Services

and a number of Community Lead Use Cases: 

1. Human data requiring security protocols provided by AAI, and data transfer services
2. Single cell transcriptomics workflow that could be adapted for different organisms
3. Metabolomics workflow adopted by the PhenoMeNal project
4. Proteomics workflow aligning with the IS around benchmarking workflows to ensure reproducible research and potential clinical applications

The study will convene and establish a consensus on high-level community-driven standards:

• Workflow / Task Orchestration Service: A minimal API specification that will support heterogenous containerised workflow (e.g. CWL, Galaxy, Nextflow, etc.) workloads for secured execution across the ELIXIR Federation of compute/cloud sites.
• Tool / Workflow Registry Service: A minimal API specification that will provide access to curated heterogeneous container formats (e.g. Docker, Singularity) and workflow specifications (e.g. CWL, Galaxy, Nextflow, etc.) to be used as part of the workflow orchestration service.
• Data Repository Service: A minimal API specification that will support the discovery and secured access to ELIXIR Core Data Resources and ELIXIR Node provided datasets as part of the workflow orchestration service.
• Data and Workflow Security Protocols: Embedding security relying on ELIXIR AAI across all ELIXIR APIs to ensure secure access to data, tools and workflows to allow analysis to be performed on sensitive data.

This will be achieved by coordinating the expertise in the ELIXIR Platforms (Compute & Tools) and work taking place within the Nodes and related projects (e.g. EOSC-Life, EOSC-Hub), and will be broken down into three work packages: 

1. Leveraging EOSC-Life workflows infrastructure
2. ELIXIR Infrastructure for Orchestrating Containers and Workflows
3. Coordinating ELIXIR Data Discovery and Transfer Services

and a number of Community Lead Use Cases: 

1. Human data requiring security protocols provided by AAI, and data transfer services
2. Single cell transcriptomics workflow that could be adapted for different organisms
3. Metabolomics workflow adopted by the PhenoMeNal project
4. Proteomics workflow aligning with the IS around benchmarking workflows to ensure reproducible research and potential clinical applications

The study will convene and establish a consensus on high-level community-driven standards:

• Workflow / Task Orchestration Service: A minimal API specification that will support heterogenous containerised workflow (e.g. CWL, Galaxy, Nextflow, etc.) workloads for secured execution across the ELIXIR Federation of compute/cloud sites.
• Tool / Workflow Registry Service: A minimal API specification that will provide access to curated heterogeneous container formats (e.g. Docker, Singularity) and workflow specifications (e.g. CWL, Galaxy, Nextflow, etc.) to be used as part of the workflow orchestration service.
• Data Repository Service: A minimal API specification that will support the discovery and secured access to ELIXIR Core Data Resources and ELIXIR Node provided datasets as part of the workflow orchestration service.
• Data and Workflow Security Protocols: Embedding security relying on ELIXIR AAI across all ELIXIR APIs to ensure secure access to data, tools and workflows to allow analysis to be performed on sensitive data.

This will be achieved by coordinating the expertise in the ELIXIR Platforms (Compute & Tools) and work taking place within the Nodes and related projects (e.g. EOSC-Life, EOSC-Hub), and will be broken down into three work packages: 

1. Leveraging EOSC-Life workflows infrastructure
2. ELIXIR Infrastructure for Orchestrating Containers and Workflows
3. Coordinating ELIXIR Data Discovery and Transfer Services

and a number of Community Lead Use Cases: 

1. Human data requiring security protocols provided by AAI, and data transfer services
2. Single cell transcriptomics workflow that could be adapted for different organisms
3. Metabolomics workflow adopted by the PhenoMeNal project
4. Proteomics workflow aligning with the IS around benchmarking workflows to ensure reproducible research and potential clinical applications

The study will convene and establish a consensus on high-level community-driven standards:

• Workflow / Task Orchestration Service: A minimal API specification that will support heterogenous containerised workflow (e.g. CWL, Galaxy, Nextflow, etc.) workloads for secured execution across the ELIXIR Federation of compute/cloud sites.
• Tool / Workflow Registry Service: A minimal API specification that will provide access to curated heterogeneous container formats (e.g. Docker, Singularity) and workflow specifications (e.g. CWL, Galaxy, Nextflow, etc.) to be used as part of the workflow orchestration service.
• Data Repository Service: A minimal API specification that will support the discovery and secured access to ELIXIR Core Data Resources and ELIXIR Node provided datasets as part of the workflow orchestration service.
• Data and Workflow Security Protocols: Embedding security relying on ELIXIR AAI across all ELIXIR APIs to ensure secure access to data, tools and workflows to allow analysis to be performed on sensitive data.

This will be achieved by coordinating the expertise in the ELIXIR Platforms (Compute & Tools) and work taking place within the Nodes and related projects (e.g. EOSC-Life, EOSC-Hub), and will be broken down into three work packages: 

1. Leveraging EOSC-Life workflows infrastructure
2. ELIXIR Infrastructure for Orchestrating Containers and Workflows
3. Coordinating ELIXIR Data Discovery and Transfer Services

and a number of Community Lead Use Cases: 

1. Human data requiring security protocols provided by AAI, and data transfer services
2. Single cell transcriptomics workflow that could be adapted for different organisms
3. Metabolomics workflow adopted by the PhenoMeNal project
4. Proteomics workflow aligning with the IS around benchmarking workflows to ensure reproducible research and potential clinical applications

The study will convene and establish a consensus on high-level community-driven standards:

• Workflow / Task Orchestration Service: A minimal API specification that will support heterogenous containerised workflow (e.g. CWL, Galaxy, Nextflow, etc.) workloads for secured execution across the ELIXIR Federation of compute/cloud sites.
• Tool / Workflow Registry Service: A minimal API specification that will provide access to curated heterogeneous container formats (e.g. Docker, Singularity) and workflow specifications (e.g. CWL, Galaxy, Nextflow, etc.) to be used as part of the workflow orchestration service.
• Data Repository Service: A minimal API specification that will support the discovery and secured access to ELIXIR Core Data Resources and ELIXIR Node provided datasets as part of the workflow orchestration service.
• Data and Workflow Security Protocols: Embedding security relying on ELIXIR AAI across all ELIXIR APIs to ensure secure access to data, tools and workflows to allow analysis to be performed on sensitive data.

This will be achieved by coordinating the expertise in the ELIXIR Platforms (Compute & Tools) and work taking place within the Nodes and related projects (e.g. EOSC-Life, EOSC-Hub), and will be broken down into three work packages: 

1. Leveraging EOSC-Life workflows infrastructure
2. ELIXIR Infrastructure for Orchestrating Containers and Workflows
3. Coordinating ELIXIR Data Discovery and Transfer Services

and a number of Community Lead Use Cases: 

1. Human data requiring security protocols provided by AAI, and data transfer services
2. Single cell transcriptomics workflow that could be adapted for different organisms
3. Metabolomics workflow adopted by the PhenoMeNal project
4. Proteomics workflow aligning with the IS around benchmarking workflows to ensure reproducible research and potential clinical applications

The study will convene and establish a consensus on high-level community-driven standards:

• Workflow / Task Orchestration Service: A minimal API specification that will support heterogenous containerised workflow (e.g. CWL, Galaxy, Nextflow, etc.) workloads for secured execution across the ELIXIR Federation of compute/cloud sites.
• Tool / Workflow Registry Service: A minimal API specification that will provide access to curated heterogeneous container formats (e.g. Docker, Singularity) and workflow specifications (e.g. CWL, Galaxy, Nextflow, etc.) to be used as part of the workflow orchestration service.
• Data Repository Service: A minimal API specification that will support the discovery and secured access to ELIXIR Core Data Resources and ELIXIR Node provided datasets as part of the workflow orchestration service.
• Data and Workflow Security Protocols: Embedding security relying on ELIXIR AAI across all ELIXIR APIs to ensure secure access to data, tools and workflows to allow analysis to be performed on sensitive data.

This will be achieved by coordinating the expertise in the ELIXIR Platforms (Compute & Tools) and work taking place within the Nodes and related projects (e.g. EOSC-Life, EOSC-Hub), and will be broken down into three work packages: 

1. Leveraging EOSC-Life workflows infrastructure
2. ELIXIR Infrastructure for Orchestrating Containers and Workflows
3. Coordinating ELIXIR Data Discovery and Transfer Services

and a number of Community Lead Use Cases: 

1. Human data requiring security protocols provided by AAI, and data transfer services
2. Single cell transcriptomics workflow that could be adapted for different organisms
3. Metabolomics workflow adopted by the PhenoMeNal project
4. Proteomics workflow aligning with the IS around benchmarking workflows to ensure reproducible research and potential clinical applications

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

The Marine Metagenomics Community has adopted the use of the Common Workflow Language (CWL) as an interoperable way to describe their analysis pipelines. One of the most complex and fully developed CWL workflows implements the EBI metagenomics analysis pipeline.

In coordination with MG-RAST, a US based metagenomics analysis pipeline, there are now two different large-scale metagenomics CWL workflows. Each uses a different CWL execution framework (namely Toil and AWE) and are run on different compute infrastructures. During the course of the coming year, the Marine Use Case expects META-pipe (the ELIXIR-NO, marine specific metagenomics pipeline) and other metagenomics related tools (e.g. ITS1 analysis from ELIXIR-IT) to adopt CWL. These additional tools can be used as alternatives for pre­existing tools or extend the functionality of the current workflows.

This Implementation Study aims to:

1. demonstrate the benefits of using CWL by combining different workflows components to make new workflows;
2. extend the current CWL workflows to enable greater reuse;
3. enhance the execution frameworks to improve both deployment and scalability;
4. deploy a single CWL workflow on different ELIXIR cloud environments to enable parallel processing and reproducibility.

To provide an exemplar to both the ELIXIR and the broader scientific communities, we will work through a community case study and ensure that the data, analysis and results conform to a bona fide Research Object (RO), ensuring that they comply with FAIR principles. We will develop appropriate training materials for two key target audiences - producers of (workflows and ROs) and consumers.

This study is closely linked with the work of the Bioschemas Community.

The Marine Metagenomics Community has adopted the use of the Common Workflow Language (CWL) as an interoperable way to describe their analysis pipelines. One of the most complex and fully developed CWL workflows implements the EBI metagenomics analysis pipeline.

In coordination with MG-RAST, a US based metagenomics analysis pipeline, there are now two different large-scale metagenomics CWL workflows. Each uses a different CWL execution framework (namely Toil and AWE) and are run on different compute infrastructures. During the course of the coming year, the Marine Use Case expects META-pipe (the ELIXIR-NO, marine specific metagenomics pipeline) and other metagenomics related tools (e.g. ITS1 analysis from ELIXIR-IT) to adopt CWL. These additional tools can be used as alternatives for pre­existing tools or extend the functionality of the current workflows.

This Implementation Study aims to:

1. demonstrate the benefits of using CWL by combining different workflows components to make new workflows;
2. extend the current CWL workflows to enable greater reuse;
3. enhance the execution frameworks to improve both deployment and scalability;
4. deploy a single CWL workflow on different ELIXIR cloud environments to enable parallel processing and reproducibility.

To provide an exemplar to both the ELIXIR and the broader scientific communities, we will work through a community case study and ensure that the data, analysis and results conform to a bona fide Research Object (RO), ensuring that they comply with FAIR principles. We will develop appropriate training materials for two key target audiences - producers of (workflows and ROs) and consumers.

This study is closely linked with the work of the Bioschemas Community.

The Marine Metagenomics Community has adopted the use of the Common Workflow Language (CWL) as an interoperable way to describe their analysis pipelines. One of the most complex and fully developed CWL workflows implements the EBI metagenomics analysis pipeline.

In coordination with MG-RAST, a US based metagenomics analysis pipeline, there are now two different large-scale metagenomics CWL workflows. Each uses a different CWL execution framework (namely Toil and AWE) and are run on different compute infrastructures. During the course of the coming year, the Marine Use Case expects META-pipe (the ELIXIR-NO, marine specific metagenomics pipeline) and other metagenomics related tools (e.g. ITS1 analysis from ELIXIR-IT) to adopt CWL. These additional tools can be used as alternatives for pre­existing tools or extend the functionality of the current workflows.

This Implementation Study aims to:

1. demonstrate the benefits of using CWL by combining different workflows components to make new workflows;
2. extend the current CWL workflows to enable greater reuse;
3. enhance the execution frameworks to improve both deployment and scalability;
4. deploy a single CWL workflow on different ELIXIR cloud environments to enable parallel processing and reproducibility.

To provide an exemplar to both the ELIXIR and the broader scientific communities, we will work through a community case study and ensure that the data, analysis and results conform to a bona fide Research Object (RO), ensuring that they comply with FAIR principles. We will develop appropriate training materials for two key target audiences - producers of (workflows and ROs) and consumers.

This study is closely linked with the work of the Bioschemas Community.

The Marine Metagenomics Community has adopted the use of the Common Workflow Language (CWL) as an interoperable way to describe their analysis pipelines. One of the most complex and fully developed CWL workflows implements the EBI metagenomics analysis pipeline.

In coordination with MG-RAST, a US based metagenomics analysis pipeline, there are now two different large-scale metagenomics CWL workflows. Each uses a different CWL execution framework (namely Toil and AWE) and are run on different compute infrastructures. During the course of the coming year, the Marine Use Case expects META-pipe (the ELIXIR-NO, marine specific metagenomics pipeline) and other metagenomics related tools (e.g. ITS1 analysis from ELIXIR-IT) to adopt CWL. These additional tools can be used as alternatives for pre­existing tools or extend the functionality of the current workflows.

This Implementation Study aims to:

1. demonstrate the benefits of using CWL by combining different workflows components to make new workflows;
2. extend the current CWL workflows to enable greater reuse;
3. enhance the execution frameworks to improve both deployment and scalability;
4. deploy a single CWL workflow on different ELIXIR cloud environments to enable parallel processing and reproducibility.

To provide an exemplar to both the ELIXIR and the broader scientific communities, we will work through a community case study and ensure that the data, analysis and results conform to a bona fide Research Object (RO), ensuring that they comply with FAIR principles. We will develop appropriate training materials for two key target audiences - producers of (workflows and ROs) and consumers.

This study is closely linked with the work of the Bioschemas Community.

An ELIXIR implementation study started in February 2017, as a collaboration between EMBL-EBI and ELIXIR-DE. Its main objective is to develop open, robust, scalable and reproducible proteomics data analysis workflows based on OpenMS, directly connected to the PRIDE database (an ELIXIR core data resource) and to deploy these pipelines in the EMBL-EBI "Embassy Cloud" as a proof of concept.

Building on this work, we here propose a follow-up project that has three objectives: 

1. The inclusion of additional open tools developed by other ELIXIR nodes
2. The improvement of the overall infrastructure supporting the implementation of proteomics data analysis pipelines
3. The inclusion of quality control pipelines.

The overarching goal is that these tools can be deployed in other cloud infrastructures, and can be easily reused by anyone in the community, thus bringing the users closer to the tools, and the tools closer to the data.

Impact of the study

The outcome will be that an increased range of open proteomics tools will be included in an extended range of cloud infrastructures, including new quality control features based on OpenMS. Impact – increased facility for proteomics analysis across multiple cloud platforms – all with increased degree of quality control.

An ELIXIR implementation study started in February 2017, as a collaboration between EMBL-EBI and ELIXIR-DE. Its main objective is to develop open, robust, scalable and reproducible proteomics data analysis workflows based on OpenMS, directly connected to the PRIDE database (an ELIXIR core data resource) and to deploy these pipelines in the EMBL-EBI "Embassy Cloud" as a proof of concept.

Building on this work, we here propose a follow-up project that has three objectives: 

1. The inclusion of additional open tools developed by other ELIXIR nodes
2. The improvement of the overall infrastructure supporting the implementation of proteomics data analysis pipelines
3. The inclusion of quality control pipelines.

The overarching goal is that these tools can be deployed in other cloud infrastructures, and can be easily reused by anyone in the community, thus bringing the users closer to the tools, and the tools closer to the data.

Impact of the study

The outcome will be that an increased range of open proteomics tools will be included in an extended range of cloud infrastructures, including new quality control features based on OpenMS. Impact – increased facility for proteomics analysis across multiple cloud platforms – all with increased degree of quality control.

An ELIXIR implementation study started in February 2017, as a collaboration between EMBL-EBI and ELIXIR-DE. Its main objective is to develop open, robust, scalable and reproducible proteomics data analysis workflows based on OpenMS, directly connected to the PRIDE database (an ELIXIR core data resource) and to deploy these pipelines in the EMBL-EBI "Embassy Cloud" as a proof of concept.

Building on this work, we here propose a follow-up project that has three objectives: 

1. The inclusion of additional open tools developed by other ELIXIR nodes
2. The improvement of the overall infrastructure supporting the implementation of proteomics data analysis pipelines
3. The inclusion of quality control pipelines.

The overarching goal is that these tools can be deployed in other cloud infrastructures, and can be easily reused by anyone in the community, thus bringing the users closer to the tools, and the tools closer to the data.

Impact of the study

The outcome will be that an increased range of open proteomics tools will be included in an extended range of cloud infrastructures, including new quality control features based on OpenMS. Impact – increased facility for proteomics analysis across multiple cloud platforms – all with increased degree of quality control.

An ELIXIR implementation study started in February 2017, as a collaboration between EMBL-EBI and ELIXIR-DE. Its main objective is to develop open, robust, scalable and reproducible proteomics data analysis workflows based on OpenMS, directly connected to the PRIDE database (an ELIXIR core data resource) and to deploy these pipelines in the EMBL-EBI "Embassy Cloud" as a proof of concept.

Building on this work, we here propose a follow-up project that has three objectives: 

1. The inclusion of additional open tools developed by other ELIXIR nodes
2. The improvement of the overall infrastructure supporting the implementation of proteomics data analysis pipelines
3. The inclusion of quality control pipelines.

The overarching goal is that these tools can be deployed in other cloud infrastructures, and can be easily reused by anyone in the community, thus bringing the users closer to the tools, and the tools closer to the data.

Impact of the study

The outcome will be that an increased range of open proteomics tools will be included in an extended range of cloud infrastructures, including new quality control features based on OpenMS. Impact – increased facility for proteomics analysis across multiple cloud platforms – all with increased degree of quality control.

An ELIXIR implementation study started in February 2017, as a collaboration between EMBL-EBI and ELIXIR-DE. Its main objective is to develop open, robust, scalable and reproducible proteomics data analysis workflows based on OpenMS, directly connected to the PRIDE database (an ELIXIR core data resource) and to deploy these pipelines in the EMBL-EBI "Embassy Cloud" as a proof of concept.

Building on this work, we here propose a follow-up project that has three objectives: 

1. The inclusion of additional open tools developed by other ELIXIR nodes
2. The improvement of the overall infrastructure supporting the implementation of proteomics data analysis pipelines
3. The inclusion of quality control pipelines.

The overarching goal is that these tools can be deployed in other cloud infrastructures, and can be easily reused by anyone in the community, thus bringing the users closer to the tools, and the tools closer to the data.

Impact of the study

The outcome will be that an increased range of open proteomics tools will be included in an extended range of cloud infrastructures, including new quality control features based on OpenMS. Impact – increased facility for proteomics analysis across multiple cloud platforms – all with increased degree of quality control.

The implementation study project plan of ELIXIR Italy consists of six activities that aim to boost the cooperation with existing ELIXIR activities and are expected to deepen the interaction between ELIXIR-IIB, the Joint Research Unit embodying the Italian Node, and ELIXIR. The partners involved have already established contacts with other ELIXIR Nodes and the relevant ELIXIR Platforms and Services in order to ensure an advantageous outcome for all the involved parties. The goal of the proposed activities is to create and/or reinforce collaborations based on concrete measures. With this implementation study the Italian ELIXIR Node will achieve greater integration within ELIXIR service infrastructures and data interoperability policies. The topics of the selected activities and an additional coordination task are summarized below:

1. Integration in ELIXIR Bioschemas activities.
2. Integration in ELIXIR Data Curation activities.
3. Integration in ELIXIR Galaxy activities through a project on practical feasibility of creating and running large-scale Galaxy-based variant calling pipelines on microservice infrastructures.
4. Integration in ELIXIR Human Data activities through Beacons.
5. Integration in ELIXIR Marine Metagenomics activities through a web-service supporting ITS1-based survey of marine communities.
6. Integration in ELIXIR Rare Diseases activities.
7. Coordination of the Italian ELIXIR Node Implementation study project.

The goal is this Staff Exchange project is to accelerate the ongoing work of integrating various components of the new Tools Platform Ecosystem, as defined in the Tools Platform Task 1 of the ELIXIR 2019-23 Programme, Work Package 2 (Developing an integrated “Tools Platform ecosystem”).

As a centralised, transparent repository of information about tools and services, the new Tools Platform Ecosystem will serve as the foundation for sustainability of the diverse Tools Platform services, and for interoperability between both the essential Platform services (bio.tools, BioContainers, OpenEBench, Bioconda) and related services outside of the Tools Platform (e.g. myExperiment, IFB Catalogue, Debian Med, Galaxy, or the resources of the bioimage analysis community).

The concrete focus of the proposed Exchange project is to integrate bio.tools into the new Tools Platform Ecosystem. In the beginning, the project will provide the implementation and test production experience needed for the deliverable D2.1 (“Governance and process management agreement for the new tools ecosystem”; due 2020 Q1) of the mentioned Tools Platform Task 1, and within its duration pave the way for D2.2 Ibid. (“Guidelines and procedures for the prospective inclusion of new registries and data repositories into the ecosystem”; due 2020 Q3).

This Staff Exchange project will foster workload sharing and organisation between the respective ELIXIR Nodes, and provide means for the necessary technological knowledge-exchange among the personnel of the participating Nodes.

The goal is this Staff Exchange project is to accelerate the ongoing work of integrating various components of the new Tools Platform Ecosystem, as defined in the Tools Platform Task 1 of the ELIXIR 2019-23 Programme, Work Package 2 (Developing an integrated “Tools Platform ecosystem”).

As a centralised, transparent repository of information about tools and services, the new Tools Platform Ecosystem will serve as the foundation for sustainability of the diverse Tools Platform services, and for interoperability between both the essential Platform services (bio.tools, BioContainers, OpenEBench, Bioconda) and related services outside of the Tools Platform (e.g. myExperiment, IFB Catalogue, Debian Med, Galaxy, or the resources of the bioimage analysis community).

The concrete focus of the proposed Exchange project is to integrate bio.tools into the new Tools Platform Ecosystem. In the beginning, the project will provide the implementation and test production experience needed for the deliverable D2.1 (“Governance and process management agreement for the new tools ecosystem”; due 2020 Q1) of the mentioned Tools Platform Task 1, and within its duration pave the way for D2.2 Ibid. (“Guidelines and procedures for the prospective inclusion of new registries and data repositories into the ecosystem”; due 2020 Q3).

This Staff Exchange project will foster workload sharing and organisation between the respective ELIXIR Nodes, and provide means for the necessary technological knowledge-exchange among the personnel of the participating Nodes.

The goal is this Staff Exchange project is to accelerate the ongoing work of integrating various components of the new Tools Platform Ecosystem, as defined in the Tools Platform Task 1 of the ELIXIR 2019-23 Programme, Work Package 2 (Developing an integrated “Tools Platform ecosystem”).

As a centralised, transparent repository of information about tools and services, the new Tools Platform Ecosystem will serve as the foundation for sustainability of the diverse Tools Platform services, and for interoperability between both the essential Platform services (bio.tools, BioContainers, OpenEBench, Bioconda) and related services outside of the Tools Platform (e.g. myExperiment, IFB Catalogue, Debian Med, Galaxy, or the resources of the bioimage analysis community).

The concrete focus of the proposed Exchange project is to integrate bio.tools into the new Tools Platform Ecosystem. In the beginning, the project will provide the implementation and test production experience needed for the deliverable D2.1 (“Governance and process management agreement for the new tools ecosystem”; due 2020 Q1) of the mentioned Tools Platform Task 1, and within its duration pave the way for D2.2 Ibid. (“Guidelines and procedures for the prospective inclusion of new registries and data repositories into the ecosystem”; due 2020 Q3).

This Staff Exchange project will foster workload sharing and organisation between the respective ELIXIR Nodes, and provide means for the necessary technological knowledge-exchange among the personnel of the participating Nodes.

The goal is this Staff Exchange project is to accelerate the ongoing work of integrating various components of the new Tools Platform Ecosystem, as defined in the Tools Platform Task 1 of the ELIXIR 2019-23 Programme, Work Package 2 (Developing an integrated “Tools Platform ecosystem”).

As a centralised, transparent repository of information about tools and services, the new Tools Platform Ecosystem will serve as the foundation for sustainability of the diverse Tools Platform services, and for interoperability between both the essential Platform services (bio.tools, BioContainers, OpenEBench, Bioconda) and related services outside of the Tools Platform (e.g. myExperiment, IFB Catalogue, Debian Med, Galaxy, or the resources of the bioimage analysis community).

The concrete focus of the proposed Exchange project is to integrate bio.tools into the new Tools Platform Ecosystem. In the beginning, the project will provide the implementation and test production experience needed for the deliverable D2.1 (“Governance and process management agreement for the new tools ecosystem”; due 2020 Q1) of the mentioned Tools Platform Task 1, and within its duration pave the way for D2.2 Ibid. (“Guidelines and procedures for the prospective inclusion of new registries and data repositories into the ecosystem”; due 2020 Q3).

This Staff Exchange project will foster workload sharing and organisation between the respective ELIXIR Nodes, and provide means for the necessary technological knowledge-exchange among the personnel of the participating Nodes.

The aim of this new strategic implementation study is to build on the current progress made through the on-going implementation study to enable adoption and deployment of protocols and services by the broader ELIXIR community at scale. This Strategic Implementation Study (SIS) aims to coordinate existing efforts across ELIXIR, identify opportunities, contribute in a targeted and limited way with specific developments to connect relevant components and propose mechanisms for sustaining this effort over time.

The aim of this new strategic implementation study is to build on the current progress made through the on-going implementation study to enable adoption and deployment of protocols and services by the broader ELIXIR community at scale. This Strategic Implementation Study (SIS) aims to coordinate existing efforts across ELIXIR, identify opportunities, contribute in a targeted and limited way with specific developments to connect relevant components and propose mechanisms for sustaining this effort over time.

The aim of this new strategic implementation study is to build on the current progress made through the on-going implementation study to enable adoption and deployment of protocols and services by the broader ELIXIR community at scale. This Strategic Implementation Study (SIS) aims to coordinate existing efforts across ELIXIR, identify opportunities, contribute in a targeted and limited way with specific developments to connect relevant components and propose mechanisms for sustaining this effort over time.

The aim of this new strategic implementation study is to build on the current progress made through the on-going implementation study to enable adoption and deployment of protocols and services by the broader ELIXIR community at scale. This Strategic Implementation Study (SIS) aims to coordinate existing efforts across ELIXIR, identify opportunities, contribute in a targeted and limited way with specific developments to connect relevant components and propose mechanisms for sustaining this effort over time.

The aim of this new strategic implementation study is to build on the current progress made through the on-going implementation study to enable adoption and deployment of protocols and services by the broader ELIXIR community at scale. This Strategic Implementation Study (SIS) aims to coordinate existing efforts across ELIXIR, identify opportunities, contribute in a targeted and limited way with specific developments to connect relevant components and propose mechanisms for sustaining this effort over time.

The aim of this new strategic implementation study is to build on the current progress made through the on-going implementation study to enable adoption and deployment of protocols and services by the broader ELIXIR community at scale. This Strategic Implementation Study (SIS) aims to coordinate existing efforts across ELIXIR, identify opportunities, contribute in a targeted and limited way with specific developments to connect relevant components and propose mechanisms for sustaining this effort over time.

The aim of this new strategic implementation study is to build on the current progress made through the on-going implementation study to enable adoption and deployment of protocols and services by the broader ELIXIR community at scale. This Strategic Implementation Study (SIS) aims to coordinate existing efforts across ELIXIR, identify opportunities, contribute in a targeted and limited way with specific developments to connect relevant components and propose mechanisms for sustaining this effort over time.

The aim of this new strategic implementation study is to build on the current progress made through the on-going implementation study to enable adoption and deployment of protocols and services by the broader ELIXIR community at scale. This Strategic Implementation Study (SIS) aims to coordinate existing efforts across ELIXIR, identify opportunities, contribute in a targeted and limited way with specific developments to connect relevant components and propose mechanisms for sustaining this effort over time.

The aim of this new strategic implementation study is to build on the current progress made through the on-going implementation study to enable adoption and deployment of protocols and services by the broader ELIXIR community at scale. This Strategic Implementation Study (SIS) aims to coordinate existing efforts across ELIXIR, identify opportunities, contribute in a targeted and limited way with specific developments to connect relevant components and propose mechanisms for sustaining this effort over time.

The aim of this new strategic implementation study is to build on the current progress made through the on-going implementation study to enable adoption and deployment of protocols and services by the broader ELIXIR community at scale. This Strategic Implementation Study (SIS) aims to coordinate existing efforts across ELIXIR, identify opportunities, contribute in a targeted and limited way with specific developments to connect relevant components and propose mechanisms for sustaining this effort over time.

The aim of this new strategic implementation study is to build on the current progress made through the on-going implementation study to enable adoption and deployment of protocols and services by the broader ELIXIR community at scale. This Strategic Implementation Study (SIS) aims to coordinate existing efforts across ELIXIR, identify opportunities, contribute in a targeted and limited way with specific developments to connect relevant components and propose mechanisms for sustaining this effort over time.

The aim of this new strategic implementation study is to build on the current progress made through the on-going implementation study to enable adoption and deployment of protocols and services by the broader ELIXIR community at scale. This Strategic Implementation Study (SIS) aims to coordinate existing efforts across ELIXIR, identify opportunities, contribute in a targeted and limited way with specific developments to connect relevant components and propose mechanisms for sustaining this effort over time.

Metabolomics aims to provide novel insights into the biochemical reactions of organisms by characterising the presence and concentrations of low molecular weight compounds from biological samples. The primary analytical tools for such high-throughput data collection are mass spectrometry (MS), often preceded by chromatographic or electrophoretic separation technologies, and nuclear magnetic resonance spectroscopy (NMR).

These technologies produce relatively large and complex data sets that require bioinformaticians, cheminformaticians, biostatisticians, data scientists and computer scientists. Together they develop and apply a wide range of algorithms, software tools, repositories and computational resources to process, analyse, report and store the data and metadata.

Increasingly, insights from genomics, epigenomics, transcriptomics, proteomics/protein interactomics and metabolomics are combined, to gain insights into the dynamics of biological processes. Metabolomics activities are well represented within Europe and ELIXIR nodes. Metabolite identification is the area that the community believes will have maximal impact of computational metabolomics and metabolomics data management and will benefit most from interactions with the existing five ELIXIR platforms and where progress will contribute most to other ELIXIR communities.

The progress through this integrative Implementation Study will benefit industry and academia alike as metabolite identification is one of the major bottlenecks in metabolomics and resolving this challenge requires a community effort.

Metabolomics aims to provide novel insights into the biochemical reactions of organisms by characterising the presence and concentrations of low molecular weight compounds from biological samples. The primary analytical tools for such high-throughput data collection are mass spectrometry (MS), often preceded by chromatographic or electrophoretic separation technologies, and nuclear magnetic resonance spectroscopy (NMR).

These technologies produce relatively large and complex data sets that require bioinformaticians, cheminformaticians, biostatisticians, data scientists and computer scientists. Together they develop and apply a wide range of algorithms, software tools, repositories and computational resources to process, analyse, report and store the data and metadata.

Increasingly, insights from genomics, epigenomics, transcriptomics, proteomics/protein interactomics and metabolomics are combined, to gain insights into the dynamics of biological processes. Metabolomics activities are well represented within Europe and ELIXIR nodes. Metabolite identification is the area that the community believes will have maximal impact of computational metabolomics and metabolomics data management and will benefit most from interactions with the existing five ELIXIR platforms and where progress will contribute most to other ELIXIR communities.

The progress through this integrative Implementation Study will benefit industry and academia alike as metabolite identification is one of the major bottlenecks in metabolomics and resolving this challenge requires a community effort.

Metabolomics aims to provide novel insights into the biochemical reactions of organisms by characterising the presence and concentrations of low molecular weight compounds from biological samples. The primary analytical tools for such high-throughput data collection are mass spectrometry (MS), often preceded by chromatographic or electrophoretic separation technologies, and nuclear magnetic resonance spectroscopy (NMR).

These technologies produce relatively large and complex data sets that require bioinformaticians, cheminformaticians, biostatisticians, data scientists and computer scientists. Together they develop and apply a wide range of algorithms, software tools, repositories and computational resources to process, analyse, report and store the data and metadata.

Increasingly, insights from genomics, epigenomics, transcriptomics, proteomics/protein interactomics and metabolomics are combined, to gain insights into the dynamics of biological processes. Metabolomics activities are well represented within Europe and ELIXIR nodes. Metabolite identification is the area that the community believes will have maximal impact of computational metabolomics and metabolomics data management and will benefit most from interactions with the existing five ELIXIR platforms and where progress will contribute most to other ELIXIR communities.

The progress through this integrative Implementation Study will benefit industry and academia alike as metabolite identification is one of the major bottlenecks in metabolomics and resolving this challenge requires a community effort.

Metabolomics aims to provide novel insights into the biochemical reactions of organisms by characterising the presence and concentrations of low molecular weight compounds from biological samples. The primary analytical tools for such high-throughput data collection are mass spectrometry (MS), often preceded by chromatographic or electrophoretic separation technologies, and nuclear magnetic resonance spectroscopy (NMR).

These technologies produce relatively large and complex data sets that require bioinformaticians, cheminformaticians, biostatisticians, data scientists and computer scientists. Together they develop and apply a wide range of algorithms, software tools, repositories and computational resources to process, analyse, report and store the data and metadata.

Increasingly, insights from genomics, epigenomics, transcriptomics, proteomics/protein interactomics and metabolomics are combined, to gain insights into the dynamics of biological processes. Metabolomics activities are well represented within Europe and ELIXIR nodes. Metabolite identification is the area that the community believes will have maximal impact of computational metabolomics and metabolomics data management and will benefit most from interactions with the existing five ELIXIR platforms and where progress will contribute most to other ELIXIR communities.

The progress through this integrative Implementation Study will benefit industry and academia alike as metabolite identification is one of the major bottlenecks in metabolomics and resolving this challenge requires a community effort.

Metabolomics aims to provide novel insights into the biochemical reactions of organisms by characterising the presence and concentrations of low molecular weight compounds from biological samples. The primary analytical tools for such high-throughput data collection are mass spectrometry (MS), often preceded by chromatographic or electrophoretic separation technologies, and nuclear magnetic resonance spectroscopy (NMR).

These technologies produce relatively large and complex data sets that require bioinformaticians, cheminformaticians, biostatisticians, data scientists and computer scientists. Together they develop and apply a wide range of algorithms, software tools, repositories and computational resources to process, analyse, report and store the data and metadata.

Increasingly, insights from genomics, epigenomics, transcriptomics, proteomics/protein interactomics and metabolomics are combined, to gain insights into the dynamics of biological processes. Metabolomics activities are well represented within Europe and ELIXIR nodes. Metabolite identification is the area that the community believes will have maximal impact of computational metabolomics and metabolomics data management and will benefit most from interactions with the existing five ELIXIR platforms and where progress will contribute most to other ELIXIR communities.

The progress through this integrative Implementation Study will benefit industry and academia alike as metabolite identification is one of the major bottlenecks in metabolomics and resolving this challenge requires a community effort.

Metabolomics aims to provide novel insights into the biochemical reactions of organisms by characterising the presence and concentrations of low molecular weight compounds from biological samples. The primary analytical tools for such high-throughput data collection are mass spectrometry (MS), often preceded by chromatographic or electrophoretic separation technologies, and nuclear magnetic resonance spectroscopy (NMR).

These technologies produce relatively large and complex data sets that require bioinformaticians, cheminformaticians, biostatisticians, data scientists and computer scientists. Together they develop and apply a wide range of algorithms, software tools, repositories and computational resources to process, analyse, report and store the data and metadata.

Increasingly, insights from genomics, epigenomics, transcriptomics, proteomics/protein interactomics and metabolomics are combined, to gain insights into the dynamics of biological processes. Metabolomics activities are well represented within Europe and ELIXIR nodes. Metabolite identification is the area that the community believes will have maximal impact of computational metabolomics and metabolomics data management and will benefit most from interactions with the existing five ELIXIR platforms and where progress will contribute most to other ELIXIR communities.

The progress through this integrative Implementation Study will benefit industry and academia alike as metabolite identification is one of the major bottlenecks in metabolomics and resolving this challenge requires a community effort.

Metabolomics aims to provide novel insights into the biochemical reactions of organisms by characterising the presence and concentrations of low molecular weight compounds from biological samples. The primary analytical tools for such high-throughput data collection are mass spectrometry (MS), often preceded by chromatographic or electrophoretic separation technologies, and nuclear magnetic resonance spectroscopy (NMR).

These technologies produce relatively large and complex data sets that require bioinformaticians, cheminformaticians, biostatisticians, data scientists and computer scientists. Together they develop and apply a wide range of algorithms, software tools, repositories and computational resources to process, analyse, report and store the data and metadata.

Increasingly, insights from genomics, epigenomics, transcriptomics, proteomics/protein interactomics and metabolomics are combined, to gain insights into the dynamics of biological processes. Metabolomics activities are well represented within Europe and ELIXIR nodes. Metabolite identification is the area that the community believes will have maximal impact of computational metabolomics and metabolomics data management and will benefit most from interactions with the existing five ELIXIR platforms and where progress will contribute most to other ELIXIR communities.

The progress through this integrative Implementation Study will benefit industry and academia alike as metabolite identification is one of the major bottlenecks in metabolomics and resolving this challenge requires a community effort.

Metabolomics aims to provide novel insights into the biochemical reactions of organisms by characterising the presence and concentrations of low molecular weight compounds from biological samples. The primary analytical tools for such high-throughput data collection are mass spectrometry (MS), often preceded by chromatographic or electrophoretic separation technologies, and nuclear magnetic resonance spectroscopy (NMR).

These technologies produce relatively large and complex data sets that require bioinformaticians, cheminformaticians, biostatisticians, data scientists and computer scientists. Together they develop and apply a wide range of algorithms, software tools, repositories and computational resources to process, analyse, report and store the data and metadata.

Increasingly, insights from genomics, epigenomics, transcriptomics, proteomics/protein interactomics and metabolomics are combined, to gain insights into the dynamics of biological processes. Metabolomics activities are well represented within Europe and ELIXIR nodes. Metabolite identification is the area that the community believes will have maximal impact of computational metabolomics and metabolomics data management and will benefit most from interactions with the existing five ELIXIR platforms and where progress will contribute most to other ELIXIR communities.

The progress through this integrative Implementation Study will benefit industry and academia alike as metabolite identification is one of the major bottlenecks in metabolomics and resolving this challenge requires a community effort.

Metabolomics aims to provide novel insights into the biochemical reactions of organisms by characterising the presence and concentrations of low molecular weight compounds from biological samples. The primary analytical tools for such high-throughput data collection are mass spectrometry (MS), often preceded by chromatographic or electrophoretic separation technologies, and nuclear magnetic resonance spectroscopy (NMR).

These technologies produce relatively large and complex data sets that require bioinformaticians, cheminformaticians, biostatisticians, data scientists and computer scientists. Together they develop and apply a wide range of algorithms, software tools, repositories and computational resources to process, analyse, report and store the data and metadata.

Increasingly, insights from genomics, epigenomics, transcriptomics, proteomics/protein interactomics and metabolomics are combined, to gain insights into the dynamics of biological processes. Metabolomics activities are well represented within Europe and ELIXIR nodes. Metabolite identification is the area that the community believes will have maximal impact of computational metabolomics and metabolomics data management and will benefit most from interactions with the existing five ELIXIR platforms and where progress will contribute most to other ELIXIR communities.

The progress through this integrative Implementation Study will benefit industry and academia alike as metabolite identification is one of the major bottlenecks in metabolomics and resolving this challenge requires a community effort.

Metabolomics aims to provide novel insights into the biochemical reactions of organisms by characterising the presence and concentrations of low molecular weight compounds from biological samples. The primary analytical tools for such high-throughput data collection are mass spectrometry (MS), often preceded by chromatographic or electrophoretic separation technologies, and nuclear magnetic resonance spectroscopy (NMR).

These technologies produce relatively large and complex data sets that require bioinformaticians, cheminformaticians, biostatisticians, data scientists and computer scientists. Together they develop and apply a wide range of algorithms, software tools, repositories and computational resources to process, analyse, report and store the data and metadata.

Increasingly, insights from genomics, epigenomics, transcriptomics, proteomics/protein interactomics and metabolomics are combined, to gain insights into the dynamics of biological processes. Metabolomics activities are well represented within Europe and ELIXIR nodes. Metabolite identification is the area that the community believes will have maximal impact of computational metabolomics and metabolomics data management and will benefit most from interactions with the existing five ELIXIR platforms and where progress will contribute most to other ELIXIR communities.

The progress through this integrative Implementation Study will benefit industry and academia alike as metabolite identification is one of the major bottlenecks in metabolomics and resolving this challenge requires a community effort.

Metabolomics aims to provide novel insights into the biochemical reactions of organisms by characterising the presence and concentrations of low molecular weight compounds from biological samples. The primary analytical tools for such high-throughput data collection are mass spectrometry (MS), often preceded by chromatographic or electrophoretic separation technologies, and nuclear magnetic resonance spectroscopy (NMR).

These technologies produce relatively large and complex data sets that require bioinformaticians, cheminformaticians, biostatisticians, data scientists and computer scientists. Together they develop and apply a wide range of algorithms, software tools, repositories and computational resources to process, analyse, report and store the data and metadata.

Increasingly, insights from genomics, epigenomics, transcriptomics, proteomics/protein interactomics and metabolomics are combined, to gain insights into the dynamics of biological processes. Metabolomics activities are well represented within Europe and ELIXIR nodes. Metabolite identification is the area that the community believes will have maximal impact of computational metabolomics and metabolomics data management and will benefit most from interactions with the existing five ELIXIR platforms and where progress will contribute most to other ELIXIR communities.

The progress through this integrative Implementation Study will benefit industry and academia alike as metabolite identification is one of the major bottlenecks in metabolomics and resolving this challenge requires a community effort.

Biological communities work across a range of domains and use a variety metrics to measure and evaluate their activities and performance. Metrics can be used in training, project management, software development as well as in more specific tasks like benchmarking of bioinformatics analysis tools or evaluation of data resources in the life science.

Even if it is possible to find data about specific metrics in publications or web resources, it is hard to find a proper description, methodology and implementation of such metrics. This makes it difficult to understand the specific meaning of a metric and makes it hard to compare metrics provided by different resources.

This project focused on proposing a solution to help to define, discover and access metrics and metrics implementations. We aimed to provide a prototype framework to help registering defined metrics and test run metrics implementations as a proof of concept. The aim being for users to be able to improve the evaluation of a resource, to assess the impact of a variety of services and gain a contribution into decision making. 

This study is now finished, the work is summarised in the end report and in two publications: 

• Top 10 metrics for life science software good practices (F1000R) 
• PIsCO: A Performance indicators framework for collection of bioinformatics resource metrics.  (PeerJ Preprints) 

An outline of the PIsCO framework is available on GitHub. The study also identified a relationship with Bioschemas and is looking to redefine the metrics database accordingly. 

Software containers are a key element in the frame of Open Science, Open Data & Open Source which is strongly supported and advocated by ELIXIR. Software containers are key to guarantee data provenance when described as part of scientific workflows and an important element towards results reproducibility.

They also ease software installation on local computer or cluster facilities.Thus, software containers are transversal to most of the strategic lines of the ELIXIR Tools Platform for the 2022 - 2023 Scientific programme.
We have divided this task into two work packages around software containers that compliment each other.

The first work package aims to maintain and extend the work initiated in the previous ELIXIR implementation study on BioContainers. The implementation study on BioContainers contributed to unify various initiatives in ELIXIR Nodes around software containers and bring them under a common infrastructure and metadata federation. This first work package will focus on operational maintenance of the infrastructure. Additional registry mirrors will be investigated for cloud/local registry availability. To do so, a partnership with Amazon (and potentially other commercial cloud providers) will be set.

While x86 architectures dominate the scientific compute clusters and clouds at this time (currently the container architecture supported by BioContainers), ARM architecture is a mature technology getting traction in both server and consumer markets. With the first super-computers starting to build on ARM architectures, the BioContainers project needs to be prepared to offer ARM based container solutions to our users. Therefore, a task of this work package will evaluate the multi-architecture container solution and add support for ARM in addition to x86. As this task requires extra physical resources, we will try to get support from the ARM company and/or support from ELIXIR members to build ARM-based BioContainers.

To compile software against different architectures, upstream support from tool developers will most likely be needed. Here, we will work together with the “development best practices” (Task 4) team to encourage developers to provide multi-arch support to their software and help them along the way.

BioContainers already integrates its metadata with the central repository of the Tools Platform, work will continue to align/homogenise with the repository evolutions which were, in a first step, a raw addition of metadata from all Tools Platform services (BioContainers, OpenEBench, bio.tools, ...) and the Tools Ecosystem.

Second work packages will focus on user communities. While BioContainers is widely used by the ELIXIR community, it could reach/extend to other communities around life science. Discussions with EOSC and other communities will evaluate how BioContainers could fit to their needs, and the possibility to contribute to the BioContainers project and the registry. This would provide end users a single entry-point and solution for container management and optimize human/compute resources.

As a summary, BioContainers is today well established in our community and provides a stable infrastructure for container availability and findability. Existing solutions could benefit extra life science communities. Energy efficiency trends towards ARM architecture (and possibly others in the future) should not be ignored and is a chance for BioContainers to provide its support to an emerging but growing community.

Software containers are a key element in the frame of Open Science, Open Data & Open Source which is strongly supported and advocated by ELIXIR. Software containers are key to guarantee data provenance when described as part of scientific workflows and an important element towards results reproducibility.

They also ease software installation on local computer or cluster facilities.Thus, software containers are transversal to most of the strategic lines of the ELIXIR Tools Platform for the 2022 - 2023 Scientific programme.
We have divided this task into two work packages around software containers that compliment each other.

The first work package aims to maintain and extend the work initiated in the previous ELIXIR implementation study on BioContainers. The implementation study on BioContainers contributed to unify various initiatives in ELIXIR Nodes around software containers and bring them under a common infrastructure and metadata federation. This first work package will focus on operational maintenance of the infrastructure. Additional registry mirrors will be investigated for cloud/local registry availability. To do so, a partnership with Amazon (and potentially other commercial cloud providers) will be set.

While x86 architectures dominate the scientific compute clusters and clouds at this time (currently the container architecture supported by BioContainers), ARM architecture is a mature technology getting traction in both server and consumer markets. With the first super-computers starting to build on ARM architectures, the BioContainers project needs to be prepared to offer ARM based container solutions to our users. Therefore, a task of this work package will evaluate the multi-architecture container solution and add support for ARM in addition to x86. As this task requires extra physical resources, we will try to get support from the ARM company and/or support from ELIXIR members to build ARM-based BioContainers.

To compile software against different architectures, upstream support from tool developers will most likely be needed. Here, we will work together with the “development best practices” (Task 4) team to encourage developers to provide multi-arch support to their software and help them along the way.

BioContainers already integrates its metadata with the central repository of the Tools Platform, work will continue to align/homogenise with the repository evolutions which were, in a first step, a raw addition of metadata from all Tools Platform services (BioContainers, OpenEBench, bio.tools, ...) and the Tools Ecosystem.

Second work packages will focus on user communities. While BioContainers is widely used by the ELIXIR community, it could reach/extend to other communities around life science. Discussions with EOSC and other communities will evaluate how BioContainers could fit to their needs, and the possibility to contribute to the BioContainers project and the registry. This would provide end users a single entry-point and solution for container management and optimize human/compute resources.

As a summary, BioContainers is today well established in our community and provides a stable infrastructure for container availability and findability. Existing solutions could benefit extra life science communities. Energy efficiency trends towards ARM architecture (and possibly others in the future) should not be ignored and is a chance for BioContainers to provide its support to an emerging but growing community.

Software containers are a key element in the frame of Open Science, Open Data & Open Source which is strongly supported and advocated by ELIXIR. Software containers are key to guarantee data provenance when described as part of scientific workflows and an important element towards results reproducibility.

They also ease software installation on local computer or cluster facilities.Thus, software containers are transversal to most of the strategic lines of the ELIXIR Tools Platform for the 2022 - 2023 Scientific programme.
We have divided this task into two work packages around software containers that compliment each other.

The first work package aims to maintain and extend the work initiated in the previous ELIXIR implementation study on BioContainers. The implementation study on BioContainers contributed to unify various initiatives in ELIXIR Nodes around software containers and bring them under a common infrastructure and metadata federation. This first work package will focus on operational maintenance of the infrastructure. Additional registry mirrors will be investigated for cloud/local registry availability. To do so, a partnership with Amazon (and potentially other commercial cloud providers) will be set.

While x86 architectures dominate the scientific compute clusters and clouds at this time (currently the container architecture supported by BioContainers), ARM architecture is a mature technology getting traction in both server and consumer markets. With the first super-computers starting to build on ARM architectures, the BioContainers project needs to be prepared to offer ARM based container solutions to our users. Therefore, a task of this work package will evaluate the multi-architecture container solution and add support for ARM in addition to x86. As this task requires extra physical resources, we will try to get support from the ARM company and/or support from ELIXIR members to build ARM-based BioContainers.

To compile software against different architectures, upstream support from tool developers will most likely be needed. Here, we will work together with the “development best practices” (Task 4) team to encourage developers to provide multi-arch support to their software and help them along the way.

BioContainers already integrates its metadata with the central repository of the Tools Platform, work will continue to align/homogenise with the repository evolutions which were, in a first step, a raw addition of metadata from all Tools Platform services (BioContainers, OpenEBench, bio.tools, ...) and the Tools Ecosystem.

Second work packages will focus on user communities. While BioContainers is widely used by the ELIXIR community, it could reach/extend to other communities around life science. Discussions with EOSC and other communities will evaluate how BioContainers could fit to their needs, and the possibility to contribute to the BioContainers project and the registry. This would provide end users a single entry-point and solution for container management and optimize human/compute resources.

As a summary, BioContainers is today well established in our community and provides a stable infrastructure for container availability and findability. Existing solutions could benefit extra life science communities. Energy efficiency trends towards ARM architecture (and possibly others in the future) should not be ignored and is a chance for BioContainers to provide its support to an emerging but growing community.

Software containers are a key element in the frame of Open Science, Open Data & Open Source which is strongly supported and advocated by ELIXIR. Software containers are key to guarantee data provenance when described as part of scientific workflows and an important element towards results reproducibility.

They also ease software installation on local computer or cluster facilities.Thus, software containers are transversal to most of the strategic lines of the ELIXIR Tools Platform for the 2022 - 2023 Scientific programme.
We have divided this task into two work packages around software containers that compliment each other.

The first work package aims to maintain and extend the work initiated in the previous ELIXIR implementation study on BioContainers. The implementation study on BioContainers contributed to unify various initiatives in ELIXIR Nodes around software containers and bring them under a common infrastructure and metadata federation. This first work package will focus on operational maintenance of the infrastructure. Additional registry mirrors will be investigated for cloud/local registry availability. To do so, a partnership with Amazon (and potentially other commercial cloud providers) will be set.

While x86 architectures dominate the scientific compute clusters and clouds at this time (currently the container architecture supported by BioContainers), ARM architecture is a mature technology getting traction in both server and consumer markets. With the first super-computers starting to build on ARM architectures, the BioContainers project needs to be prepared to offer ARM based container solutions to our users. Therefore, a task of this work package will evaluate the multi-architecture container solution and add support for ARM in addition to x86. As this task requires extra physical resources, we will try to get support from the ARM company and/or support from ELIXIR members to build ARM-based BioContainers.

To compile software against different architectures, upstream support from tool developers will most likely be needed. Here, we will work together with the “development best practices” (Task 4) team to encourage developers to provide multi-arch support to their software and help them along the way.

BioContainers already integrates its metadata with the central repository of the Tools Platform, work will continue to align/homogenise with the repository evolutions which were, in a first step, a raw addition of metadata from all Tools Platform services (BioContainers, OpenEBench, bio.tools, ...) and the Tools Ecosystem.

Second work packages will focus on user communities. While BioContainers is widely used by the ELIXIR community, it could reach/extend to other communities around life science. Discussions with EOSC and other communities will evaluate how BioContainers could fit to their needs, and the possibility to contribute to the BioContainers project and the registry. This would provide end users a single entry-point and solution for container management and optimize human/compute resources.

As a summary, BioContainers is today well established in our community and provides a stable infrastructure for container availability and findability. Existing solutions could benefit extra life science communities. Energy efficiency trends towards ARM architecture (and possibly others in the future) should not be ignored and is a chance for BioContainers to provide its support to an emerging but growing community.

Software containers are a key element in the frame of Open Science, Open Data & Open Source which is strongly supported and advocated by ELIXIR. Software containers are key to guarantee data provenance when described as part of scientific workflows and an important element towards results reproducibility.

They also ease software installation on local computer or cluster facilities.Thus, software containers are transversal to most of the strategic lines of the ELIXIR Tools Platform for the 2022 - 2023 Scientific programme.
We have divided this task into two work packages around software containers that compliment each other.

The first work package aims to maintain and extend the work initiated in the previous ELIXIR implementation study on BioContainers. The implementation study on BioContainers contributed to unify various initiatives in ELIXIR Nodes around software containers and bring them under a common infrastructure and metadata federation. This first work package will focus on operational maintenance of the infrastructure. Additional registry mirrors will be investigated for cloud/local registry availability. To do so, a partnership with Amazon (and potentially other commercial cloud providers) will be set.

While x86 architectures dominate the scientific compute clusters and clouds at this time (currently the container architecture supported by BioContainers), ARM architecture is a mature technology getting traction in both server and consumer markets. With the first super-computers starting to build on ARM architectures, the BioContainers project needs to be prepared to offer ARM based container solutions to our users. Therefore, a task of this work package will evaluate the multi-architecture container solution and add support for ARM in addition to x86. As this task requires extra physical resources, we will try to get support from the ARM company and/or support from ELIXIR members to build ARM-based BioContainers.

To compile software against different architectures, upstream support from tool developers will most likely be needed. Here, we will work together with the “development best practices” (Task 4) team to encourage developers to provide multi-arch support to their software and help them along the way.

BioContainers already integrates its metadata with the central repository of the Tools Platform, work will continue to align/homogenise with the repository evolutions which were, in a first step, a raw addition of metadata from all Tools Platform services (BioContainers, OpenEBench, bio.tools, ...) and the Tools Ecosystem.

Second work packages will focus on user communities. While BioContainers is widely used by the ELIXIR community, it could reach/extend to other communities around life science. Discussions with EOSC and other communities will evaluate how BioContainers could fit to their needs, and the possibility to contribute to the BioContainers project and the registry. This would provide end users a single entry-point and solution for container management and optimize human/compute resources.

As a summary, BioContainers is today well established in our community and provides a stable infrastructure for container availability and findability. Existing solutions could benefit extra life science communities. Energy efficiency trends towards ARM architecture (and possibly others in the future) should not be ignored and is a chance for BioContainers to provide its support to an emerging but growing community.

Software containers are a key element in the frame of Open Science, Open Data & Open Source which is strongly supported and advocated by ELIXIR. Software containers are key to guarantee data provenance when described as part of scientific workflows and an important element towards results reproducibility.

They also ease software installation on local computer or cluster facilities.Thus, software containers are transversal to most of the strategic lines of the ELIXIR Tools Platform for the 2022 - 2023 Scientific programme.
We have divided this task into two work packages around software containers that compliment each other.

The first work package aims to maintain and extend the work initiated in the previous ELIXIR implementation study on BioContainers. The implementation study on BioContainers contributed to unify various initiatives in ELIXIR Nodes around software containers and bring them under a common infrastructure and metadata federation. This first work package will focus on operational maintenance of the infrastructure. Additional registry mirrors will be investigated for cloud/local registry availability. To do so, a partnership with Amazon (and potentially other commercial cloud providers) will be set.

While x86 architectures dominate the scientific compute clusters and clouds at this time (currently the container architecture supported by BioContainers), ARM architecture is a mature technology getting traction in both server and consumer markets. With the first super-computers starting to build on ARM architectures, the BioContainers project needs to be prepared to offer ARM based container solutions to our users. Therefore, a task of this work package will evaluate the multi-architecture container solution and add support for ARM in addition to x86. As this task requires extra physical resources, we will try to get support from the ARM company and/or support from ELIXIR members to build ARM-based BioContainers.

To compile software against different architectures, upstream support from tool developers will most likely be needed. Here, we will work together with the “development best practices” (Task 4) team to encourage developers to provide multi-arch support to their software and help them along the way.

BioContainers already integrates its metadata with the central repository of the Tools Platform, work will continue to align/homogenise with the repository evolutions which were, in a first step, a raw addition of metadata from all Tools Platform services (BioContainers, OpenEBench, bio.tools, ...) and the Tools Ecosystem.

Second work packages will focus on user communities. While BioContainers is widely used by the ELIXIR community, it could reach/extend to other communities around life science. Discussions with EOSC and other communities will evaluate how BioContainers could fit to their needs, and the possibility to contribute to the BioContainers project and the registry. This would provide end users a single entry-point and solution for container management and optimize human/compute resources.

As a summary, BioContainers is today well established in our community and provides a stable infrastructure for container availability and findability. Existing solutions could benefit extra life science communities. Energy efficiency trends towards ARM architecture (and possibly others in the future) should not be ignored and is a chance for BioContainers to provide its support to an emerging but growing community.

Software containers are a key element in the frame of Open Science, Open Data & Open Source which is strongly supported and advocated by ELIXIR. Software containers are key to guarantee data provenance when described as part of scientific workflows and an important element towards results reproducibility.

They also ease software installation on local computer or cluster facilities.Thus, software containers are transversal to most of the strategic lines of the ELIXIR Tools Platform for the 2022 - 2023 Scientific programme.
We have divided this task into two work packages around software containers that compliment each other.

The first work package aims to maintain and extend the work initiated in the previous ELIXIR implementation study on BioContainers. The implementation study on BioContainers contributed to unify various initiatives in ELIXIR Nodes around software containers and bring them under a common infrastructure and metadata federation. This first work package will focus on operational maintenance of the infrastructure. Additional registry mirrors will be investigated for cloud/local registry availability. To do so, a partnership with Amazon (and potentially other commercial cloud providers) will be set.

While x86 architectures dominate the scientific compute clusters and clouds at this time (currently the container architecture supported by BioContainers), ARM architecture is a mature technology getting traction in both server and consumer markets. With the first super-computers starting to build on ARM architectures, the BioContainers project needs to be prepared to offer ARM based container solutions to our users. Therefore, a task of this work package will evaluate the multi-architecture container solution and add support for ARM in addition to x86. As this task requires extra physical resources, we will try to get support from the ARM company and/or support from ELIXIR members to build ARM-based BioContainers.

To compile software against different architectures, upstream support from tool developers will most likely be needed. Here, we will work together with the “development best practices” (Task 4) team to encourage developers to provide multi-arch support to their software and help them along the way.

BioContainers already integrates its metadata with the central repository of the Tools Platform, work will continue to align/homogenise with the repository evolutions which were, in a first step, a raw addition of metadata from all Tools Platform services (BioContainers, OpenEBench, bio.tools, ...) and the Tools Ecosystem.

Second work packages will focus on user communities. While BioContainers is widely used by the ELIXIR community, it could reach/extend to other communities around life science. Discussions with EOSC and other communities will evaluate how BioContainers could fit to their needs, and the possibility to contribute to the BioContainers project and the registry. This would provide end users a single entry-point and solution for container management and optimize human/compute resources.

As a summary, BioContainers is today well established in our community and provides a stable infrastructure for container availability and findability. Existing solutions could benefit extra life science communities. Energy efficiency trends towards ARM architecture (and possibly others in the future) should not be ignored and is a chance for BioContainers to provide its support to an emerging but growing community.

Software containers are a key element in the frame of Open Science, Open Data & Open Source which is strongly supported and advocated by ELIXIR. Software containers are key to guarantee data provenance when described as part of scientific workflows and an important element towards results reproducibility.

They also ease software installation on local computer or cluster facilities.Thus, software containers are transversal to most of the strategic lines of the ELIXIR Tools Platform for the 2022 - 2023 Scientific programme.
We have divided this task into two work packages around software containers that compliment each other.

The first work package aims to maintain and extend the work initiated in the previous ELIXIR implementation study on BioContainers. The implementation study on BioContainers contributed to unify various initiatives in ELIXIR Nodes around software containers and bring them under a common infrastructure and metadata federation. This first work package will focus on operational maintenance of the infrastructure. Additional registry mirrors will be investigated for cloud/local registry availability. To do so, a partnership with Amazon (and potentially other commercial cloud providers) will be set.

While x86 architectures dominate the scientific compute clusters and clouds at this time (currently the container architecture supported by BioContainers), ARM architecture is a mature technology getting traction in both server and consumer markets. With the first super-computers starting to build on ARM architectures, the BioContainers project needs to be prepared to offer ARM based container solutions to our users. Therefore, a task of this work package will evaluate the multi-architecture container solution and add support for ARM in addition to x86. As this task requires extra physical resources, we will try to get support from the ARM company and/or support from ELIXIR members to build ARM-based BioContainers.

To compile software against different architectures, upstream support from tool developers will most likely be needed. Here, we will work together with the “development best practices” (Task 4) team to encourage developers to provide multi-arch support to their software and help them along the way.

BioContainers already integrates its metadata with the central repository of the Tools Platform, work will continue to align/homogenise with the repository evolutions which were, in a first step, a raw addition of metadata from all Tools Platform services (BioContainers, OpenEBench, bio.tools, ...) and the Tools Ecosystem.

Second work packages will focus on user communities. While BioContainers is widely used by the ELIXIR community, it could reach/extend to other communities around life science. Discussions with EOSC and other communities will evaluate how BioContainers could fit to their needs, and the possibility to contribute to the BioContainers project and the registry. This would provide end users a single entry-point and solution for container management and optimize human/compute resources.

As a summary, BioContainers is today well established in our community and provides a stable infrastructure for container availability and findability. Existing solutions could benefit extra life science communities. Energy efficiency trends towards ARM architecture (and possibly others in the future) should not be ignored and is a chance for BioContainers to provide its support to an emerging but growing community.

Software containers are a key element in the frame of Open Science, Open Data & Open Source which is strongly supported and advocated by ELIXIR. Software containers are key to guarantee data provenance when described as part of scientific workflows and an important element towards results reproducibility.

They also ease software installation on local computer or cluster facilities.Thus, software containers are transversal to most of the strategic lines of the ELIXIR Tools Platform for the 2022 - 2023 Scientific programme.
We have divided this task into two work packages around software containers that compliment each other.

The first work package aims to maintain and extend the work initiated in the previous ELIXIR implementation study on BioContainers. The implementation study on BioContainers contributed to unify various initiatives in ELIXIR Nodes around software containers and bring them under a common infrastructure and metadata federation. This first work package will focus on operational maintenance of the infrastructure. Additional registry mirrors will be investigated for cloud/local registry availability. To do so, a partnership with Amazon (and potentially other commercial cloud providers) will be set.

While x86 architectures dominate the scientific compute clusters and clouds at this time (currently the container architecture supported by BioContainers), ARM architecture is a mature technology getting traction in both server and consumer markets. With the first super-computers starting to build on ARM architectures, the BioContainers project needs to be prepared to offer ARM based container solutions to our users. Therefore, a task of this work package will evaluate the multi-architecture container solution and add support for ARM in addition to x86. As this task requires extra physical resources, we will try to get support from the ARM company and/or support from ELIXIR members to build ARM-based BioContainers.

To compile software against different architectures, upstream support from tool developers will most likely be needed. Here, we will work together with the “development best practices” (Task 4) team to encourage developers to provide multi-arch support to their software and help them along the way.

BioContainers already integrates its metadata with the central repository of the Tools Platform, work will continue to align/homogenise with the repository evolutions which were, in a first step, a raw addition of metadata from all Tools Platform services (BioContainers, OpenEBench, bio.tools, ...) and the Tools Ecosystem.

Second work packages will focus on user communities. While BioContainers is widely used by the ELIXIR community, it could reach/extend to other communities around life science. Discussions with EOSC and other communities will evaluate how BioContainers could fit to their needs, and the possibility to contribute to the BioContainers project and the registry. This would provide end users a single entry-point and solution for container management and optimize human/compute resources.

As a summary, BioContainers is today well established in our community and provides a stable infrastructure for container availability and findability. Existing solutions could benefit extra life science communities. Energy efficiency trends towards ARM architecture (and possibly others in the future) should not be ignored and is a chance for BioContainers to provide its support to an emerging but growing community.

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

OpenEBench is designed to support benchmarking activities in terms of 1) scientific performance of individual tools, workflows and platforms in the context of self-organized communities, and 2)
technical monitoring of the life sciences research software using dedicated metrics and indicators.
Indeed, one of the main goals of OpenEBench is to become an observatory of bioinformatics software quality regarding openness. OpenEBench is strongly committed to promote the adoption of all guidelines and technologies promoted by ELIXIR including but not limited to ELIXIR AAI, software development and containerization best-practices, FAIR data principles for reference datasets as well as the principles on Open Data, Open Source and Open Science.

OpenEBench is designed to support benchmarking activities in terms of 1) scientific performance of individual tools, workflows and platforms in the context of self-organized communities, and 2)
technical monitoring of the life sciences research software using dedicated metrics and indicators.
Indeed, one of the main goals of OpenEBench is to become an observatory of bioinformatics software quality regarding openness. OpenEBench is strongly committed to promote the adoption of all guidelines and technologies promoted by ELIXIR including but not limited to ELIXIR AAI, software development and containerization best-practices, FAIR data principles for reference datasets as well as the principles on Open Data, Open Source and Open Science.

OpenEBench is designed to support benchmarking activities in terms of 1) scientific performance of individual tools, workflows and platforms in the context of self-organized communities, and 2)
technical monitoring of the life sciences research software using dedicated metrics and indicators.
Indeed, one of the main goals of OpenEBench is to become an observatory of bioinformatics software quality regarding openness. OpenEBench is strongly committed to promote the adoption of all guidelines and technologies promoted by ELIXIR including but not limited to ELIXIR AAI, software development and containerization best-practices, FAIR data principles for reference datasets as well as the principles on Open Data, Open Source and Open Science.

OpenEBench is designed to support benchmarking activities in terms of 1) scientific performance of individual tools, workflows and platforms in the context of self-organized communities, and 2)
technical monitoring of the life sciences research software using dedicated metrics and indicators.
Indeed, one of the main goals of OpenEBench is to become an observatory of bioinformatics software quality regarding openness. OpenEBench is strongly committed to promote the adoption of all guidelines and technologies promoted by ELIXIR including but not limited to ELIXIR AAI, software development and containerization best-practices, FAIR data principles for reference datasets as well as the principles on Open Data, Open Source and Open Science.

OpenEBench is designed to support benchmarking activities in terms of 1) scientific performance of individual tools, workflows and platforms in the context of self-organized communities, and 2)
technical monitoring of the life sciences research software using dedicated metrics and indicators.
Indeed, one of the main goals of OpenEBench is to become an observatory of bioinformatics software quality regarding openness. OpenEBench is strongly committed to promote the adoption of all guidelines and technologies promoted by ELIXIR including but not limited to ELIXIR AAI, software development and containerization best-practices, FAIR data principles for reference datasets as well as the principles on Open Data, Open Source and Open Science.

OpenEBench is designed to support benchmarking activities in terms of 1) scientific performance of individual tools, workflows and platforms in the context of self-organized communities, and 2)
technical monitoring of the life sciences research software using dedicated metrics and indicators.
Indeed, one of the main goals of OpenEBench is to become an observatory of bioinformatics software quality regarding openness. OpenEBench is strongly committed to promote the adoption of all guidelines and technologies promoted by ELIXIR including but not limited to ELIXIR AAI, software development and containerization best-practices, FAIR data principles for reference datasets as well as the principles on Open Data, Open Source and Open Science.

This study will support OpenEBench in the goal to become an observatory of bioinformatics software quality regarding openness including: 

• ELIXIR AAI
• software development and containerization best-practices
• FAIR data principles for reference datasets as well as the principles on Open Data, Open Source and Open Science.

WP1. A Core Benchmarking Service: 

Work Package 1 has the following aims:

• To establish, consolidate and extend the core ELIXIR Service for benchmarking
• To lower the benchmarking startup hurdle
• To provide basic tests of tool operability
• To alleviate reimplementation of abstractable workflows

Through four subtasks: 

1. Execution environment for benchmarking workflows
2. Automated data import
3. Scientific benchmarking test case
4. Extend visualization gallery

This study will support OpenEBench in the goal to become an observatory of bioinformatics software quality regarding openness including: 

• ELIXIR AAI
• software development and containerization best-practices
• FAIR data principles for reference datasets as well as the principles on Open Data, Open Source and Open Science.

WP1. A Core Benchmarking Service: 

Work Package 1 has the following aims:

• To establish, consolidate and extend the core ELIXIR Service for benchmarking
• To lower the benchmarking startup hurdle
• To provide basic tests of tool operability
• To alleviate reimplementation of abstractable workflows

Through four subtasks: 

1. Execution environment for benchmarking workflows
2. Automated data import
3. Scientific benchmarking test case
4. Extend visualization gallery

This study will support OpenEBench in the goal to become an observatory of bioinformatics software quality regarding openness including: 

• ELIXIR AAI
• software development and containerization best-practices
• FAIR data principles for reference datasets as well as the principles on Open Data, Open Source and Open Science.

WP1. A Core Benchmarking Service: 

Work Package 1 has the following aims:

• To establish, consolidate and extend the core ELIXIR Service for benchmarking
• To lower the benchmarking startup hurdle
• To provide basic tests of tool operability
• To alleviate reimplementation of abstractable workflows

Through four subtasks: 

1. Execution environment for benchmarking workflows
2. Automated data import
3. Scientific benchmarking test case
4. Extend visualization gallery

This study will support OpenEBench in the goal to become an observatory of bioinformatics software quality regarding openness including: 

• ELIXIR AAI
• software development and containerization best-practices
• FAIR data principles for reference datasets as well as the principles on Open Data, Open Source and Open Science.

WP1. A Core Benchmarking Service: 

Work Package 1 has the following aims:

• To establish, consolidate and extend the core ELIXIR Service for benchmarking
• To lower the benchmarking startup hurdle
• To provide basic tests of tool operability
• To alleviate reimplementation of abstractable workflows

Through four subtasks: 

1. Execution environment for benchmarking workflows
2. Automated data import
3. Scientific benchmarking test case
4. Extend visualization gallery

This study will support OpenEBench in the goal to become an observatory of bioinformatics software quality regarding openness including: 

• ELIXIR AAI
• software development and containerization best-practices
• FAIR data principles for reference datasets as well as the principles on Open Data, Open Source and Open Science.

WP1. A Core Benchmarking Service: 

Work Package 1 has the following aims:

• To establish, consolidate and extend the core ELIXIR Service for benchmarking
• To lower the benchmarking startup hurdle
• To provide basic tests of tool operability
• To alleviate reimplementation of abstractable workflows

Through four subtasks: 

1. Execution environment for benchmarking workflows
2. Automated data import
3. Scientific benchmarking test case
4. Extend visualization gallery

bio.tools provides persistent identifiers for 10,000+ verified tool descriptions and has attracted 20 new contributors / month over the last year. Through this Study we will: 

1. Engage scientific expertise including ELIXIR Communities and ELIXIR Nodes to improve the scientific quality and national representation.
2. Develop tooling for domain-specific bio.tools views for communities

Through a combination of

• best-practice guidelines,
• extension of the bio.tools studentship scheme,
• community-led workshops,
• adherence to the bio.tools Tool Information Standards.

Four subtasks will establish a network of thematic editors for scientific areas and nations, to oversee improvement in the scientific quality of EDAM and bio.tools, and ensure national interests are adequately represented.  This will represent existing and emerging ELIXIR communities, e.g. Proteomics, Metabolomics and Marine Metagenomics.

bio.tools provides persistent identifiers for 10,000+ verified tool descriptions and has attracted 20 new contributors / month over the last year. Through this Study we will: 

1. Engage scientific expertise including ELIXIR Communities and ELIXIR Nodes to improve the scientific quality and national representation.
2. Develop tooling for domain-specific bio.tools views for communities

Through a combination of

• best-practice guidelines,
• extension of the bio.tools studentship scheme,
• community-led workshops,
• adherence to the bio.tools Tool Information Standards.

Four subtasks will establish a network of thematic editors for scientific areas and nations, to oversee improvement in the scientific quality of EDAM and bio.tools, and ensure national interests are adequately represented.  This will represent existing and emerging ELIXIR communities, e.g. Proteomics, Metabolomics and Marine Metagenomics.

bio.tools provides persistent identifiers for 10,000+ verified tool descriptions and has attracted 20 new contributors / month over the last year. Through this Study we will: 

1. Engage scientific expertise including ELIXIR Communities and ELIXIR Nodes to improve the scientific quality and national representation.
2. Develop tooling for domain-specific bio.tools views for communities

Through a combination of

• best-practice guidelines,
• extension of the bio.tools studentship scheme,
• community-led workshops,
• adherence to the bio.tools Tool Information Standards.

Four subtasks will establish a network of thematic editors for scientific areas and nations, to oversee improvement in the scientific quality of EDAM and bio.tools, and ensure national interests are adequately represented.  This will represent existing and emerging ELIXIR communities, e.g. Proteomics, Metabolomics and Marine Metagenomics.

bio.tools provides persistent identifiers for 10,000+ verified tool descriptions and has attracted 20 new contributors / month over the last year. Through this Study we will: 

1. Engage scientific expertise including ELIXIR Communities and ELIXIR Nodes to improve the scientific quality and national representation.
2. Develop tooling for domain-specific bio.tools views for communities

Through a combination of

• best-practice guidelines,
• extension of the bio.tools studentship scheme,
• community-led workshops,
• adherence to the bio.tools Tool Information Standards.

Four subtasks will establish a network of thematic editors for scientific areas and nations, to oversee improvement in the scientific quality of EDAM and bio.tools, and ensure national interests are adequately represented.  This will represent existing and emerging ELIXIR communities, e.g. Proteomics, Metabolomics and Marine Metagenomics.

To raise the quality and sustainability of research software

This study will promote the production, adopting, promoting and measuring information standards and best practices applied to software development life cycle. We have published four simple recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices. 

The next steps are to:

• Adopt, promote, and recognise these practices, by developing guidelines to help software developers to adopt and comply with the 4OSS recommendations
• Train and promote software best practices and the 4OSS
• Measure, recognise and  visualise adoption (longer term aim)
• To develop a software management plan template, connected to a concise description of the guidelines for open research software.
• Produce a white paper for the software development management plan for ELIXIR which can be consequently used to produce training material.
• We will work with the newly formed  ReSA (Research Software Alliance ) to facilitate adoption of this plan to the wider community.

To raise the quality and sustainability of research software

This study will promote the production, adopting, promoting and measuring information standards and best practices applied to software development life cycle. We have published four simple recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices. 

The next steps are to:

• Adopt, promote, and recognise these practices, by developing guidelines to help software developers to adopt and comply with the 4OSS recommendations
• Train and promote software best practices and the 4OSS
• Measure, recognise and  visualise adoption (longer term aim)
• To develop a software management plan template, connected to a concise description of the guidelines for open research software.
• Produce a white paper for the software development management plan for ELIXIR which can be consequently used to produce training material.
• We will work with the newly formed  ReSA (Research Software Alliance ) to facilitate adoption of this plan to the wider community.

To raise the quality and sustainability of research software

This study will promote the production, adopting, promoting and measuring information standards and best practices applied to software development life cycle. We have published four simple recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices. 

The next steps are to:

• Adopt, promote, and recognise these practices, by developing guidelines to help software developers to adopt and comply with the 4OSS recommendations
• Train and promote software best practices and the 4OSS
• Measure, recognise and  visualise adoption (longer term aim)
• To develop a software management plan template, connected to a concise description of the guidelines for open research software.
• Produce a white paper for the software development management plan for ELIXIR which can be consequently used to produce training material.
• We will work with the newly formed  ReSA (Research Software Alliance ) to facilitate adoption of this plan to the wider community.

To raise the quality and sustainability of research software

This study will promote the production, adopting, promoting and measuring information standards and best practices applied to software development life cycle. We have published four simple recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices. 

The next steps are to:

• Adopt, promote, and recognise these practices, by developing guidelines to help software developers to adopt and comply with the 4OSS recommendations
• Train and promote software best practices and the 4OSS
• Measure, recognise and  visualise adoption (longer term aim)
• To develop a software management plan template, connected to a concise description of the guidelines for open research software.
• Produce a white paper for the software development management plan for ELIXIR which can be consequently used to produce training material.
• We will work with the newly formed  ReSA (Research Software Alliance ) to facilitate adoption of this plan to the wider community.

To raise the quality and sustainability of research software

This study will promote the production, adopting, promoting and measuring information standards and best practices applied to software development life cycle. We have published four simple recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices. 

The next steps are to:

• Adopt, promote, and recognise these practices, by developing guidelines to help software developers to adopt and comply with the 4OSS recommendations
• Train and promote software best practices and the 4OSS
• Measure, recognise and  visualise adoption (longer term aim)
• To develop a software management plan template, connected to a concise description of the guidelines for open research software.
• Produce a white paper for the software development management plan for ELIXIR which can be consequently used to produce training material.
• We will work with the newly formed  ReSA (Research Software Alliance ) to facilitate adoption of this plan to the wider community.

To raise the quality and sustainability of research software

This study will promote the production, adopting, promoting and measuring information standards and best practices applied to software development life cycle. We have published four simple recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices. 

The next steps are to:

• Adopt, promote, and recognise these practices, by developing guidelines to help software developers to adopt and comply with the 4OSS recommendations
• Train and promote software best practices and the 4OSS
• Measure, recognise and  visualise adoption (longer term aim)
• To develop a software management plan template, connected to a concise description of the guidelines for open research software.
• Produce a white paper for the software development management plan for ELIXIR which can be consequently used to produce training material.
• We will work with the newly formed  ReSA (Research Software Alliance ) to facilitate adoption of this plan to the wider community.

The aim of this task is to raise the Quality and Sustainability of research software by producing, promoting, measuring and adopting best practices applied to the software development life cycle. So far, efforts of this group have led to the publications of the four simple recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices.

Additionally, we’ve produced training material to promote and increase the awareness of these practices, and delivered several workshops across ELIXIR Nodes, targeting researchers and developers. Moreover, after capturing the community practices towards managing research software, this group produced a first draft of a software management plan template, connected to a concise description of the guidelines for open research software.

Next steps include activities towards alignment between the best practices and the wider Tools Platform ecosystem, the implementation of tools to support the application of these practices, expanding the training portfolio of the Software Best Practices including the Software Management Plan, and ultimately create a community around the sustainability, adoption and maintenance of the Software Management Plan effort going beyond the confines of the ELIXIR network, and engaging with relevant initiatives and groups around the globe (such as the Research Software Alliance, the Australia BioCommons, Force11 and the Research Data Alliance).

The aim of this task is to raise the Quality and Sustainability of research software by producing, promoting, measuring and adopting best practices applied to the software development life cycle. So far, efforts of this group have led to the publications of the four simple recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices.

Additionally, we’ve produced training material to promote and increase the awareness of these practices, and delivered several workshops across ELIXIR Nodes, targeting researchers and developers. Moreover, after capturing the community practices towards managing research software, this group produced a first draft of a software management plan template, connected to a concise description of the guidelines for open research software.

Next steps include activities towards alignment between the best practices and the wider Tools Platform ecosystem, the implementation of tools to support the application of these practices, expanding the training portfolio of the Software Best Practices including the Software Management Plan, and ultimately create a community around the sustainability, adoption and maintenance of the Software Management Plan effort going beyond the confines of the ELIXIR network, and engaging with relevant initiatives and groups around the globe (such as the Research Software Alliance, the Australia BioCommons, Force11 and the Research Data Alliance).

The aim of this task is to raise the Quality and Sustainability of research software by producing, promoting, measuring and adopting best practices applied to the software development life cycle. So far, efforts of this group have led to the publications of the four simple recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices.

Additionally, we’ve produced training material to promote and increase the awareness of these practices, and delivered several workshops across ELIXIR Nodes, targeting researchers and developers. Moreover, after capturing the community practices towards managing research software, this group produced a first draft of a software management plan template, connected to a concise description of the guidelines for open research software.

Next steps include activities towards alignment between the best practices and the wider Tools Platform ecosystem, the implementation of tools to support the application of these practices, expanding the training portfolio of the Software Best Practices including the Software Management Plan, and ultimately create a community around the sustainability, adoption and maintenance of the Software Management Plan effort going beyond the confines of the ELIXIR network, and engaging with relevant initiatives and groups around the globe (such as the Research Software Alliance, the Australia BioCommons, Force11 and the Research Data Alliance).

The aim of this task is to raise the Quality and Sustainability of research software by producing, promoting, measuring and adopting best practices applied to the software development life cycle. So far, efforts of this group have led to the publications of the four simple recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices.

Additionally, we’ve produced training material to promote and increase the awareness of these practices, and delivered several workshops across ELIXIR Nodes, targeting researchers and developers. Moreover, after capturing the community practices towards managing research software, this group produced a first draft of a software management plan template, connected to a concise description of the guidelines for open research software.

Next steps include activities towards alignment between the best practices and the wider Tools Platform ecosystem, the implementation of tools to support the application of these practices, expanding the training portfolio of the Software Best Practices including the Software Management Plan, and ultimately create a community around the sustainability, adoption and maintenance of the Software Management Plan effort going beyond the confines of the ELIXIR network, and engaging with relevant initiatives and groups around the globe (such as the Research Software Alliance, the Australia BioCommons, Force11 and the Research Data Alliance).

The aim of this task is to raise the Quality and Sustainability of research software by producing, promoting, measuring and adopting best practices applied to the software development life cycle. So far, efforts of this group have led to the publications of the four simple recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices.

Additionally, we’ve produced training material to promote and increase the awareness of these practices, and delivered several workshops across ELIXIR Nodes, targeting researchers and developers. Moreover, after capturing the community practices towards managing research software, this group produced a first draft of a software management plan template, connected to a concise description of the guidelines for open research software.

Next steps include activities towards alignment between the best practices and the wider Tools Platform ecosystem, the implementation of tools to support the application of these practices, expanding the training portfolio of the Software Best Practices including the Software Management Plan, and ultimately create a community around the sustainability, adoption and maintenance of the Software Management Plan effort going beyond the confines of the ELIXIR network, and engaging with relevant initiatives and groups around the globe (such as the Research Software Alliance, the Australia BioCommons, Force11 and the Research Data Alliance).

The aim of this task is to raise the Quality and Sustainability of research software by producing, promoting, measuring and adopting best practices applied to the software development life cycle. So far, efforts of this group have led to the publications of the four simple recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices.

Additionally, we’ve produced training material to promote and increase the awareness of these practices, and delivered several workshops across ELIXIR Nodes, targeting researchers and developers. Moreover, after capturing the community practices towards managing research software, this group produced a first draft of a software management plan template, connected to a concise description of the guidelines for open research software.

Next steps include activities towards alignment between the best practices and the wider Tools Platform ecosystem, the implementation of tools to support the application of these practices, expanding the training portfolio of the Software Best Practices including the Software Management Plan, and ultimately create a community around the sustainability, adoption and maintenance of the Software Management Plan effort going beyond the confines of the ELIXIR network, and engaging with relevant initiatives and groups around the globe (such as the Research Software Alliance, the Australia BioCommons, Force11 and the Research Data Alliance).

The aim of this task is to raise the Quality and Sustainability of research software by producing, promoting, measuring and adopting best practices applied to the software development life cycle. So far, efforts of this group have led to the publications of the four simple recommendations to encourage best practices in research software and the Top 10 metrics for life science software good practices.

Additionally, we’ve produced training material to promote and increase the awareness of these practices, and delivered several workshops across ELIXIR Nodes, targeting researchers and developers. Moreover, after capturing the community practices towards managing research software, this group produced a first draft of a software management plan template, connected to a concise description of the guidelines for open research software.

Next steps include activities towards alignment between the best practices and the wider Tools Platform ecosystem, the implementation of tools to support the application of these practices, expanding the training portfolio of the Software Best Practices including the Software Management Plan, and ultimately create a community around the sustainability, adoption and maintenance of the Software Management Plan effort going beyond the confines of the ELIXIR network, and engaging with relevant initiatives and groups around the globe (such as the Research Software Alliance, the Australia BioCommons, Force11 and the Research Data Alliance).

The aim of this Implementation Study was to prepare for the start of the ELIXIR-EXCELERATE project and the anticipated scaling up of the ELIXIR Tools and Data Services Registry, both in terms of the content, functionality and the community behind it, certain urgent developments are required. These include technical development of the registry, preparations for a series of hackathons and publications following from these efforts.

The study has been completed, see the end report.

Webinar summarising the outcomes

Slides

The bio.tools registry content is continuously growing as new entries are added by curators and by the community. Currently contains over 20,000 tool annotations. Given the large number of bio.tools entries, the registry needs to ensure that its users can seamlessly search and obtain tools of interest.

To achieve this there is a need for high quality content along with the functionality and interface necessary to curate and maintain this content, and provide it to the users in a manner that encourages data (re) usability, contribution and integration with other projects. Both the bio.tools registry and the EDAM ontology are essential, continuously evolving components of the ELIXIR Tools Platform, that will be deeply integrated with the Tools Platform Ecosystem and other Platforms.

All the work package components described below synergize and complement each other. It is important to acknowledge that there is little value gained by having quality tool annotations without the mechanisms and interfaces to identify and use these tools. In a similar fashion there is little value to having highly performant searching and complex interfaces without quality of data. These types of issues can be solved by tackling the problem from multiple angles. In consequence the below described tasks will contribute to creating a well integrated and up-to-date system which provides both valuable high quality data and the means to deliver this data to the users in a practical and useful manner.

The bio.tools registry content is continuously growing as new entries are added by curators and by the community. Currently contains over 20,000 tool annotations. Given the large number of bio.tools entries, the registry needs to ensure that its users can seamlessly search and obtain tools of interest.

To achieve this there is a need for high quality content along with the functionality and interface necessary to curate and maintain this content, and provide it to the users in a manner that encourages data (re) usability, contribution and integration with other projects. Both the bio.tools registry and the EDAM ontology are essential, continuously evolving components of the ELIXIR Tools Platform, that will be deeply integrated with the Tools Platform Ecosystem and other Platforms.

All the work package components described below synergize and complement each other. It is important to acknowledge that there is little value gained by having quality tool annotations without the mechanisms and interfaces to identify and use these tools. In a similar fashion there is little value to having highly performant searching and complex interfaces without quality of data. These types of issues can be solved by tackling the problem from multiple angles. In consequence the below described tasks will contribute to creating a well integrated and up-to-date system which provides both valuable high quality data and the means to deliver this data to the users in a practical and useful manner.

The bio.tools registry content is continuously growing as new entries are added by curators and by the community. Currently contains over 20,000 tool annotations. Given the large number of bio.tools entries, the registry needs to ensure that its users can seamlessly search and obtain tools of interest.

To achieve this there is a need for high quality content along with the functionality and interface necessary to curate and maintain this content, and provide it to the users in a manner that encourages data (re) usability, contribution and integration with other projects. Both the bio.tools registry and the EDAM ontology are essential, continuously evolving components of the ELIXIR Tools Platform, that will be deeply integrated with the Tools Platform Ecosystem and other Platforms.

All the work package components described below synergize and complement each other. It is important to acknowledge that there is little value gained by having quality tool annotations without the mechanisms and interfaces to identify and use these tools. In a similar fashion there is little value to having highly performant searching and complex interfaces without quality of data. These types of issues can be solved by tackling the problem from multiple angles. In consequence the below described tasks will contribute to creating a well integrated and up-to-date system which provides both valuable high quality data and the means to deliver this data to the users in a practical and useful manner.

The bio.tools registry content is continuously growing as new entries are added by curators and by the community. Currently contains over 20,000 tool annotations. Given the large number of bio.tools entries, the registry needs to ensure that its users can seamlessly search and obtain tools of interest.

To achieve this there is a need for high quality content along with the functionality and interface necessary to curate and maintain this content, and provide it to the users in a manner that encourages data (re) usability, contribution and integration with other projects. Both the bio.tools registry and the EDAM ontology are essential, continuously evolving components of the ELIXIR Tools Platform, that will be deeply integrated with the Tools Platform Ecosystem and other Platforms.

All the work package components described below synergize and complement each other. It is important to acknowledge that there is little value gained by having quality tool annotations without the mechanisms and interfaces to identify and use these tools. In a similar fashion there is little value to having highly performant searching and complex interfaces without quality of data. These types of issues can be solved by tackling the problem from multiple angles. In consequence the below described tasks will contribute to creating a well integrated and up-to-date system which provides both valuable high quality data and the means to deliver this data to the users in a practical and useful manner.

The bio.tools registry content is continuously growing as new entries are added by curators and by the community. Currently contains over 20,000 tool annotations. Given the large number of bio.tools entries, the registry needs to ensure that its users can seamlessly search and obtain tools of interest.

To achieve this there is a need for high quality content along with the functionality and interface necessary to curate and maintain this content, and provide it to the users in a manner that encourages data (re) usability, contribution and integration with other projects. Both the bio.tools registry and the EDAM ontology are essential, continuously evolving components of the ELIXIR Tools Platform, that will be deeply integrated with the Tools Platform Ecosystem and other Platforms.

All the work package components described below synergize and complement each other. It is important to acknowledge that there is little value gained by having quality tool annotations without the mechanisms and interfaces to identify and use these tools. In a similar fashion there is little value to having highly performant searching and complex interfaces without quality of data. These types of issues can be solved by tackling the problem from multiple angles. In consequence the below described tasks will contribute to creating a well integrated and up-to-date system which provides both valuable high quality data and the means to deliver this data to the users in a practical and useful manner.

The bio.tools registry content is continuously growing as new entries are added by curators and by the community. Currently contains over 20,000 tool annotations. Given the large number of bio.tools entries, the registry needs to ensure that its users can seamlessly search and obtain tools of interest.

To achieve this there is a need for high quality content along with the functionality and interface necessary to curate and maintain this content, and provide it to the users in a manner that encourages data (re) usability, contribution and integration with other projects. Both the bio.tools registry and the EDAM ontology are essential, continuously evolving components of the ELIXIR Tools Platform, that will be deeply integrated with the Tools Platform Ecosystem and other Platforms.

All the work package components described below synergize and complement each other. It is important to acknowledge that there is little value gained by having quality tool annotations without the mechanisms and interfaces to identify and use these tools. In a similar fashion there is little value to having highly performant searching and complex interfaces without quality of data. These types of issues can be solved by tackling the problem from multiple angles. In consequence the below described tasks will contribute to creating a well integrated and up-to-date system which provides both valuable high quality data and the means to deliver this data to the users in a practical and useful manner.

The bio.tools registry content is continuously growing as new entries are added by curators and by the community. Currently contains over 20,000 tool annotations. Given the large number of bio.tools entries, the registry needs to ensure that its users can seamlessly search and obtain tools of interest.

To achieve this there is a need for high quality content along with the functionality and interface necessary to curate and maintain this content, and provide it to the users in a manner that encourages data (re) usability, contribution and integration with other projects. Both the bio.tools registry and the EDAM ontology are essential, continuously evolving components of the ELIXIR Tools Platform, that will be deeply integrated with the Tools Platform Ecosystem and other Platforms.

All the work package components described below synergize and complement each other. It is important to acknowledge that there is little value gained by having quality tool annotations without the mechanisms and interfaces to identify and use these tools. In a similar fashion there is little value to having highly performant searching and complex interfaces without quality of data. These types of issues can be solved by tackling the problem from multiple angles. In consequence the below described tasks will contribute to creating a well integrated and up-to-date system which provides both valuable high quality data and the means to deliver this data to the users in a practical and useful manner.

The bio.tools registry content is continuously growing as new entries are added by curators and by the community. Currently contains over 20,000 tool annotations. Given the large number of bio.tools entries, the registry needs to ensure that its users can seamlessly search and obtain tools of interest.

To achieve this there is a need for high quality content along with the functionality and interface necessary to curate and maintain this content, and provide it to the users in a manner that encourages data (re) usability, contribution and integration with other projects. Both the bio.tools registry and the EDAM ontology are essential, continuously evolving components of the ELIXIR Tools Platform, that will be deeply integrated with the Tools Platform Ecosystem and other Platforms.

All the work package components described below synergize and complement each other. It is important to acknowledge that there is little value gained by having quality tool annotations without the mechanisms and interfaces to identify and use these tools. In a similar fashion there is little value to having highly performant searching and complex interfaces without quality of data. These types of issues can be solved by tackling the problem from multiple angles. In consequence the below described tasks will contribute to creating a well integrated and up-to-date system which provides both valuable high quality data and the means to deliver this data to the users in a practical and useful manner.

The Tools Platform has initiated the development of the “Tools Platform Ecosystem”. This metadata exchange platform will coordinate the different registries and services maintained by the ELIXIR Tools Platform, using standards such as EDAM, Bioschemas, and biotoolsSchema. Building on top of the content aggregated and curated over the last years, it will open up the content and make it accessible beyond API calls. In production, this platform will serve as the central tool-metadata hub for the Tools Platform resources, and provide integration with other services and communities within and beyond ELIXIR.

The Tools Platform has initiated the development of the “Tools Platform Ecosystem”. This metadata exchange platform will coordinate the different registries and services maintained by the ELIXIR Tools Platform, using standards such as EDAM, Bioschemas, and biotoolsSchema. Building on top of the content aggregated and curated over the last years, it will open up the content and make it accessible beyond API calls. In production, this platform will serve as the central tool-metadata hub for the Tools Platform resources, and provide integration with other services and communities within and beyond ELIXIR.

The Tools Platform has initiated the development of the “Tools Platform Ecosystem”. This metadata exchange platform will coordinate the different registries and services maintained by the ELIXIR Tools Platform, using standards such as EDAM, Bioschemas, and biotoolsSchema. Building on top of the content aggregated and curated over the last years, it will open up the content and make it accessible beyond API calls. In production, this platform will serve as the central tool-metadata hub for the Tools Platform resources, and provide integration with other services and communities within and beyond ELIXIR.

The Tools Platform has initiated the development of the “Tools Platform Ecosystem”. This metadata exchange platform will coordinate the different registries and services maintained by the ELIXIR Tools Platform, using standards such as EDAM, Bioschemas, and biotoolsSchema. Building on top of the content aggregated and curated over the last years, it will open up the content and make it accessible beyond API calls. In production, this platform will serve as the central tool-metadata hub for the Tools Platform resources, and provide integration with other services and communities within and beyond ELIXIR.

The Tools Platform has initiated the development of the “Tools Platform Ecosystem”. This metadata exchange platform will coordinate the different registries and services maintained by the ELIXIR Tools Platform, using standards such as EDAM, Bioschemas, and biotoolsSchema. Building on top of the content aggregated and curated over the last years, it will open up the content and make it accessible beyond API calls. In production, this platform will serve as the central tool-metadata hub for the Tools Platform resources, and provide integration with other services and communities within and beyond ELIXIR.

The Tools Platform has initiated the development of the “Tools Platform Ecosystem”. This metadata exchange platform will coordinate the different registries and services maintained by the ELIXIR Tools Platform, using standards such as EDAM, Bioschemas, and biotoolsSchema. Building on top of the content aggregated and curated over the last years, it will open up the content and make it accessible beyond API calls. In production, this platform will serve as the central tool-metadata hub for the Tools Platform resources, and provide integration with other services and communities within and beyond ELIXIR.

The Tools Platform has initiated the development of the “Tools Platform Ecosystem”. This metadata exchange platform will coordinate the different registries and services maintained by the ELIXIR Tools Platform, using standards such as EDAM, Bioschemas, and biotoolsSchema. Building on top of the content aggregated and curated over the last years, it will open up the content and make it accessible beyond API calls. In production, this platform will serve as the central tool-metadata hub for the Tools Platform resources, and provide integration with other services and communities within and beyond ELIXIR.

The Tools Platform has initiated the development of the “Tools Platform Ecosystem”. This metadata exchange platform will coordinate the different registries and services maintained by the ELIXIR Tools Platform, using standards such as EDAM, Bioschemas, and biotoolsSchema. Building on top of the content aggregated and curated over the last years, it will open up the content and make it accessible beyond API calls. In production, this platform will serve as the central tool-metadata hub for the Tools Platform resources, and provide integration with other services and communities within and beyond ELIXIR.

The Tools Platform has initiated the development of the “Tools Platform Ecosystem”. This metadata exchange platform will coordinate the different registries and services maintained by the ELIXIR Tools Platform, using standards such as EDAM, Bioschemas, and biotoolsSchema. Building on top of the content aggregated and curated over the last years, it will open up the content and make it accessible beyond API calls. In production, this platform will serve as the central tool-metadata hub for the Tools Platform resources, and provide integration with other services and communities within and beyond ELIXIR.

The Tools Platform has initiated the development of the “Tools Platform Ecosystem”. This metadata exchange platform will coordinate the different registries and services maintained by the ELIXIR Tools Platform, using standards such as EDAM, Bioschemas, and biotoolsSchema. Building on top of the content aggregated and curated over the last years, it will open up the content and make it accessible beyond API calls. In production, this platform will serve as the central tool-metadata hub for the Tools Platform resources, and provide integration with other services and communities within and beyond ELIXIR.