Services: software tools

Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis.

Alfred is a comprehensive NGS alignment quality control method that supports commonly used QC metrics, RNA and DNA feature counting and flexible feature annotation.

A Consensus Method for Amyloid Propensity Prediction

ANASTASIA (Automated Nucleotide Animoacid Sequences Translational plAtform for Synthetic Interpretation and Analysis) is a metagenomics analysis platform and repository.

http://motherbox.chemeng.ntua.gr/anastasia_dev/

ANISEED is the main model organism database for the worldwide community of scientists working on a class of marine invertebrates, the tunicates (sister-group of vertebrates). It integrates for each species: a main knowledge base with extended information on gene function, gene expression, phylogeny and embryonic anatomy at single cell resolution; a genomic browser and a Genomicus gene synteny browser.

Annotates variants with biological data such as protein structural information, functionally important residues, conservation of functional domains and evidence of cross-species conservation.

Annotation Retrieval of Gene Ontology Terms using semantic similarity in Gene Ontology.

ARIA (Ambiguous Restraints for Iterative Assignment) is a software for automated NOE assignment and NMR structure calculation. It speeds up and automatizes the assignment process through the use of an iterative structure calculation scheme. 

A customised Galaxy instance for the genomic characterisation of microoganisms in particular and data intensive biomedical research in general.

Automated high-throughput assembly, annotation and feature analysis of microbial genome cohorts

ASAP (Automated Single-cell Analysis Portal) is a web-based, collaborative portal aimed at democratizing single-cell omics data analyses and to render it more accessible to researchers. ASAP does not require any installation and enables standardized analyses that can be run in minutes by any user without requiring significant computing power. The entire single-cell analysis pipeline is available in ASAP, allowing users to choose from a panel of tools, and guiding them through tutorials.

Atomic Charge Calculator - web application using the Electronegativity Equalization Method.

AuReMe, is an adaptable workspace for sustainable reconstructions or improvements of genome-scale metabolic models involving personalized pipelines. It is adapted to the metabolic study of non-conventional organisms and microbiomes to ensure that the process is reproducible and documented regardless of the combination of tools used. Among others, modules included in the AuReMe environment are a model-management PADmet module, a wiki-export module, a gap-filling tool for non-conventional organism (meneco), a tool for the reduction of microbial communities based on metabolic complementarities (miscoto) and a package to handle the analysis of large-scale microbiota (Metage2Metabo).

Predicts the subcellular localization of proteins in eukaryotes.

Online access to tools and databases related to miRNAs binding site predictions, RNA Binding protein binding sites, circular RNAs, CLIP data analysis and transcriptome analysis

Web portal for tools registry and discovery, incorporating tool benchmarking and service monitoring information and the use of EDAM for precise scientific tool description. 

Website providing sequence-based predictions to grasp the behaviour of proteins that compose the SARS-CoV-2 virus

Build, test and convert Cloud and HPC software into Linux containers.

This bioconductor authoring tool links the journal’s manuscript management system with the Bioconductor nightly build system, thus enabling “continuous Integration”, automated quality control and guaranteed workflow functionality even as underlying resources and tools evolve. A package and tutorial publication are underway, and we have actively helped several authors from the community with workflow authoring.

 BIII Bio Image informatics Index (www.biii.eu) is a knowledge database of software tools, test image databases and training materials for bio image analysis. Software tools are organized as full protocol of analysis (workflow), specific brick (component) to construct a workflow, or software platform or library (collection).  They are described using Edam Bio Imaging, which is iteratively defined using this website. All entries are exposed following FAIR principles and accessible for other usage with  (ODC-By) v1.0 license.

Provides an R interface to BioMart services. In particular this is the most widely used programmatic access route to query EMBL-EBI’s Ensembl database.

Knowledge integration platform for literature mining and concept discovery

BioTranslator enables functional interpretation of genomic experiments through pathways analysis with a variety of biomedical ontologies, regulatory genes prioritization and protein network visualization.

The BioXSD / GTrack ecosystem is an infrastructure of generic state-of-the-art data formats for integrative bioinformatics, with focus on genomics and epigenomics, sequence and structure bioinformatics, and other applications. 

An interactive literature‐based biomedical discovery support system

A web server integrating multiple tools for prediction of protein subcellular localization and topological features

BUSCO provides quantitative measures for the assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content.

Unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. Allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways.

Tool for calibration of targeted MS‐based measurements.

Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB.