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.

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. 

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.

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

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. 

 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.

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

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. 

Tool for analysis of molecular channels in proteins. CAVER Analyst allows interactive visualization of the channels and cavities in protein structures.

ClustVis is a web tool for visualizing clustering of multivariate data. This web tool allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps.

A server for calculating contact maps of X-ray, NMR and predicted structures.

Expertise on very diverse subjects of data processing, analysis and curation as well as connections to existing infrastructure RI's like EUDAT. This expertise can be made available to research projects and organisations.  

Aligns contigs from a draft genome to a closely related genome, and resolves their relative orientation based on this alignment.

CRISPRCas++ is a new website holding a program called CRISPRCasFinder to detect CRISPR arrays and cas genes in the genome of prokaryotes. CRISPRCasMeta is adapted to the analysis of large metagenomic data. The programs are available online or can be downloaded for local usage. A database called CRISPRCasdb, the successor of CRISPRdb, is accessible on the CRISPRCas++ website. It can be browsed and queried in search for repeat and spacer sequences. 

Chipster is a user-friendly analysis software for high-throughput data. It contains hundreds of analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. 

System for identification of alterations using protein mass spectrometry.

Web interface for assignment and analysis of DNA conformers.

Tool to predict backbone dynamics from a single protein sequence

SIB's resource portal with access to all major tools and databases provided by different SIB groups and external partners. Specific query features allow interacting with many resources at the same time. 

FAIDARE is a portal developed by ELIXIR-FR as an asset of the ELIXIR Plant Science community. FAIDARE enables data discovery through federations of distant Plant informations systems that have set up a standardized Restful API, the BrAPI. FAIDARE currently allows to do detailed searches of accessions and phenotyping data.

An information and educational resource of inter-related data standards, databases and policies. 

g:Profiler is a bioinformatics toolkit for characterising and manipulating gene lists of high-throughput genomic data.

An optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data.

The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cassava, Cacao, Coffee, Grass, Rice and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers).

Genomicus is a database and a web server that integrates comparative genome data and ancestral genome reconstruction in a fast and intuitive way. It enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. A user-friendly graphical interface allows syntenic comparisons and gene order alignments between pairs of genomes or multiple genomes at different scales: local gene order, karyotypes, matrix plots, etc.  Different phylums such as Vertebrates, Plants, Fungi, Metazoa (as per Ensembl Genomes) are represented and regularly updated, as well as specific versions on Tunicates, Fish and Amphioxus.  

GINsim (Gene Interaction Network simulation) is a computer tool for the modeling and simulation of genetic regulatory networks.
Using its user-friendly graphical interface, users can specify a signed regulatory graph, define boolean or multivalued logical functions, and then simulate and analyse its qualitative dynamical behaviour.

GraphWeb is a public web server for graph-based analysis of biological networks.