This is the main tool and resource list of our website. This is a curated list which means that not all tools or resources that exist for a certain topic are listed here. This is mainly because we do not intend to be a registry. In most cases you will only find back the tools or resources that are mentioned in the different pages. Most pages will show a filtered list of this main table at the end of the page. If you see a missing link with one of the registries or a mistake, please open an issue or check our how to add a tool or resource guide.

Tool or resource Description Tags Registry
Access to Biological Collection Data Schema (ABCD) A standard schema for primary biodiversity data micro biotech
Addgene A searchable repository with a focus on plasmids micro biotech
Amazon Web Services Amazon Web Services storage data analysis transfer
Amnesia Amnesia is a GDPR compliant high accuracy data anonymization tool sensitive
APID Interactomes APID (Agile Protein Interactomes DataServer) is a server that provides a comprehensive collection of protein interactomes for more than 400 organisms based in the integration of known experimentally validated protein-protein physical interactions (PPIs) IDP
Argos Plan and follow your data. Bring your Data Management Plans closer to where data are generated, analysed and stored. DMP researcher data manager
ArrayExpress A repository of array based genomics data micro biotech
ATCC Biological materials resource including cell-lines, strains and genomics tools micro biotech
BacDive A searchable database for bacteria specific information micro biotech
Bacillus Genetic Stock Center (BGSC) A repository specific to Bacillus strains micro biotech
BBMRI-ERIC's ELSI Knowledge Base The ELSI Knowledge Base is an open-access resource platform that aims at providing practical know-how for responsible research. data protection sensitive policy officer data manager human data
Beacon The Beacon protocol defines an open standard for genomics data discovery. researcher data manager IT support human data
Benchling R&D Platform for Life Sciences micro biotech
BigNASim Repository for Nucleic Acids MD simulations biomol sim
BindingDB Public, web-accessible database of measured binding affinities biomol sim
Bioactive Conformational Ensemble Platform designed to efficiently generate bioactive conformers and speed up the drug discovery process. biomol sim
Bioconda Bioconda is a bioinformatics channel for the Conda package manager IT support data analysis
Biodiversity Information Standards (TDWG) Biodiversity Information Standards (TDWG), historically the Taxonomic Databases Working Group, work to develop biodiversity information standards micro biotech
BioExcel COVID-19 Platform designed to provide web-access to atomistic-MD trajectories for macromolecules involved in the COVID-19 disease. biomol sim
BioModels A repository of mathematical models for application in biological sciences micro biotech
BIONDA BIONDA is a free and open-access biomarker database, which employs various text mining methods to extract structured information on biomarkers from abstracts of scientific publications storage researcher human data
Biosamples BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. metadata plants
Biostudies The BioStudies database holds descriptions of biological studies and links to data from these studies in other databases. metadata plants
BioStudies A database hosting datasets from biological studies. Useful for storing or accessing data that is not compliant for mainstream repositories. micro biotech
Bitbucket Git based code hosting and collaboration tool, built for teams. data organisation data manager IT support
BMRB Biological Magnetic Resonance Data Bank IDP researcher
BoostDM BoostDM is a method to score all possible point mutations (single base substitutions) in cancer genes for their potential to be involved in tumorigenesis. data analysis human data
Box Cloud storage and file sharing service storage IT support transfer
BrAPI Specification for a standard API for plant data: plant material, plant phenotyping data IT support plants
BRENDA Database of enzyme and enzyme-ligand information, across all taxonomic groups, manually extracted from primary literature and extended by text mining procedures micro biotech
Bulk Rename Utility File renaming software for Windows data organisation data manager researcher
CalibraCurve A highly useful and flexible tool for calibration of targeted MS?based measurements. CalibraCurve enables an automated batch-mode determination of dynamic linear ranges and quantification limits for both targeted proteomics and similar assays. The software uses a variety of measures to assess the accuracy of the calibration and provides intuitive visualizations. data analysis
Cancer Genome Interpreter Cancer Genome Interpreter (CGI) is designed to support the identification of tumor alterations that drive the disease and detect those that may be therapeutically actionable. data analysis human data
CATH A hierarchical domain classification of protein structures in the Protein Data Bank.
CellRepo A version management tool for modifying strains micro biotech
Cellular Microscopy Phenotype Ontology (CMPO) An ontology for expressing cellular (or multi-cellular) terms with applications in microscopy micro biotech
CERNBox CERNBox cloud data storage, sharing and synchronization storage
ChEBI Dictionary of molecular entities focused on 'small' chemical compounds micro biotech
ChEMBL Database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties and abstracted bioactivities.
Choose a license Choose an open source license licensing researcher data manager policy officer
COmputational Modeling in BIology NEtwork (COMBINE) An initiative to bring together various formats and standard for computational models in biology micro biotech
Conda Open source package management systemn IT support data analysis
Consent Clauses for Genomic Research A resource for researchers when drafting consent forms so they can use language matching cutting-edge GA4GH international standards human data
COPO Portal for scientists to broker more easily rich metadata alongside data to public repos. metadata researcher plants
COVID-19 Molecular Structure and Therapeutics Hub COVID-19 Molecular Structure and Therapeutics Hub biomol sim
Creative Commons License Chooser It helps you choose the right Creative Commons license for your needs. licensing researcher data manager policy officer
Crop Ontology The Crop Ontology compiles concepts to curate phenotyping assays on crop plants, including anatomy, structure and phenotype. researcher data manager IT support plants
CS3 Cloud Storage Services for Synchronization and Sharing (CS3) storage
DAISY Data Information System to keep sensitive data inventory and meet GDPR accountability requirement. IT support policy officer human data data protection
Data Curation Centre Metadata list List of metadata standards metadata researcher data manager
Data Use Ontology DUO allows to semantically tag datasets with restriction about their usage. data manager researcher human data Data License list Overview of typical licenses used for data resources licensing biomol sim
DATAVERSE Open source research data respository software. storage researcher data manager IT support
DAWID The Data Agreement Wizard is a tool developed by ELIXIR-Luxembourg to facilitate data sharing agreements. data protection policy officer human data
dbGAP The database of Genotypes and Phenotypes (dbGaP) archives and distributes data from studies investigating the interaction of genotype and phenotype in Humans data publication researcher IT support human data
DisGeNET A discovery platform containing collections of genes and variants associated to human diseases. data analysis human data researcher
DisProt A database of intrinsically disordered proteins IDP researcher
DMP Canvas Generator Questionnaire, which generates a pre-filled a DMP DMP researcher data manager
DMP OPIDoR Online questionnaire for the development of data management plans - repository of DMPs DMP researcher data manager
DMPlanner Semi-automatically generated, searchable catalogue of resources that are relevant to data management plans. DMP researcher data manager
DMPonline A free tool to write, share and export a data management plan. Built-in data management plan templates for many major funders. DMP researcher data manager
DMPonline Belgium A free tool to write, share and export a data management plan. Instance aimed at Belgian researchers with built-in data management plan templates for the major funders. DMP researcher data manager
DMPTool Build your Data Management Plan DMP researcher data manager
DMPTuuli Finland Data management planning tool DMP researcher data manager
DNA Data Bank of Japan (DDBJ) A database of DNA sequences micro biotech
Docker Docker is a software for the execution of applications in virtualized environments called containers. It is linked to DockerHub, a library for sharing container images IT support data analysis
DropBox Cloud storage and file sharing service storage IT support transfer
Dryad Open-source, community-led data curation, publishing, and preservation platform for CC0 publicly available research data data publication biomol sim
DS-Wizard Data Stewardship Wizard DMP researcher data manager IT support nels
Dynameomics Database of folding / unfolding pathway of representatives from all known protein folds by MD simulation biomol sim
e!DAL Electronic data archive library is a framework for publishing and sharing research data storage IT support
e!DAL-PGP Plant Genomics and Phenomics Research Data Repository plants researcher data manager IT support
EasyDMP DMP creation, versioning and sharing DMP researcher data manager
ECPGR Hub for the identification of plant genetic resources in Europe plants researcher data manager
ELIXIR Deposition Databases for Biomolecular Data List of discipline-specific deposition databases recommended by ELIXIR. data publication researcher data manager IT support
EMBL-EBI Ontology Lookup Service EMBL-EBI’s web portal for finding ontologies metadata data manager researcher
EMBL-EBI's data submission wizard EMBL-EBI's wizard for finding the right EMBL-EBI repository for your data. data publication researcher data manager
Ensembl Genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.
Ensembl Genomes Comparative analysis, data mining and visualisation for the genomes of non-vertebrate species
EU General Data Protection Regulation Regulation (eu) 2016/679 of the european parliament and of the council on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing directive 95/46/ec (general data protection regulation). data protection policy officer human data
EUDAT licence selector wizard EUDAT's wizard for finding the right licence for your data or code. licensing researcher data manager policy officer
EUPID EUPID provides a method for identity management, pseudonymisation and record linkage to bridge the gap between multiple contexts. IT support policy officer human data
EURISCO European Search Catalogue for Plant Genetic Resources plants researcher data manager
Europe PMC Europe PMC is a repository, providing access to worldwide life sciences articles, books, patents and clinical guidelines. researcher
European Nucleotide Archive (ENA) A record of sequence information scaling from raw sequcning reads to assemblies and functional annotation micro biotech
FAIDARE FAIDARE is a tool allowing to search data across dinstinct databases that implemented BrAPI. researcher data manager plants
FAIRDOMHub Data, model and SOPs management for projects, from preliminary data to publication, support for running SBML models etc. (public SEEK instance) storage researcher nels metadata micro biotech
fairsharing A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies. metadata data publication policy officer data manager researcher micro biotech
FigShare Data publishing platform data publication biomol sim
Freegenes Repository of IP-free synthetic biological parts micro biotech
GA4GH data security toolkit Principled and practical framework for the responsible sharing of genomic and health-related data. data publication policy officer data manager IT support human data
GA4GH regular and ethical toolkit Framework for Responsible Sharing of Genomic and Health-Related Data data protection sensitive policy officer data manager IT support human data
Galaxy Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. nels data analysis researcher IT support
GenBank A database of genetic sequence information. GenBank may also refer to the data format used for storing information around genetic sequence data. micro biotech
Gene Expression Omnibus (GEO) A repository of MIAME-compliant genomics data from arrays and high-throughput sequencing micro biotech
GENEID Geneid is an ab initio gene finding program used to predict genes along DNA sequences in a large set of organisms. data analysis researcher
Git Distributed version control system designed to handle everything from small to very large projects data organisation data manager IT support
GitHub Versioning system, used for sharing code, as well as for sharing of small data data publication data organisation IT support data manager
GitLab GitLab is an open source end-to-end software development platform with built-in version control, issue tracking, code review, CI/CD, and more. Self-host GitLab on your own servers, in a container, or on a cloud provider. data organisation data publication IT support data manager
GnpIS A multispecies integrative information system dedicated to plant and fungi pests. It allows researchers to access genetic, phenotypic and genomic data. It is used by both large international projects and the French National Research Institute for Agriculture, Food and Environment. plants
Google Drive Cloud Storage for Work and Home storage transfer
GPCRmd Repository of GPCR protein simulations biomol sim
GRAPE 2.0 The GRAPE pipeline provides an extensive pipeline for RNA-Seq analyses. It allows the creation of an automated and integrated workflow to manage, analyse and visualize RNA-Seq data. data analysis
How to License Research Data - DCC Guidelines about how to license research data from Digital Curation Centre licensing researcher data manager policy officer
Human Protein Atlas The Human Protein Atlas contains information for a large majority of all human protein-coding genes regarding the expression and localization of the corresponding proteins based on both RNA and protein data.
HumanMine HumanMine integrates many types of human data and provides a powerful query engine, export for results, analysis for lists of data and FAIR access via web services. data organisation data manager researcher human data data analysis
iCloud Data sharing storage data analysis transfer
IDPO Intrinsically disordered proteins ontology IDP metadata
iGEM Parts Registry A collection of standard biological parts to which all entrants in the iGEM competition must submit their parts micro biotech
Image Data Resource (IDR) A repository of image datasets from scientific publications micro biotech
Informed Consent Ontology The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. IT support policy officer human data
International Compilation of Human Research Standards The International Compilation of Human Research Standards enumerates over 1,000 laws, regulations, and guidelines (collectively referred to as standards) that govern human subject protections in 133 countries, as well as standards from a number of international and regional organizations human data
International Nucleotide Sequence Database Collaboration (INSDC) A collaborative database of genetic sequence datasets from DDBJ, EMBL-EBI and NCBI micro biotech
International Society for the Advancement of Cytometry (ISAC) Data standards and formats for reporting flow cytometry data micro biotech
International Union of Biochemistry and Molecular Biology (IUBMB) Resource for naming standards in biochemistry and molecular biology micro biotech
InterPro Functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites
IntoGen IntoGen collects and analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes. data analysis human data
iRODS Integrated Rule-Oriented Data System (iRODS) is open source data management software for a cancer genome analysis workflow. storage IT support
ISA-tools Open source framework and tools helping to manage a diverse set of life science, environmental and biomedical experiments using the Investigation Study Assay (ISA) standard IT support data manager micro biotech
ISO/IEC 27001 International information security standard data protection policy officer human data
IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN) A collaborative resource from IUPAC and IUBMB for naming standards in biochemistry micro biotech
JBEI-ICE A registry platform for biological parts micro biotech
Jupyter Jupyter notebooks allow to share code, documentation IT support data analysis
Linked Open Vocabularies (LOV) Web portal for finding ontologies metadata data manager researcher
List of Prokaryotic names with Standing in Nomenclature (LPSN) A database of prokaryote specific biodiversity information micro biotech
maDMP - Research Bridge Machine-Actionable Data Management Plan | Webinar (2016) on making a good data management plan. DMP IT support
MCPD The Multi-Crop Passport Descriptor is the metadata standard for plant genetic resources maintained ex situ by genbanks. metadata researcher IT support policy officer plants
MCPD The Multi-crop Passport Descriptors are an international standard to facilitate germplasm passport information exchange metadata plants
MemProtMD Database of over 5000 intrinsic membrane protein structures biomol sim
Mendeley data Multidisciplinary, free-to-use open repository specialized for research data data publication biomol sim
MetabolomeXchange A repository of genomics data relating to the study of the metabolome micro biotech
MIADE Minimum Information About Disorder Experiments (MIADE) standard metadata researcher data manager IDP
MIAPPE Minimum Information About a Plant Phenotyping Experiment metadata researcher data manager plants
Microsoft Azure Cloud storage and file sharing service from Microsoft storage IT support transfer
Microsoft OneDrive Cloud storage and file sharing service from Microsoft storage IT support
MIGS/MIMS Minimum Information about a (Meta)Genome Sequence metadata researcher data manager marine micro biotech
MINT MINT, the Molecular INTeraction database, focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators
MIxS Minimum Information about any (x) Sequence metadata researcher data manager marine
MobiDB A database of protein disorder and mobility annotations IDP researcher
MoDEL Database of Protein Molecular Dynamics simulations representing different structural clusters of the PDB biomol sim
MoDEL Covid19 Database of COVID-19 related atomistic Molecular Dynamic Trajectories biomol sim
MoDEL-CNS Repository for Central Nervous System-related mainly membrane protein MD simulations biomol sim
ModelArchive Repository for molecular models - providing doi of models biomol sim
MolMeDB Database about interactions of molecules with membranes biomol sim
MONARC A risk assessment tool that can be used to do Data Protection Impact Assessments data protection policy officer human data
National Center for Biotechnology Information (NCBI) Online database hosting a vast amount of biotechnological information including nucleic acids, proteins, genomes and publications. Also boasts integrated tools for analysis. micro biotech
NCBI Taxonomy NCBI's taxonomy browser is a database of biodiversity information micro biotech
NCIMB Hosts information relating to strains, cultures and more micro biotech
NeLS Norwegian e-Infrastructure for Life Sciences enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their omics-scale data nels
NextCloud As fully on-premises solution, Nextcloud Hub provides the benefits of online collaboration without the compliance and security risks. storage IT support transfer
Nextflow Nextflow is a framework for data analysis workflow execution IT support data analysis
NMRlipids Repository for lipid MD simulations to validate force fields with NMR data biomol sim
Ontobee A web portal to search and visualise ontologies metadata data manager researcher
ONTOMATON OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets. researcher data manager IT support
Open Definition Conformant Licenses Licenses that are conformant with the principles laid out in the Open Definition. licensing researcher data manager policy officer
OpenEBench ELIXIR benchmarking platform to support community-led scientific benchmarking efforts and the technical monitoring of bioinformatics reosurces data analysis data manager IT support
OpenRefine Data curation tool for working with messy data data quality
OpenScienceFramework free and open source project management tool that supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery data publication biomol sim
Orphadata The Orphadata platform provides the scientific community with comprehensive, high-quality datasets related to rare diseases and orphan drugs, in a reusable and computable format
OSF OSF (Open Science Framework) is a free, open platform to support your research and enable collaboration. storage researcher data manager
OTP One Touch Pipeline (OTP) is a data management platform for running bioinformatics pipelines in a high-throughput setting, and for organising the resulting data and metadata. human data metadata DMP data analysis
OwnCloud Cloud storage and file sharing service storage IT support transfer data analysis
PAA PAA is an R/Bioconductor tool for protein microarray data analysis aimed at biomarker discovery. data analysis researcher human data
PCDDB The Protein Circular Dichroism Data Bank IDP researcher
PDB The Protein Data Bank (PDB) researcher IDP
PDB-Dev Prototype archiving system for structural models obtained using integrative or hybrid modeling biomol sim
PIA - Protein Inference Algorithms PIA is a toolbox for mass spectrometrey based protein inference and identification analysis. data analysis researcher
PMut Platform for the study of the impact of pathological mutations in protein stuctures. data analysis human data
Privacy Impact Assessment Tool Privacy Impact Assessment Tool is a software, that allows you to carry out Privacy Impact Assessment (PIA) independently. data protection policy officer human data A secure platform for developing and sharing reproducible methods. micro biotech
R Markdown R Markdown documents are fully reproducible. Use a productive notebook interface to weave together narrative text and code to produce elegantly formatted output. Use multiple languages including R, Python, and SQL. data analysis researcher
RD-Connect Genome Phenome Analysis Platform The RD-Connect GPAP is an online tool for diagnosis and gene discovery in rare disease research. researcher human data
RDA Standards Directory of standard metadata, divided into different research areas metadata researcher data manager
Renamer4Mac File renaming software for Mac data organisation data manager researcher
Repository Finder Repository Finder can help you find an appropriate repository to deposit your research data. The tool is hosted by DataCite and queries the re3data registry of research data repositories. data publication researcher data manager
Research Data Management Platform (RDMP) Data management platform for automated loading, storage, linkage and provision of data sets storage IT support
Research Management Plan Machine actionable DMPs. DMP researcher data manager
Research Object Crate (RO-Crate) RO-Crate is a lightweight approach to packaging research data with their metadata, using An RO-Crate is a structured archive of all the items that contributed to the research outcome, including their identifiers, provenance, relations and annotations. metadata storage data organisation data manager researcher micro biotech
Reva Reva connects cloud storages and application providers data analysis transfer
Rightfield RightField is an open-source tool for adding ontology term selection to Excel spreadsheets researcher metadata data manager micro biotech
Rstudio Rstudio notebooks allow to share code, documentation data analysis IT support researcher
Rucio Rucio - Scientific Data Management storage data analysis transfer
SASBDB Small Angle Scattering Biological Data Bank IDP researcher
SBOL Visual A standard library of visual glyphs used to represent SBOL designs and interactions. micro biotech
SBOLDesigner A CAD tool to create SBOL designs through the use of SBOL Visual glyphs. micro biotech
Schemapedia Web portal for finding ontologies metadata data manager researcher
ScienceMesh ScienceMesh - frictionless scientific collaboration and access to research services storage data analysis transfer
Scientific Data's Recommended Repositories List of respositories recommended by Scinetific Data, contains both discipline-specific and general repositories. data publication researcher data manager IT support
SeaFile SeaFile File Synchronization and Share Solution storage transfer
FAIRDOM-SEEK Data, model and SOPs management for projects, from preliminary data to publication, support for running SBML models etc. storage IT support nels micro biotech
ShortBOL A scripting language for creating Synthetic Biology Open Language (SBOL) in a more abstract way. micro biotech
SIFTS Structure integration with function, taxonomy and sequence researcher IDP
Silva SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).
Singularity Singularity is a container platform. IT support data analysis
Snakemake Snakemake is a framework for data analysis workflow execution IT support data analysis
Standards for Reporting Enzyme Data (STRENDA) Resource of standards for reporting enzyme data micro biotech
STRING Known and predicted protein-protein interactions.
SynBioHub A searchable design repository for biological constructs micro biotech
Synthetic Biology Open Language (SBOL) An open standard for the representation of in silico biological designs and their place in the Design-Build-Test-Learn cycle of synthetic biology. micro biotech
Systems Biology Markup Language (SBML) An open format for computational models of biological processes micro biotech
The Environment Ontology (EnvO) An ontology for expressing environmental terms micro biotech
The European Genome-phenome Archive (EGA) EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects data publication human data policy officer
The Genomic Standards Consortium (GSC) Minimum Information about any (x) Sequence metadata researcher IT support policy officer human data
The Open Biological and Biomedical Ontology (OBO) Foundry Collaborative effort to develob interoperable ontologies for the biological sciences metadata data manager researcher
Tryggve ELSI Checklist A list of Ethical, Legal, and Societal Implications (ELSI) to consider for research projects on human subjects sensitive policy officer data manager human data
UniProt Comprehensive resource for protein sequence and annotation data metadata researcher IDP micro biotech
VisBOL A JavaScript library for the visualisation of SBOL. micro biotech
Wellcome Open Research - Data Guidelines Wellcome Open Research requires that the source data underlying the results are made available as soon as an article is published. This page provides information about data you need to include, where your data can be stored, and how your data should be presented. data publication researcher data manager
Zenodo Generalist research data repository built and developed by OpenAIRE and CERN data publication biomol sim