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All tools and resources

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.

We link tools and resources to related information in ELIXIR registries: related policies and standards in FAIRsharing, scientific and technical descriptions of the resource in, and related training in TeSS. 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.

It is recommended to add:

  • your training materials and events into the training registry TeSS
  • your standards, databases and policies in fairsharing registry
  • your software tools, databases and services for bioinformatics and the life sciences in registry
Tool or resource Description Related pages Registry
3D-Beacons Network providing unified programmatic access to experimentally determined and predicted structure models Structural Bioinformatics Tool info
3DBioNotes 3DBIONOTES-WS is a web application designed to automatically annotate biochemical and biomedical information onto structural models. Structural Bioinformatics Machine actionability Tool info Training
4DN-BINA-OME-QUAREP (NBO-Q) Rigorous record-keeping and quality control are required to ensure the quality, reproducibility and value of imaging data. The 4DN Initiative and BINA have published light Microscopy Metadata Specifications that extend the OME Data Model, scale with experimental intent and complexity, and make it possible for scientists to create comprehensive records of imaging experiments. The Microscopy Metadata Specifications have been adopted by QUAREP-LiMi and are being revised in QUAREP-LiMi in collaboration with instrument manufacturers OMERO Bioimaging data Standards/Databases
Access to Biological Collection Data Schema (ABCD) A standard schema for primary biodiversity data Microbial biotechnology
Access to Research Infrastructure Administration (ARIA) Access and data management platform that allows facilities to manage outputs and associate them with proposal information and other research outputs. Structural Bioinformatics Tool info
Ada Discovery Analytics (Ada) Ada is a performant and highly configurable system for secured integration, visualization, and collaborative analysis of heterogeneous data sets, primarily targeting clinical and experimental sources. TransMed
Addgene A searchable repository with a focus on plasmids Microbial biotechnology Tool info Standards/Databases
Agronomic Linked Data The RDF Knowledge-based Database for plant molecular networks Machine actionability Standards/Databases
AgroPortal Browser for ontologies for agricultural science based on NBCO BioPortal. Plant Phenomics Documentation and meta... Tool info Standards/Databases
AICSImageIO Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python Bioimaging data
Alchemer Commercial online survey tool. Health data
Amazon Web Services Amazon Web Services Data transfer Training
Analysis Data Model for data and metadata of clinical trial statistical analysis (ADaM) A CDISC Foundational Standard that defines dataset and metadata standards. Health data Tool info
AnnData Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray. Single-cell sequencing Tool info Training
Annotare Annotare is a tool for submitting functional genomics data to the ArrayExpress collection in BioStudies. Single-cell sequencing Training
AOP4EUpest AOP4EUpest web server is devoted to the identification of pesticides involved in an Adverse Outcome Pathway via text mining approaches. Toxicology data Tool info
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) Proteomics Tool info
Argos Plan and follow your data. Bring your Data Management Plans closer to where data are generated, analysed and stored. Data management plan Training
ArrayExpress A repository of array based genomics data Microbial biotechnology Single-cell sequencing Data publication Tool info Standards/Databases Training
Arvados With Arvados, bioinformaticians run and scale compute-intensive workflows, developers create biomedical applications, and IT administrators manage large compute and storage resources. Data analysis
ATCC Biological materials resource including cell-lines, strains and genomics tools Microbial biotechnology Tool info
Atlas Free, publicly available web-based, open-source software application developed by the OHDSI community to support the design and execution of observational analyses to generate real world evidence from patient level observational data. TransMed Tool info Training
b2share Store and publish your research data. Can be used to bridge between domains Bioimaging data Standards/Databases
BacDive A searchable database for bacteria specific information Microbial biotechnology Tool info Training
Bacillus Genetic Stock Center (BGSC) A repository specific to Bacillus strains Microbial biotechnology
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. Human data Ethical aspects GDPR compliance
Beacon The Beacon protocol defines an open standard for genomics data discovery. Human data Tool info Standards/Databases Training
Benchling R&D Platform for Life Sciences Microbial biotechnology
Better BibTeX (BBT) A plugin for Zotero and Juris-M that makes it easier to manage bibliographic data.
bfconvert The bfconvert command line tool can be used to convert files between supported formats. Bioimaging data
BIAFLOWS BIAFLOWS is an open-soure web framework to reproducibly deploy and benchmark bioimage analysis workflows Data analysis Tool info
BigNASim Repository for Nucleic Acids MD simulations Biomolecular simulatio... Tool info
BIII The BioImage Informatics Index is a registry of software tools, image databases for benchmarking, and training materials for bioimage analysis Bioimaging data Tool info
BindingDB Public, web-accessible database of measured binding affinities Biomolecular simulatio... Tool info Standards/Databases
Bio-Formats Bio-Formats is a software tool for reading and writing image data using standardized, open formats. OMERO Tool info
Bio-Formats Bio-Formats is a software tool for reading and writing image data using standardized, open formats Bioimaging data Tool info Essential scientific and technical information about software tools, databases and services for bioinformatics and the life sciences. Data analysis Tool info Standards/Databases Training
Bioactive Conformational Ensemble Platform designed to efficiently generate bioactive conformers and speed up the drug discovery process. Biomolecular simulatio... Tool info
Bioconda Bioconda is a bioinformatics channel for the Conda package manager Data analysis Tool info Training
BioContainers BioContainers Flow Single-cell sequencing Data analysis Tool info Training
Biodiversity Information Standards (TDWG) Biodiversity Information Standards (TDWG), historically the Taxonomic Databases Working Group, work to develop biodiversity information standards Microbial biotechnology
BioExcel COVID-19 Platform designed to provide web-access to atomistic-MD trajectories for macromolecules involved in the COVID-19 disease. Biomolecular simulatio...
bioformats2raw Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification. Bioimaging data
BioImage Model Zoo BioImage is a collaborative effort to bring AI models to the bioimaging community. Machine learning Training
BioImageArchive The BioImage Archive stores and distributes biological images that are useful to life-science researchers. Bioimaging data Data publication Standards/Databases
BioModels A repository of mathematical models for application in biological sciences Microbial biotechnology Data publication Tool info Standards/Databases Training
BioPortal A comprehensive repository of biomedical ontologies Bioimaging data Health data Documentation and meta... Tool info Standards/Databases Training
BioSamples BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. Plant Genomics Plant sciences Tool info Standards/Databases Training
Bioschemas Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials Intrinsically disorder... Machine actionability Standards/Databases Training
BioStudies A database hosting datasets from biological studies. Useful for storing or accessing data that is not compliant for mainstream repositories. Microbial biotechnology Plant sciences Single-cell sequencing Data publication Tool info Standards/Databases Training
BisQue Resource for management and analysis of 5D biological images Bioimaging data Tool info
Bitbucket Git based code hosting and collaboration tool, built for teams. Data organisation Standards/Databases
BMDS EPA's Benchmark Dose Software (BMDS) collects and provides easy access to numerous mathematical models that help risk assessors estimate the quantitative relationship between a chemical dose and the test subject’s response. Toxicology data
BMRB Biological Magnetic Resonance Data Bank Intrinsically disorder... Structural Bioinformatics Tool info
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. Human data Tool info
Box Cloud storage and file sharing service Data transfer Data storage Training
BrAPI Specification for a standard API for plant data: plant material, plant phenotyping data Plant Phenomics Plant sciences Training
BrAPI compatible server Submit a new BrAPI compatible server Plant sciences
BRAVA BRAVA is a tool designed to help developers test servers that comply with the BrAPI specifications. Plant Phenomics
BRENDA Database of enzyme and enzyme-ligand information, across all taxonomic groups, manually extracted from primary literature and extended by text mining procedures Microbial biotechnology Tool info Standards/Databases Training
Bulk Rename Utility File renaming software for Windows Data organisation
CAMEO Continuous evaluation of the accuracy and reliability of protein structure prediction methods in a fully automated manner Structural Bioinformatics Tool info Standards/Databases
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. Human data Tool info
CAPRI Critical assessment of structure prediction methods for protein-protein interactions Structural Bioinformatics
CAS Registry The CAS Registry (Chemical Abstracts Service Registry) includes more than 188 million unique chemicals. CAS Registry Numbers are broadly used as a unique identifier for chemical substances. The Registry is maintained by CAS, a subdivision of the American Chemical Society. Toxicology data Standards/Databases
CASP Biennial critical assessment of techniques for protein structure prediction Structural Bioinformatics Tool info Training
Castor Castor is an EDC system for researchers and institutions. With Castor, you can create and customize your own database in no time. Without any prior technical knowledge, you can build a study in just a few clicks using our intuitive Form Builder. Simply define your data points and start collecting high quality data, all you need is a web browser. Health data Identifiers Tool info
CatBoost CatBoost is a high-performance open source library for gradient boosting on decision trees. Machine learning
CATH A hierarchical domain classification of protein structures in the Protein Data Bank. Proteomics Tool info Standards/Databases Training
CDISC/SEND CDISC SEND Controlled Terminology Toxicology data
CEDAR CEDAR is making data submission smarter and faster, so that scientific researchers and analysts can create and use better metadata. Documentation and meta... Tool info Standards/Databases
CellDataSet The main class used by Monocle to hold single cell expression data. CellDataSet extends the basic Bioconductor ExpressionSet class. Single-cell sequencing
CellMarker A database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data. Single-cell sequencing Tool info
CellProfiler Image analysis software OMERO Tool info Training
CellRanger A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data. Single-cell sequencing
CellRepo A version management tool for modifying strains Microbial biotechnology
Cellular Microscopy Phenotype Ontology (CMPO) An ontology for expressing cellular (or multi-cellular) terms with applications in microscopy Microbial biotechnology Training
CERNBox CERNBox cloud data storage, sharing and synchronization Data storage
ChEBI Dictionary of molecular entities focused on 'small' chemical compounds Microbial biotechnology Tool info Standards/Databases Training
ChEMBL Database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties and abstracted bioactivities. Toxicology data Tool info Standards/Databases Training
Chocolatey The Package Manager for Windows Data analysis
Choose a license Choose an open source license Licensing
Clinical Data Interchange Standards Consortium (CDISC) Consortium which defines several open standards for regulatory approval and case report forms in particular in the context of clinical trials meant for submission to FDA and EMA. Health data
Clinical Data Interoperability Services (CDIS) REDCap feature which allows a REDCap project to interact with an EHR system and pull EHR data into REDCap. Health data
Clinical Trial Registry-XML (CTR-XML) A CDISC Data Exchange Standard that lets technology vendors implement tools that support a “write once, use many times” solution based on XML. Health data is a resource depending on the National Library of medicine which makes available private and public-funded clinical trials. Toxicology data Standards/Databases
Comet Open source tandem mass spectrometry (MS/MS) sequence database search tool. Proteomics Tool info
Common Data Elements (CDE) in a box A collection of software applications which enables creation, storing and publishing of Common Data Elements according to the CDE semantic model. Rare disease data Tool info
Common Workflow Language (CWL) An open standard for describing workflows that are build from command line tools Data analysis Standards/Databases Training
Comptox The CompTox Chemicals Dashboard provides toxicological information for over 800.000 chemical compounds. It is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks. Toxicology data Tool info Standards/Databases
COmputational Modeling in BIology NEtwork (COMBINE) An initiative to bring together various formats and standard for computational models in biology Microbial biotechnology
Conda Open source package management system Data analysis Training
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
Convenient And Reusable Rapid OMOP Transformer (CaRROT-Mapper) Open-source tool to map datasets to the OMOP CDM. Health data
Cookiecutter A command-line utility that creates projects from cookiecutters (project templates), e.g. creating a Python package project from a Python package project template. Data organisation
COPO Portal for scientists to broker more easily rich metadata alongside data to public repos. Plant Phenomics Plant sciences Documentation and meta... Tool info Standards/Databases
COVID-19 Structural Hub Structural information organiser, collecting structures deposited in public repositories together with computationally predicted models from SARS-CoV-2, as well as their interactions with host proteins. Structural Bioinformatics Training
Create a Codebook Examples and tools to create a codebook by the Data Documentation Initiative (DDI) Documentation and meta...
Creative Commons License Chooser It helps you choose the right Creative Commons license for your needs. Licensing
Cromwell Cromwell is a Workflow Management System geared towards scientific workflows. Data analysis
Crop Ontology The Crop Ontology compiles concepts to curate phenotyping assays on crop plants, including anatomy, structure and phenotype. Plant sciences Standards/Databases Training
Crypt4GH A Python tool to encrypt, decrypt or re-encrypt files, according to the GA4GH encryption file format. Human data Training
CS3 Cloud Storage Services for Synchronization and Sharing (CS3) Data storage
CTD A database that aims to advance understanding about how environmental exposures affect human health. Toxicology data Tool info
CUDA toolkit The CUDA Toolkit from NVIDIA provides everything you need to develop GPU-accelerated applications Machine learning
cURL Command line tool and library for transferring data with URLs Data transfer Training
CWL in Toil The Common Workflow Language CWL is an emerging standard for writing workflows that are portable across multiple workflow engines and platforms. Toil has full support for the CWL v1.0, v1.1, and v1.2 standards. Data analysis
cwltool This is the reference implementation of the Common Workflow Language open standards. It is intended to be feature complete and provide comprehensive validation of CWL files as well as provide other tools related to working with CWL. Data analysis
Cytomine-IMS Image Data management Bioimaging data
DAISY Data Information System to keep sensitive data inventory and meet GDPR accountability requirement. TransMed Human data GDPR compliance Tool info Training
DAMAP It guides you step by step through a DMP and lets you export a pre-filled DMP as a Word document that you can customize and use for submission to funders. Also, DAMAP is compatible with the RDA recommendation for machine-actionable DMPs and offers an export of JSON DMPs. DAMAP is open source and to be self deployed. Data management plan
Data Agreement Wizard (DAWID) The Data Agreement Wizard is a tool developed by ELIXIR-Luxembourg to facilitate data sharing agreements. Human data GDPR compliance
Data Catalog Unique collection of project-level metadata from large research initiatives in a diverse range of fields, including clinical, molecular and observational studies. Its aim is to improve the findability of these projects following FAIR data principles. TransMed Training
Data Catalog Vocabulary (DCAT) DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. Rare disease data Machine actionability
Data Curation Centre Metadata list List of metadata standards Documentation and meta...
Data Stewardship Wizard Publicly available online tool for composing smart data management plans CSC FAIRtracks Plant Genomics Plant Phenomics Plant sciences Data management plan GDPR compliance Tool info Training
Data Stewardship Wizard Storage Costs Evaluator This service provides simple estimation of storage costs based on desired properties and local/actual configuration. Costs of data management
Data Use Ontology (DUO) DUO allows to semantically tag datasets with restriction about their usage. Human data Ethical aspects Standards/Databases Training Data License list Overview of typical licenses used for data resources Licensing
DataCite A search engine for the complete collection of publicly available DataCite DOIs Existing data Standards/Databases
DataPLAN Data Management Plan (DMP) generator that focuses on plant science. Plant sciences Tool info
DATAVERSE Open source research data respository software. Plant Phenomics Plant sciences Machine actionability Data storage Training
dbGAP The database of Genotypes and Phenotypes (dbGaP) archives and distributes data from studies investigating the interaction of genotype and phenotype in Humans Human data Tool info Standards/Databases Training
DESEq2 Differential gene expression analysis based on the negative binomial distribution Toxicology data Tool info Training
DisGeNET A discovery platform containing collections of genes and variants associated to human diseases. Human data Toxicology data Tool info Standards/Databases Training
DisProt A database of intrinsically disordered proteins Intrinsically disorder... Tool info Standards/Databases Training
DMP Canvas Generator Questionnaire, which generates a pre-filled a DMP Data management plan
DMPlanner Semi-automatically generated, searchable catalogue of resources that are relevant to data management plans. Data management plan
DMPonline Data Management Plans that meet institutional funder requirements. CSC Plant sciences Data management plan Training
DMPRoadmap DMP Roadmap is a Data Management Planning tool Data management plan
DMPTool Build your Data Management Plan Data management plan Training
DNA Data Bank of Japan (DDBJ) A database of DNA sequences Microbial biotechnology Tool info
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 Single-cell sequencing Data analysis Standards/Databases Standards/Databases Training
Docker Compose overview Compose is a tool for defining and running multi-container Docker applications. Data analysis
Docker Hub Docker Hub is the world's easiest way to create, manage, and deliver your team's container applications. Data analysis Standards/Databases Training
Dockerfile reference Docker can build images automatically by reading the instructions from a Dockerfile Data analysis
Dockstore Dockstore is a free and open source platform for sharing reusable and scalable analytical tools and workflows. It’s developed by the Cancer Genome Collaboratory and used by the GA4GH. Data analysis Tool info Training
DOME-ML Data, Optimisation, Model and Evaluation in Machine Learning (DOME-ML) is a set of community guidelines, recommendations and checklists for supervised ML validation in biology. Machine learning Standards/Databases
DPIA Knowledge Model A DSW knowledge model guiding users through a set of questions to collect information necessary for a research project Data Protection Impact Assessment (DPIA). Human data GDPR compliance
Dropbox Cloud storage and file sharing service Data transfer Documentation and meta... Data storage
Drug Matrix A toxicogenomic resource that provides access to the gene expression profiles of over 600 different compounds in several cell types from rats and primary rat hepatocytes. Toxicology data
Dryad Open-source, community-led data curation, publishing, and preservation platform for CC0 publicly available research data Bioimaging data Biomolecular simulatio... Data publication Standards/Databases
Dynameomics Database of folding / unfolding pathway of representatives from all known protein folds by MD simulation Biomolecular simulatio...
e!DAL Electronic data archive library is a framework for publishing and sharing research data Plant Phenomics Plant sciences Tool info Training
e!DAL-PGP Plant Genomics and Phenomics Research Data Repository Plant Genomics Plant Phenomics Standards/Databases Training
easy.DMP Data Management Plan Generator Data management plan
ECOTOX The ECOTOXicology Knowledgebase (ECOTOX) is a comprehensive, publicly available Knowledgebase providing single chemical environmental toxicity data on aquatic life, terrestrial plants, and wildlife. Toxicology data Standards/Databases
ECPGR Hub for the identification of plant genetic resources in Europe Plant sciences
ECPGR Central Crop Databases and other Crop Databases A number of ECPGR Central Crop Databases have been established through the initiative of individual institutes and of ECPGR Working Groups. The databases hold passport data and, to varying degrees, characterization and primary evaluation data of the major collections of the respective crops in Europe. Plant sciences
EDKB Endocrine Disruptor Knowledge Base is a platform designed to foster the development of computational predictive toxicology. This platform allows direct access to ten libraries containing the following resources: a biological activity database, QSAR training sets, in vitro and in vivo experimental data for more than 3,000 chemicals, literature citations, chemical-structure search capabilities. Toxicology data
Electron Microscopy Data Bank (EMDB) A public repository for electron cryo-microscopy maps and tomograms of macromolecular complexes and subcellular structures. Structural Bioinformatics Tool info
ELIXIR Core Data Resources Set of European data resources of fundamental importance to the wider life-science community and the long-term preservation of biological data Existing data Standards/Databases
ELIXIR Deposition Databases for Biomolecular Data List of discipline-specific deposition databases recommended by ELIXIR. CSC IFB Marine Metagenomics NeLS Data publication Documentation and meta... Standards/Databases
EMBL-EBI's data submission wizard EMBL-EBI's wizard for finding the right EMBL-EBI repository for your data. Data publication
EMPIAR Electron Microscopy Public Image Archive is a public resource for raw, 2D electron microscopy images. You can browse, upload and download the raw images used to build a 3D structure OMERO Bioimaging data Structural Bioinformatics Data publication Tool info Standards/Databases Training
ENA COMPARE Data Hubs This tool carries out data hub set up at the European Nucleotide Archive (ENA). Project data managemen...
ENA upload tool The program submits experimental data and respective metadata to the European Nucleotide Archive (ENA). Data brokering
Ensembl Genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Identifiers Tool info Standards/Databases Training
Ensembl Plants Open-access database of full genomes of plant species. Plant Genomics Standards/Databases Training
ERN Registries Generic Informed Consent Forms EJP RD - European Joint Programme on Rare Diseases - ERN Registries Generic Informed Consent Forms Rare disease data
ERPA Web-based tool allowing users to create and manage a register of personal data processing activities (ROPA). Human data GDPR compliance
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). TSD Human data Data sensitivity
EU Survey European Commission's official multilingual online survey-management system built for the creation and publishing of globally accessible forms. Health data
EUDAT licence selector wizard EUDAT's wizard for finding the right licence for your data or code. Licensing
EudraVigilance The European database of suspected adverse drug reaction reports is a public resource aimed to provide access to reported suspected side-effects of drugs. Side-effects are defined according to the MedDRA ontology. Toxicology data
EUPID EUPID provides a method for identity management, pseudonymisation and record linkage to bridge the gap between multiple contexts. Human data
EURISCO European Search Catalogue for Plant Genetic Resources Plant sciences Tool info
Europe PMC Europe PMC is a repository, providing access to worldwide life sciences articles, books, patents and clinical guidelines. Machine actionability Tool info Standards/Databases Training
European Electronic Health Record Exchange Format (EEHRxF) Recommended by the European Commission as the format to be used for the exchange of EHR data for cross-border healthcare. Health data
European Joint Programme on Rare Diseases (EJP RD) A programme aiming to create an effective rare diseases research ecosystem for progress, innovation and for the benefit of everyone with a rare disease. Rare disease data
European Joint Programme on Rare Diseases Metadata Model This core model is designed to represent data about a rare disease patient and biosample registries. The model is based on and builds on existing standards, such as the European Rare Disease Registry Infrastructure and the Common Data Elements from the rare disease community and other more generalised standards for data sharing such as the W3C DCAT vocabulary. Rare disease data
European Joint Programme on Rare Diseases Virtual Platform (EJP RD) The Virtual Platform is a federated ecosystem, in which resources are enhanced to be amenable to rare disease research, and made Findable, Accessible, Interoperable and Reusable: data stays at the source level but can be queyrable at distance from an EJP RD query point. Rare disease data
European Nucleotide Archive (ENA) A record of sequence information scaling from raw sequcning reads to assemblies and functional annotation Galaxy Plant Genomics Microbial biotechnology Single-cell sequencing Data brokering Data publication Project data managemen... Tool info Standards/Databases Training
European Rare Disease Registry Infrastructure directory of registries (ERDRI.dor) ERDRI.dor provides an overview of participating rare disease registries with their main characteristics and description. Rare disease data
European Rare Disease Registry Infrastructure metadata repository (ERDRI.mdr) ERDRI.mdr serves to ease the integration of heterogeneous data from different rare disease registries. For this purpose, it contains a collection of metadata which specifies the used data elements of a registry including the designation of the used data elements, their definition and units of measurement. Rare disease data
European Reference Networks (ERNs) Virtual networks involving healthcare providers across Europe. They aim to facilitate discussion on complex or rare diseases and conditions that require highly specialised treatment, and concentrated knowledge and resources. Rare disease data Training
European Variation Archive (EVA) Open-access database of all types of genetic variation data from all species. Plant Genomics Tool info Standards/Databases Training
Evidence and Conclusion Ontology (ECO) Controlled vocabulary that describes types of evidence and assertion methods Existing data Documentation and meta... Standards/Databases
Expression Atlas Gene expression across species and biological conditions Machine actionability Standards/Databases Training
FAERS The FDA Adverse Event Reporting System (FAERS) is an american resource that contains adverse event reports, medication error reports and product quality complaints submitted by healthcare professionals, consumers, and manufacturers. MedDRA ontology is used for coding adverse effects. Note that reports available in FAERS do not require a causal relationship between a product and an adverse event and further evaluations are conducted by FDA to monitor the safety of products. Toxicology data Tool info
FAIDARE FAIDARE is a tool allowing to search data across dinstinct databases that implemented BrAPI. Plant Phenomics Plant sciences Tool info Training
FAIR Cookbook FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable and Reusable (FAIR) TransMed Health data Compliance monitoring ... Tool info Training
FAIR Data Point (FDP) A FAIR Data Point stores metadata in a standardized and sharable way. Rare disease data Standards/Databases Training
FAIR Data Points Metadata for machines Rare disease data Training
FAIR Evaluation Services Resources and guidelines to assess the FAIRness of digital resources. Compliance monitoring ...
FAIR Implementation Profile The FIP is a collection of FAIR implementation choices made by a community of practice for each of the FAIR Principles. Data management plan Project data managemen... Standards/Databases
FAIR-Wizard The FAIR wizard utilizes FAIRification resources developed by the FAIRplus project and other platforms, suggests FAIRification materials based on the FAIRification requirements, and designs FAIRification solutions for data owners, data stewards, and other people involved in FAIRification. Compliance monitoring ... Training Help you discover resources to measure and improve FAIRness. Compliance monitoring ...
FAIRDOM-SEEK A data Management Platform for organising, sharing and publishing research datasets, models, protocols, samples, publications and other research outcomes. NeLS Plant Phenomics Microbial biotechnology Plant sciences Documentation and meta... Data storage Tool info
FAIRDOMHub Data, model and SOPs management for projects, from preliminary data to publication, support for running SBML models, etc. (public SEEK instance) NeLS Plant Genomics Plant Phenomics Microbial biotechnology Plant sciences Documentation and meta... Standards/Databases Training
FAIRshake A System to Evaluate the FAIRness of Digital Objects Compliance monitoring ...
FAIRsharing A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies. FAIRtracks Health data Microbial biotechnology Plant sciences Data provenance Data publication Existing data Machine actionability Documentation and meta... Standards/Databases Training
Federated Health Information Model (FHIM) A UML-based logical health information model defined by the Open Group, intended to achieve interoperability between multiple healthcare standards and protocols. Health data
FHIR4FAIR Guidance on how FHIR can be used for supporting FAIR health data. Health data
FigShare Data publishing platform Biomolecular simulatio... Data publication Identifiers Documentation and meta... Standards/Databases Training
Fiji Fiji is an image processing package OMERO Tool info Training
FileZilla A free FTP (FTPS and SFTP) solution with graphical interface Data transfer Training
FIP Wizard FIP Wizard is a toolset to facilitate the capture of data in FAIR Convergence Matrix questionnaire prompting communities to explicitly declare their FAIR Implementation Profiles. These profiles can be then stored and published as nanopublications. Data management plan Project data managemen...
Flame Flame is a flexible framework supporting predictive modeling and similarity search within the eTRANSAFE project. Toxicology data Tool info
Free-IPA FreeIPA is an integrated Identity and Authentication solution for Linux/UNIX networked environments. TransMed
Freegenes Repository of IP-free synthetic biological parts Microbial biotechnology
GA4GH Data Security Toolkit Principled and practical framework for the responsible sharing of genomic and health-related data. Human data
GA4GH Genomic Data Toolkit Open standards for genomic data sharing. Human data
GA4GH Regulatory and Ethics toolkit Framework for Responsible Sharing of Genomic and Health-Related Data Human data Ethical aspects
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. Marine Metagenomics Single-cell sequencing Data analysis Data provenance Data storage Tool info Training
GenBank A database of genetic sequence information. GenBank may also refer to the data format used for storing information around genetic sequence data. Microbial biotechnology Tool info Standards/Databases Training
Gene Expression Omnibus (GEO) A repository of MIAME-compliant genomics data from arrays and high-throughput sequencing Microbial biotechnology Single-cell sequencing Standards/Databases
Gene Ontology The Gene Ontology Consortium continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. Single-cell sequencing Tool info Standards/Databases Training
Genesys Genesys is an online platform where you can find information about Plant Genetic Resources for Food and Agriculture PGRFA conserved in genebanks worldwide. Plant sciences
Genomic Standards Consortium (GSC) The Genomic Standards Consortium (GSC) is an open-membership working body enabling genomic data integration, discovery and comparison through international community-driven standards. Marine metagenomics Standards/Databases
GHS Classification GHS (Globally Harmonized System of Classification and Labelling of Chemicals) classification was developed by the United Nations in an attempt to align standards and chemical regulations in different countries. GHS includes criteria for the classification of health, physical and environmental hazards, and what information should be included on labels of hazardous chemicals and safety data sheets. Toxicology data
GISAID Accessible database designed by scientist for scientist, to improve the sharing of influenza data. Machine actionability Standards/Databases
Git Distributed version control system designed to handle everything from small to very large projects Single-cell sequencing Data organisation Training
GitHub Versioning system, used for sharing code, as well as for sharing of small data Machine learning Data organisation Documentation and meta... Standards/Databases Standards/Databases Training
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 Standards/Databases Training
Globus High-performance data transfers between systems within and across organizations Data transfer
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. Plant Phenomics Tool info Standards/Databases
Google Dataset Search Search engine for datasets Existing data
Google Drive Cloud Storage for Work and Home Data transfer
GPCRmd Repository of GPCR protein simulations Biomolecular simulatio... Tool info
Harmony Fast, sensitive and accurate integration of single-cell data. Single-cell sequencing Tool info Training
Harvard Medical School - Electronic Lab Notebooks ELN Comparison Grid by Hardvard Medical School Identifiers Documentation and meta...
Haz-Map Haz-Map is an occupational health database that makes available information about the adverse effects of exposures to chemical and biological agents at the workplace. These associations have been established using current scientific evidence. Toxicology data
Hierarchical Data Format HDF5 consists of a file format for storing HDF5 data, a data model for logically organizing and accessing HDF5 data from an application, and the software (libraries, language interfaces, and tools) for working with this format. Single-cell sequencing Standards/Databases
HL7 FHIR A standard used for health care data exchange. Health data
Homebrew The Missing Package Manager for macOS or Linux Data analysis
How to License Research Data - DCC Guidelines about how to license research data from Digital Curation Centre Licensing
HuggingFace The platform where the machine learning community collaborates on models, datasets, and applications. Machine learning Training
Human Phenotype Ontology (HPO) Standardised vocabulary of phenotypic abnormalities encountered in human disease. Health data Tool info
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. Proteomics Standards/Databases Training
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. Human data Tool info Standards/Databases Training
HUPO Proteomics Standards Initiative The HUPO Proteomics Standards Initiative defines community standards for data representation in proteomics and interactomics to facilitate data comparison, exchange and verification. Microbial biotechnology Proteomics
IBM Aspera With fast file transfer and streaming solutions built on the award-winning IBM FASP protocol, IBM Aspera software moves data of any size across any distance Data transfer The Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession). FAIRtracks Identifiers Tool info Standards/Databases Training
iGEM Parts Registry A collection of standard biological parts to which all entrants in the iGEM competition must submit their parts Microbial biotechnology
ilastik ilastik is a user-friendly tool for interactive image classification, segmentation and analysis OMERO Tool info
Image Data Resource (IDR) A repository of image datasets from scientific publications OMERO Bioimaging data Microbial biotechnology Tool info Standards/Databases
Informed Consent Ontology (ICO) The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. Human data Ethical aspects Standards/Databases
Integrated Database of Small Molecules Interoperability in small molecules Machine actionability
International Classification of Diseases 10th Revision (ICD-10) Codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases. Replaced by ICD-11 on 1/1/2022. Health data Tool info
International Classification of Diseases 11th Revision (ICD-11) Replaces the ICD-10 as the global standard for recording health information and causes of death. It is developed by the World Health Organization and is annually updated. Health data Tool info
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 Multicrop Databases A catalogue of relevant International Multicrop Databases Plant sciences
International Nucleotide Sequence Database Collaboration The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, through alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations. Galaxy Microbial biotechnology Plant sciences Data publication
International Nucleotide Sequence Database Collaboration (INSDC) A collaborative database of genetic sequence datasets from DDBJ, EMBL-EBI and NCBI Galaxy Microbial biotechnology Plant sciences Data publication Tool info
International Society for the Advancement of Cytometry (ISAC) Data standards and formats for reporting flow cytometry data Microbial biotechnology
International Union of Biochemistry and Molecular Biology (IUBMB) Resource for naming standards in biochemistry and molecular biology Microbial biotechnology
InterPro Functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites Proteomics Tool info Standards/Databases Training
IntoGen IntoGen collects and analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes. Human data Tool info
Intrinsically disordered proteins ontology (IDPO) Intrinsically disordered proteins ontology Intrinsically disorder... Tool info
IRIS The Integrated Risk Information System (IRIS) resource evaluates information on health that might arise after exposure to environmental contaminants. Toxicology data Tool info Training
iRODS Integrated Rule-Oriented Data System (iRODS) is open source data management software for a cancer genome analysis workflow. TransMed Bioimaging data Data storage Tool info
IRRMC Integrated Resource for Reproducibility in Macromolecular Crystallography. Repository of diffraction experiments used to determine protein structures in the PDB, contributed by the CSGID, SSGCID, JCSG, MCSG, SGC, and other large-scale projects, as well as individual research laboratories. Structural Bioinformatics
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 Plant sciences Standards/Databases
ISA4J Open source software library that can be used to generate a ISA-TAB export from in-house data sets. These comprises e.g. local database or local file system based experimental. Plant Phenomics Tool info
ISO 13606 A standard designed by the European Committee for Standardization to define a information architecture for communicating part or all of the EHR of a single patient between EHR systems or between EHR systems and a centralised EHR data repository. Health data
ISO 13972:2022 Defines data elements, the relationships between such data elements and terminologies for detailed small, reusable clinical models. Health data
ISO/DIS 14199 Domain model for data interchange that enables semantic interoperability and intends to integrate biomedical, clinical research and routine healthcare data. Health data
ISO/IEC 27001 International information security standard Human data Compliance monitoring ...
ITER ITER is an Internet database of human health risk values and cancer classifications for over 680 chemicals of environmental concern from multiple organizations worldwide. Toxicology data Training
IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN) A collaborative resource from IUPAC and IUBMB for naming standards in biochemistry Microbial biotechnology
JBEI-ICE A registry platform for biological parts Microbial biotechnology
JGA The Japanese Genotype-phenotype Archive (JGA) is a service for permanent archiving and sharing of all types of individual-level genetic and de-identified phenotypic data resulting from biomedical research projects. Human data
Jotform Commercial online survey tool. Health data
Jupyter Jupyter notebooks allow to share code, documentation Data analysis Training
Jupyter kernels Kernel Zero is IPython, which you can get through ipykernel, and is still a dependency of jupyter. The IPython kernel can be thought of as a reference implementation, as CPython is for Python. Data analysis
JWS Online JWS-Online is a systems biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models. NeLS Standards/Databases
Keras Keras is an open-source library that provides a Python interface for artificial neural networks. Machine learning Training
Keycloak Keycloak is an open source identity and data access management solution. TransMed Training
KnetMiner A software to make biological search more integrated, intuitive and intelligent, enabling a better way to discover and share new insights. Machine actionability Tool info Standards/Databases Training
Kubernetes Kubernetes, also known as K8s, is an open-source system for automating deployment, scaling, and management of containerized applications. Data analysis Training
LeafNet LeafNet is a convenient tool that can robustly localize stomata and segment pavement cells for light-microscope images of leaves Plant Phenomics Tool info
Life Science Login (LS Login) An authentication service from EOSC-Life IFB NeLS TransMed TSD
Life-Monitor LifeMonitor is a service to support the sustainability and reusability of published computational workflows. Data analysis Training
LimeSurvey A free and open source platform to develop and publish online surveys. Health data
limma Linear Models for Microarray Data Toxicology data Tool info Training
LimTox The LiMTox system is a text mining approach that tries to extract associations between compounds and a particular toxicological endpoint at various levels of granularity and evidence types, all inspired by the content of toxicology reports. It integrates direct ranking of associations between compounds and hepatotoxicity through combination of heterogeneous complementary strategies from term co-mention, rules, and patterns to machine learning-based text classification. It also provides indirect associations to hepatotoxicity through the extraction of relations reflecting the effect of compounds at the level of metabolism and liver enzymes. Toxicology data Tool info
Linked Open Vocabularies (LOV) Web portal for finding ontologies Documentation and meta...
List of Prokaryotic names with Standing in Nomenclature (LPSN) A database of prokaryote specific biodiversity information Microbial biotechnology Tool info
Logical Observation Identifiers Names and Codes (LOINC) Terminology standard for health measurements, observations, and documents. Health data
Loom Loom is an efficient file format for large omics datasets. Single-cell sequencing
LUMI EuroHPC world-class supercomputer Data analysis Tool info
MacPorts The MacPorts Project is an open-source community initiative to design an easy-to-use system for compiling, installing, and upgrading either command-line, X11 or Aqua based open-source software on the Mac operating system. Data analysis
MarDB MarDB includes all non-complete marine microbial genomes regardless of level of completeness. Each entry contains 120 metadata fields including information about sampling environment or host, organism and taxonomy, phenotype, pathogenicity, assembly and annotation. Marine Metagenomics Tool info
MarFun MarFun is a manually curated marine fungi genome database. Marine Metagenomics
Marine Metagenomics Portal (MMP) High-quality curated and freely accessible microbial genomics and metagenomics resources for the marine scientific community Marine Metagenomics Tool info
MarRef MarRef is a manually curated marine microbial reference genome database that equenced genomes. Each entry contains 120 metadata fields including information about sampling environment or host, organism and taxonomy, phenotype, pathogenicity, assembly and annotation information Marine Metagenomics Tool info
Mascot Powerful search engine which uses mass spectrometry data to identify proteins from DNA, RNA and protein sequence databases as well as spectral libraries. Proteomics Tool info Training
Mass Centric Peptide Database A database to quickly access all tryptic peptides of the UniProtKB Proteomics
MassIVE Powerful search engine which uses mass spectrometry data to identify proteins from DNA, RNA and protein sequence databases as well as spectral libraries. Proteomics Training
MemProtMD Database of over 5000 intrinsic membrane protein structures Biomolecular simulatio... Tool info
Mendeley data Multidisciplinary, free-to-use open repository specialized for research data Biomolecular simulatio... Data publication Existing data Standards/Databases
Metabolome Exchange A repository of genomics data relating to the study of the metabolome Microbial biotechnology
Metagen-FastQC Cleans metagenomic reads to remove adapters, low-quality bases and host (e.g. human) contamination Data publication
MIADE Minimum Information About Disorder Experiments (MIADE) standard Intrinsically disorder... Training
MIAME Minimum Information About a Microarray Experiment Documentation and meta... Standards/Databases Training
MIAPPE Minimum Information About a Plant Phenotyping Experiment Plant Genomics Plant Phenomics Plant sciences Documentation and meta... Standards/Databases Training
MIAPPE-compliant spreadsheet template MIAPPE-compliant spreadsheet template Plant sciences
MIAPPE_Checklist-Data-Model This document describes the MIAPPE Checklist and Data Model Plant sciences
Microsoft Azure Cloud storage and file sharing service from Microsoft Data transfer
Microsoft OneDrive Cloud storage and file sharing service from Microsoft Data transfer Data storage
MIGS/MIMS Minimum Information about a (Meta)Genome Sequence Marine metagenomics Standards/Databases
MineProt A stand-alone server for structural proteome curation Structural Bioinformatics Tool info
Minimum Information about a Single-Cell Experiment (minSCe) MinSCe is a minimum set of metadata categories used to describe a single-cell assay in sufficient detail to enable the analysis of transcriptomic data. Single-cell sequencing Standards/Databases
MINSEQE Minimum Information about a high-throughput SEQuencing Experiment Documentation and meta... Standards/Databases Training
MIxS Minimum Information about any (x) Sequence Marine metagenomics Standards/Databases Training
MobiDB A database of protein disorder and mobility annotations Intrinsically disorder... Tool info Standards/Databases Training
MoDEL Database of Protein Molecular Dynamics simulations representing different structural clusters of the PDB Biomolecular simulatio... Tool info Training
MoDEL-CNS Repository for Central Nervous System-related mainly membrane protein MD simulations Biomolecular simulatio...
ModelArchive Repository for theoretical models of macromolecular structures with DOIs for models Biomolecular simulatio... Structural Bioinformatics Tool info Standards/Databases
MOLGENIS Molgenis is a modular web application for scientific data. Molgenis provides researchers with user friendly and scalable software infrastructures to capture, exchange, and exploit the large amounts of data that is being produced by scientific organisations all around the world. MOLGENIS Identifiers Tool info
MolMeDB Database about interactions of molecules with membranes Biomolecular simulatio... Tool info Standards/Databases
MolSSI - BioExcel COVID-19 therapeutics hub Aggregating critical information to accelerate COVID-19 drug discovery for the molecular modeling and simulation community. Biomolecular simulatio...
MONARC A risk assessment tool that can be used to do Data Protection Impact Assessments TransMed Human data
Monocle The Monocle 3 package provides a toolkit for analyzing single-cell gene expression experiments. Single-cell sequencing Tool info Training
MRI2DICOM a Magnetic Resonance Imaging (MRI) converter from ParaVision® (Bruker, Inc. Billerica, MA) file format to DICOM standard XNAT-PIC
msconvert Provides a set of open-source, cross-platform software libraries and tools that facilitate proteomics data analysis. Proteomics Tool info
Multi-Crop Passport Descriptor (MCPD) The Multi-Crop Passport Descriptor is the metadata standard for plant genetic resources maintained ex situ by genbanks. Plant sciences Standards/Databases Training
MyTARDIS A file-system based platform handling the transfer of data Bioimaging 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. Identifiers
NBP The National Biomonitoring Program (NBP) is a public resource that offers an assessment of nutritional status and the exposure of the U.S. population to environmental chemicals and toxic substances. Toxicology data
NCBI Taxonomy NCBI's taxonomy browser is a database of biodiversity information Microbial biotechnology Standards/Databases
NCIMB Hosts information relating to strains, cultures and more Microbial biotechnology
Nextcloud As fully on-premises solution, Nextcloud Hub provides the benefits of online collaboration without the compliance and security risks Data storage
Nextflow Nextflow is a framework for data analysis workflow execution Data analysis Tool info Training
NMRlipids Repository for lipid MD simulations to validate force fields with NMR data Biomolecular simulatio...
NPDS The National Poison Data System (NPDS) is a resource that provides poisson exposure occurring in the US and some freely associated states. Toxicology data
OHDSI Multi-stakeholder, interdisciplinary collaborative to bring out the value of health data through large-scale analytics. All our solutions are open-source. TransMed Toxicology data Data quality Tool info
OHDSI Athena Repository of ontologies for use with the OMOP CDM. Health data
OME Data Model and File Formats The OME Model is a specification for storing data on biological imaging. Machine actionability
OMERO OMERO is an open-source client-server platform for managing, visualizing and analyzing microscopy images and associated metadata Galaxy OMERO Bioimaging data Tool info Training
OmicsDI Omics Discovery Index (OmicsDI) provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics) Galaxy Existing data Machine actionability Tool info Standards/Databases Training
Omnipy Omnipy is a high level Python library for type-driven data wrangling and scalable workflow orchestration. FAIRtracks Tool info Training
OMOP Common Data Model Open community standard for observational health care data obtained from health records. Health data Training
OMOP-CDM OMOP is a common data model for the harmonisation for of observational health data. TransMed Data quality
OnotoMaton OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets. Plant sciences Identifiers
Ontobee A web portal to search and visualise ontologies Documentation and meta... Standards/Databases Training
ONTOBROWSER The OntoBrowser tool was developed to manage ontologies and code lists. Toxicology data Tool info
Ontology Lookup Service EMBL-EBI's web portal for finding ontologies FAIRtracks Bioimaging data Health data Documentation and meta... Tool info Standards/Databases Training
Open Definition Conformant Licenses Licenses that are conformant with the principles laid out in the Open Definition. Licensing
Open Neural Network Exchange (ONNX) ONNX is an open format built to represent machine learning models. Machine learning
OpenAIRE Explore Explore Open Access research outcomes from OpenAIRE network Existing data
OpenEBench ELIXIR benchmarking platform to support community-led scientific benchmarking efforts and the technical monitoring of bioinformatics reosurces Data analysis Tool info
OpenEHR Non-profit organisation that publishes technical standards for an EHR platform along with domain‑developed clinical models to define content. Health data Standards/Databases
OpenMS OpenMS offers an open-source C++ library (+ Python bindings) for LC/MS data management, analysis and visualization. Proteomics Tool info Training
OpenRefine Data curation tool for working with messy data TransMed Data quality Machine actionability Training
OpenScienceFramework free and open source project management tool that supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery Biomolecular simulatio... Documentation and meta... Standards/Databases
OpenSlide C library that provides a simple interface to read whole-slide images (also known as virtual slides) Bioimaging data
OpenStack OpenStack is an open source cloud computing infrastructure software project and is one of the three most active open source projects in the world Data analysis Data storage Training
Operational Data Model-XML (ODM-XML) A CDISC Data Exchange Standard that is a vendor-neutral, platform-independent format for exchanging and archiving clinical and translational research data, along with their associated metadata, administrative data, reference data, and audit information. Health data
OSF OSF (Open Science Framework) is a free, open platform to support your research and enable collaboration. Data storage Training
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 Tool info
ownCloud Cloud storage and file sharing service Data transfer Data storage
PAA PAA is an R/Bioconductor tool for protein microarray data analysis aimed at biomarker discovery. Proteomics Tool info
PANGAEA Data Publisher for Earth and Environmental Science Data publication Tool info Standards/Databases Training
PCDDB The Protein Circular Dichroism Data Bank Intrinsically disorder... Tool info
PDB The Protein Data Bank (PDB) Galaxy Intrinsically disorder... Structural Bioinformatics Data publication Tool info Training
PDB-Dev Prototype archiving system for structural models obtained using integrative or hybrid modeling Biomolecular simulatio... Structural Bioinformatics
PDBe-KB Protein Data Bank in Europe Knowledge Base Machine actionability Tool info Training
PDBx/mmCIF format and tools Information about the standard PDB archive format PDBx/mmCIF, its dictionaries and related software tools Structural Bioinformatics Standards/Databases
PDBx/mmCIF ModelCIF Extension Dictionary Extension of the PDBx/mmCIF dictionary for theoretical models of macromolecular structures Structural Bioinformatics
PeptideAtlas Database of multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Proteomics Tool info Standards/Databases
PharmGKB A resource that curates knowledge about the impact of genetic variation on drug response. Toxicology data Tool info
Pharos Pharos provides hazard, use, and exposure information on 140,872 chemicals and 180 different kinds of building products. Toxicology data Tool info
Phenomenal 3D Phenomenal-3D is an automatic open source library for 3D shoot architecture reconstruction and analysis for image-based plant phenotyping Plant Phenomics Tool info
PHIS The open-source Phenotyping Hybrid Information System (PHIS) manages and collects data from plants phenotyping and high throughput phenotyping experiments on a day to day basis. Plant Phenomics Training
PIA - Protein Inference Algorithms PIA is a toolbox for mass spectrometrey based protein inference and identification analysis. Proteomics Tool info
pISA-tree A data management solution for intra-institutional organization and structured storage of life science project-associated research data, with emphasis on the generation of adequate metadata. Plant Phenomics Tool info
Plant 3D Plant 3D is a plant phenotyping toolkit for 3D point clouds. Plant 3D (P3D) automatically extracts common phenotyping features of interest from high-resolution 3D scans of plant architectures. Plant Phenomics Tool info
plant-miappe.json BioSamples Plant MIAPPE checklist in JSON format Plant sciences
PlantCV Plant Computer Vision (PlantCV)is an image processing toolkit for plant phenotyping analysis. Plant Phenomics Tool info
PLAZA Access point for plant comparative genomics, centralizing genomic data produced by different genome sequencing initiatives. Plant Genomics Standards/Databases Training
PMut Platform for the study of the impact of pathological mutations in protein stuctures. Human data Tool info
Podman Manage containers, pods, and images with Podman. Seamlessly work with containers and Kubernetes from your local environment. Data analysis
Prefect Prefect is a workflow orchestration tool empowering developers to build, observe, and react to data pipelines. FAIRtracks
PRIDE PRoteomics IDEntifications (PRIDE) Archive database Proteomics Data publication Tool info Standards/Databases Training
PRIDE Submission Tool Main tool used to submit proteomics datasets to PRIDE Archive Proteomics
Privacy Impact Assessment Tool (PIA) The open source PIA software helps to carry out data protection impact assessment Human data Tool info
PROAST PROAST (copyright RIVM National Institute for Public Health and the Environment) is a software package for the statistical analysis of dose-response data. Toxicology data
ProteomeXchange ProteomeXchange provides globally coordinated standard data submission and dissemination pipelines Proteomics Tool info Standards/Databases Training A secure platform for developing and sharing reproducible methods. Microbial biotechnology Standards/Databases
PROV-DM: The PROV Data Model PROV-DM is the conceptual data model that forms a basis for the W3C provenance (PROV) family of specifications. Data provenance
PUBLISSO Documenting research data: Electronic Lab(oratory) Notebooks. Documentation and meta...
Pydantic Pydantic is the most widely used data validation library for Python. FAIRtracks
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 storage Training
raw2ometiff Java application to convert a directory of tiles to an OME-TIFF pyramid. This is the second half of iSyntax/.mrxs => OME-TIFF conversion. Bioimaging data
RD-Connect Genome Phenome Analysis Platform The RD-Connect GPAP is an online tool for diagnosis and gene discovery in rare disease research. Human data Tool info Training
RDA Standards Directory of standard metadata, divided into different research areas Data provenance Documentation and meta...
re3data Registry of Research Data Repositories Data publication Existing data Licensing Training
REACH registered substances Portal with public data submitted to ECHA in REACH registration dossiers by substance manufacturers, importers, or their representatives, as laid out by the REACH Regulation (see Understanding REACH regulation). Toxicology data
Real World Data for Clinical Research (Vulcan) A minimal set of clinical research FHIR resources and elements in an EHR that can be utilised in an interoperable and consistent manner for clinical research. Health data Tool info
Recherche Data Gouv An ecosystem for sharing and opening research data Plant sciences Standards/Databases
REDCap REDCap is a secure web application for building and managing online surveys and databases. While REDCap can be used to collect virtually any type of data in any environment, it is specifically geared to support online and offline data capture for research studies and operations. TransMed Health data Data quality Identifiers Tool info Training
REDCap Cloud A fully managed REDCap system based in the cloud, provided by nPhase. Health data
REDIportal Database of A-to-I (deamination of adenosines to inosines) events that enables to search RNA editing sites by genomic region, gene name and other relevant features as the tissue of origin. Epitranscriptome data Tool info
REDItools Python scripts to detect RNA editing events in RNAseq experiments Epitranscriptome data Tool info
REDItools2 REDItools2 is the optimized, parallel multi-node version of REDItools. Epitranscriptome data
REMS REMS (Resource Entitlement Management System), developed by CSC, is a tool that can be used to manage researchers’ access rights to datasets. TransMed Tool info Training
Renamer4Mac File renaming software for Mac Data organisation
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
Research Data Management Organiser Supports the systematic planning, organisation and implementation of research data management throughout the course of a project Data management plan
Research Data Management Platform (RDMP) Data management platform for automated loading, storage, linkage and provision of data sets Data storage Tool info
Research Management Plan Machine actionable DMPs. Data management plan
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. Galaxy Microbial biotechnology Data provenance Standards/Databases
Reva Reva connects cloud storages and application providers Data transfer Tool info Training
Rightfield RightField is an open-source tool for adding ontology term selection to Excel spreadsheets Microbial biotechnology Plant sciences Identifiers Tool info
RRI self reflection tool The Self-Reflection Tool provides questions and statements addressing all stakeholder groups (policy makers, education representatives, civil society organisations, industry and business, and the research community). Ethical aspects
RRI Toolkit The RRI Toolkit helps stakeholders across Europe put Responsible Research and Innovation into practice. Ethical aspects
Rstudio Rstudio notebooks allow to share code, documentation Data analysis Tool info Training
Rucio Rucio - Scientific Data Management Data transfer Data storage
RxNorm RxNorm is a normalized naming system for medications that is maintained by the National Library of Medicine. Rxnorm provides unique identifiers and allows unambiguous communication of drug-related information across the American health computer systems. Health data Toxicology data Tool info Standards/Databases
salDB SalDB is a salmon specific database of genome sequenced prokaryotes representing the microbiota of fishes found in the taxonomic family of Salmonidae. Marine Metagenomics
SASBDB Small Angle Scattering Biological Data Bank Intrinsically disorder...
SBGrid Data Bank Repository of X-ray diffraction, MicroED, LLSM datasets, as well as structural models. Structural Bioinformatics
SBOL Visual A standard library of visual glyphs used to represent SBOL designs and interactions. Microbial biotechnology
SBOLDesigner A CAD tool to create SBOL designs through the use of SBOL Visual glyphs. Microbial biotechnology
Scanpy Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. Single-cell sequencing Tool info Training
Scater Scater offers a collection of tools for analysis (such as quality control) for single-cell gene expression data. Single-cell sequencing Tool info Training
SCEasy sceasy is a package that helps easy conversion of different single-cell data formats to each other. Single-cell sequencing is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond. Machine learning Machine actionability Standards/Databases Training
ScienceMesh ScienceMesh - frictionless scientific collaboration and access to research services Data transfer Data storage
Scientific Data's Recommended Repositories List of respositories recommended by Scientific Data, contains both discipline-specific and general repositories. Existing data
scikit-learn scikit-learn is a free software machine learning library for the Python programming language. Machine learning Tool info Training
Scipion Cryo em image processing framework. Integration, traceability and analysis. Structural Bioinformatics Tool info Standards/Databases
ScipionCloud Cloud virtual machine with the Scipion software to process EM imaging data either in a single server or in a cluster. Structural Bioinformatics
SDRF Information about a proposed standard for sample metadata annotations in public repositories called Sample and Data Relationship File (SDRF)-Proteomics format. Proteomics
SeaFile SeaFile File Synchronization and Share Solution Data transfer Data storage
Semantic data model of the set of common data elements for rare diseases registration A semantic data model describing the common data elements for rare diseases registration. Rare disease data
Semares All-in-one platform for life science data management, semantic data integration, data analysis and visualization Documentation and meta... Data storage
Sequence Read Archive Sequence Read Archive (SRA) data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequencing data. Single-cell sequencing Standards/Databases Training
Set of common data elements for rare diseases registration Contains 16 data elements to be registered by each rare disease registry across Europe, which are considered to be essential for further research. Rare disease data
Seurat Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Single-cell sequencing Tool info Training
ShortBOL A scripting language for creating Synthetic Biology Open Language (SBOL) in a more abstract way. Microbial biotechnology
SIFTS Structure integration with function, taxonomy and sequence Intrinsically disorder...
Single Cell Portal Interactive portal for single-cell genomics data. Single-cell sequencing
Single-cell best pratices An entry point for novices in the field of single-cell (multi-)omic analysis and guides advanced users to the most recent best practices. Single-cell sequencing
SingleCellExperiment The SingleCellExperiment class is a lightweight Bioconductor container for storing and manipulating single-cell genomics data. Single-cell sequencing Tool info
Singularity Singularity is a container platform. Data analysis Training
Skyline Freely-available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), DIA/SWATH and targeted DDA quantitative methods and analyzing the resulting mass spectrometer data. Proteomics Tool info
SMASCH SMASCH (Smart Scheduling) system, is a web-based tooldesigned for longitudinal clinical studies requiring recurrent follow-upvisits of the participants. SMASCH controls and simplifies the scheduling of big database of patients. Smasch is also used to organize the daily plannings (delegation of tasks) for the different medical professionals such as doctors, nurses and neuropsychologists. TransMed Health data
Snakemake Snakemake is a framework for data analysis workflow execution Data analysis Tool info Training
SPIDER pseudonymisation tool ERDRI.spider (Secure Privacy-preserving Identity management in Distributed Environments for Research) pseudonymisation tool generates pseudonyms for RD patients. Rare disease data
SSBD:database Added-value database for biological dynamics images Bioimaging data Standards/Databases
SSBD:repository An open data archive that stores and publishes bioimaging and biological quantitative datasets Bioimaging data
Standards for Reporting Enzyme Data (STRENDA) Resource of standards for reporting enzyme data Microbial biotechnology
STARsolo A comprehensive turnkey solution for quantifying gene expression in single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR. Single-cell sequencing Training
STRING Known and predicted protein-protein interactions. Proteomics Tool info Standards/Databases Training
Study Data Tabulation Model (SDTM) A CDISC Foundational Standard that provides a standard for organizing and formatting data to streamline processes in collection, management, analysis and reporting. Health data
SynBioHub A searchable design repository for biological constructs Microbial biotechnology Tool info Standards/Databases
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. Microbial biotechnology Tool info
Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT) Terminology standard consisting of codes, terms, synonyms and definitions used in clinical documentation and reporting. Health data
Systems Biology Markup Language (SBML) An open format for computational models of biological processes Microbial biotechnology Tool info
T3DB The Toxin and Toxin Target Database is a bioinformatics resource that combines exhaustive toxin data with toxin target information. Currently it presents more than 42,000 toxin-target associations extracted from other databases, government documents, books and scientific literature. Each toxin record includes data on chemical properties and descriptors, toxicity values and medical information. Toxicology data Tool info
Talend Talend is an open source data integration platform. TransMed
Tensorflow A free and open-source software library for machine learning and artificial intelligence. Machine learning Tool info Training
TG-GATES A toxicogenomics database that stores gene expression data and biochemistry, hematology, and histopathology findings derived from in vivo (rat) and in vitro (primary rat hepatocytes, primary human hepatocytes) exposure to 170 compounds at multiple dosages and time points. Toxicology data Tool info
The Environment Ontology (EnvO) An ontology for expressing environmental terms Microbial biotechnology
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 CSC TSD Human data Data publication Tool info Standards/Databases Training
The Open Biological and Biomedical Ontology (OBO) Foundry Collaborative effort to develob interoperable ontologies for the biological sciences Documentation and meta... Standards/Databases
Tox21_Toolbox The Toxicology in the 21st Century program, or Tox21, is a unique collaboration between several federal agencies to develop new ways to rapidly test whether substances adversely affect human health. The Tox21 Toolbox contains data-analysis tools for accessing and visualizing Tox21 quantitative high-throughput screening (qHTS) 10K library data, as well as integrating with other publicly available data. Toxicology data
ToxCast_data The Toxicology in the 21st Century program, or Tox21, is a unique collaboration between several federal agencies to develop new ways to rapidly test whether substances adversely affect human health. This portal contains diverse downloadable results of the ToxCast project. Toxicology data
Track Hub Registry A global centralised collection of publicly accessible track hubs FAIRtracks Standards/Databases
TrackFind TrackFind is a search and curation engine for metadata of geneomic tracks. It supports crawling of the TrackHub Registry and other portals. FAIRtracks Tool info
tranSMART Knowledge management and high-content analysis platform enabling analysis of integrated data for the purposes of hypothesis generation, hypothesis validation, and cohort discovery in translational research. TransMed Data storage Tool info
Tryggve ELSI Checklist A list of Ethical, Legal, and Societal Implications (ELSI) to consider for research projects on human subjects NeLS TSD Human data GDPR compliance
TU Delft data management costing tool TU Delft costing tool helps to budget for data management personnel costs in proposals. Costs of data management
TXG-MAPr A tool that contains weighted gene co-expression networks obtained from the Primary Human Hepatocytes, rat kidney, and liver TG-GATEs dataset. Toxicology data Tool info
udocker udocker is a basic user tool to execute simple docker containers in user space without requiring root privileges. Data analysis
UK Data Service Data Management costing Tool UK Data Service activity-based costing tool. Costs of data management
UMLS The Unified Medical Language System (UMLS) is a set of tools that establishes a mapping structure among different vocabularies in the biomedical sciences field to enable interoperativity between computer systems. Toxicology data
UniChem UniChem is a very simple, large-scale non-redundant database of pointers between chemical structures and EMBL-EBI chemistry resources. Primarily, this service has been designed to maintain cross references between EBI chemistry resources. These include primary chemistry resources (ChEMBL and ChEBI), and other resources where the main focus is not small molecules, but which may nevertheless contain some small molecule information (eg: Gene Expression Atlas, PDBe). Toxicology data Training
Unimod Protein modification for mass spectrometry Proteomics Tool info Standards/Databases
UniProt Comprehensive resource for protein sequence and annotation data Galaxy Intrinsically disorder... Proteomics Single-cell sequencing Structural Bioinformatics Machine actionability Tool info Standards/Databases Training
University of Cambridge - Electronic Research Notebook Products List of Electronic Research Notebook Products by University of Cambridge Identifiers Documentation and meta...
VisBOL A JavaScript library for the visualisation of SBOL. Microbial biotechnology
Volumes Volumes are the preferred mechanism for persisting data generated by and used by Docker containers. Data analysis Training
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 Standards/Databases
Windows Package Manager Windows Package Manager is a comprehensive package manager solution that consists of a command line tool and set of services for installing applications on Windows 10 and Windows 11. Data analysis
WinSCP WinSCP is a popular SFTP client and FTP client for Microsoft Windows! Copy file between a local computer and remote servers using FTP, FTPS, SCP, SFTP, WebDAV or S3 file transfer protocols. Data transfer
WorkflowHub WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows. Galaxy Data analysis Data provenance Tool info Standards/Databases Training
XNAT Open source imaging informatics platform. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data. TransMed XNAT-PIC Bioimaging data
XNAT-PIC Pipelines Analysing of single or multiple subjects within the same project in XNAT XNAT-PIC
XNAT-PIC Uploader Import tool for multimodal DICOM image datasets to XNAT XNAT-PIC
Zenodo Generalist research data repository built and developed by OpenAIRE and CERN FAIRtracks Plant Phenomics Bioimaging data Biomolecular simulatio... Plant sciences Single-cell sequencing Data publication Identifiers Standards/Databases Training
Zooma Find possible ontology mappings for free text terms in the ZOOMA repository. Bioimaging data Tool info Training
Zotero Free and open-source reference management software to manage bibliographic data and related research materials.