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

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Tool or resource Description Related pages Registry
Access to Biological Collection Data Schema (ABCD) A standard schema for primary biodiversity data Microbial biotechnology bio.tools
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. Data analysis TransMed
Addgene A searchable repository with a focus on plasmids Microbial biotechnology FAIRsharing
Amazon Web Services Amazon Web Services Data storage Data analysis Data transfer TeSS
Amnesia Amnesia is a GDPR compliant high accuracy data anonymization tool Sensitive data
AOP4EUpest AOP4EUpest web server is devoted to the identification of pesticides involved in an Adverse Outcome Pathway via text mining approaches. Toxicology data bio.tools
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) Intrinsically disordered proteins bio.tools
Argos Plan and follow your data. Bring your Data Management Plans closer to where data are generated, analysed and stored. Data management plan Researcher Data steward research
ArrayExpress A repository of array based genomics data Microbial biotechnology bio.tools FAIRsharing TeSS
Arvados With Arvados, bioinformaticians run and scale compute-intensive workflows, developers create biomedical applications, and IT administrators manage large compute and storage resources. Data steward infrastructure Data steward policy Researcher Data analysis
Aspera Fasp 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 Data steward infrastructure
ATCC Biological materials resource including cell-lines, strains and genomics tools Microbial biotechnology bio.tools
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. Data steward research Researcher TransMed bio.tools FAIRsharing TeSS
BacDive A searchable database for bacteria specific information Microbial biotechnology bio.tools
Bacillus Genetic Stock Center (BGSC) A repository specific to Bacillus strains Microbial biotechnology
BASE A search engine for academic web resources Existing data bio.tools TeSS
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 data Data steward policy Data steward research Human data
Beacon The Beacon protocol defines an open standard for genomics data discovery. Researcher Data steward research Data steward infrastructure Human data bio.tools TeSS
Benchling R&D Platform for Life Sciences Microbial biotechnology
BIAFLOWS BIAFLOWS is an open-soure web framework to reproducibly deploy and benchmark bioimage analysis workflows Data analysis bio.tools
BigNASim Repository for Nucleic Acids MD simulations Biomolecular simulation data bio.tools
BIII The BioImage Informatics Index is a registry of software tools, image databases for benchmarking, and training materials for bioimage analysis Data steward infrastructure Data analysis bio.tools
BindingDB Public, web-accessible database of measured binding affinities Biomolecular simulation data bio.tools FAIRsharing
Bio-Formats Bio-Formats is a software tool for reading and writing image data using standardized, open formats OMERO bio.tools TeSS
Bioactive Conformational Ensemble Platform designed to efficiently generate bioactive conformers and speed up the drug discovery process. Biomolecular simulation data bio.tools
Bioconda Bioconda is a bioinformatics channel for the Conda package manager Data steward infrastructure Data analysis bio.tools TeSS
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 simulation data
BioImageArchive The BioImage Archive stores and distributes biological images that are useful to life-science researchers. Data publication FAIRsharing
BioModels A repository of mathematical models for application in biological sciences Microbial biotechnology bio.tools FAIRsharing TeSS
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 Data storage Researcher Human data Proteomics bio.tools
BioSamples BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. Documentation and metadata Plant sciences Plant Genomics bio.tools FAIRsharing TeSS
BioStudies A database hosting datasets from biological studies. Useful for storing or accessing data that is not compliant for mainstream repositories. Microbial biotechnology Documentation and metadata Plant sciences bio.tools FAIRsharing TeSS
Bitbucket Git based code hosting and collaboration tool, built for teams. Data organisation Data steward research Data steward infrastructure
BMRB Biological Magnetic Resonance Data Bank Intrinsically disordered proteins Researcher bio.tools
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 bio.tools
Box Cloud storage and file sharing service Data storage Data steward infrastructure Data transfer TeSS
BrAPI Specification for a standard API for plant data: plant material, plant phenotyping data Data steward infrastructure Plant sciences TeSS
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 bio.tools FAIRsharing TeSS
Bulk Rename Utility File renaming software for Windows Data organisation Data steward research 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 Proteomics bio.tools
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 bio.tools
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 FAIRsharing
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. Identifiers Data steward infrastructure Data steward research bio.tools
CATH A hierarchical domain classification of protein structures in the Protein Data Bank. bio.tools FAIRsharing TeSS
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 TeSS
CERNBox CERNBox cloud data storage, sharing and synchronization Data storage
ChEBI Dictionary of molecular entities focused on 'small' chemical compounds Microbial biotechnology bio.tools FAIRsharing TeSS
ChEMBL Database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties and abstracted bioactivities. Data analysis Researcher Toxicology data bio.tools FAIRsharing TeSS
Chipster Chipster is a user-friendly analysis software for high-throughput data such as RNA-seq and single cell RNA-seq. It contains analysis tools and a large reference genome collection. CSC Data analysis Researcher Data steward infrastructure bio.tools TeSS
ChIPSummitDB ChIPSummitDB is a database of transcription factor binding sites and the distances of the binding sites relative to the peak summits. Human data bio.tools
Choose a license Choose an open source license Licensing Researcher Data steward research Data steward policy TeSS
ClinicalTrials.gov ClinicalTrials.gov is a resource depending on the National Library of medicine which makes available private and public-funded clinical trials. Toxicology data FAIRsharing
Common Workflow Language (CWL) An open standard for describing workflows that are build from command line tools Data steward infrastructure Researcher Data analysis FAIRsharing TeSS
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 bio.tools FAIRsharing
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 steward infrastructure Data analysis TeSS
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. Documentation and metadata Researcher Plant sciences bio.tools FAIRsharing
COVID-19 Molecular Structure and Therapeutics Hub COVID-19 Molecular Structure and Therapeutics Hub Biomolecular simulation data
Create a Codebook Examples and tools to create a codebook by the Data Documentation Initiative (DDI) Documentation and metadata Researcher Data steward research
Creative Commons License Chooser It helps you choose the right Creative Commons license for your needs. Licensing Researcher Data steward research Data steward policy
Crop Ontology The Crop Ontology compiles concepts to curate phenotyping assays on crop plants, including anatomy, structure and phenotype. Researcher Data steward research Data steward infrastructure Plant sciences FAIRsharing TeSS
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 bio.tools
cURL command line tool and library for transferring data with URLs Data transfer Data steward infrastructure
DAISY Data Information System to keep sensitive data inventory and meet GDPR accountability requirement. Data steward infrastructure Data steward policy Human data Data protection TransMed bio.tools
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. Documentation and metadata TransMed TeSS
Data Curation Centre Metadata list List of metadata standards Documentation and metadata Researcher Data steward research
Data INRAE Dataverse for life sciences and agronomic related data Plant sciences Plant Genomics Researcher Data steward research FAIRsharing
Data Stewardship Wizard Publicly available online tool for composing smart data management plans Data management plan Researcher Data steward research Data steward infrastructure NeLS TSD bio.tools TeSS
Data Use Ontology DUO allows to semantically tag datasets with restriction about their usage. Data steward research Researcher Human data FAIRsharing TeSS
data.world Data License list Overview of typical licenses used for data resources Licensing Biomolecular simulation data
DataCite A search engine for the complete collection of publicly available DataCite DOIs Existing data FAIRsharing
DATAVERSE Open source research data respository software. Data storage Researcher Data steward research Data steward infrastructure IFB TeSS
DAWID The Data Agreement Wizard is a tool developed by ELIXIR-Luxembourg to facilitate data sharing agreements. Data protection Data steward policy 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 Data steward infrastructure Human data bio.tools FAIRsharing
DisGeNET A discovery platform containing collections of genes and variants associated to human diseases. Data analysis Human data Researcher Toxicology data bio.tools FAIRsharing
DisProt A database of intrinsically disordered proteins Intrinsically disordered proteins Researcher bio.tools
DMP Canvas Generator Questionnaire, which generates a pre-filled a DMP Data management plan Researcher Data steward research
DMP OPIDoR Online questionnaire for the development of data management plans - repository of DMPs Data management plan Researcher Data steward research IFB
DMPlanner Semi-automatically generated, searchable catalogue of resources that are relevant to data management plans. Data management plan Researcher Data steward research
DMPonline A free tool to write, share and export a data management plan. Built-in data management plan templates for many major funders. Data management plan Researcher Data steward research TeSS
DMPTool Build your Data Management Plan Data management plan Researcher Data steward research
DMPTuuli Data management planning tool (Finland) Data management plan Researcher Data steward research CSC
DNA Data Bank of Japan (DDBJ) A database of DNA sequences Microbial biotechnology bio.tools
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 Data steward infrastructure Data analysis FAIRsharing TeSS
DropBox Cloud storage and file sharing service Data storage Data steward infrastructure Data transfer
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 Data publication Biomolecular simulation data FAIRsharing
Dynameomics Database of folding / unfolding pathway of representatives from all known protein folds by MD simulation Biomolecular simulation data
e!DAL Electronic data archive library is a framework for publishing and sharing research data Data storage Data steward infrastructure bio.tools
e!DAL-PGP Plant Genomics and Phenomics Research Data Repository Plant sciences Plant Genomics Researcher Data steward research Data steward infrastructure FAIRsharing
EasyDMP DMP creation, versioning and sharing Data management plan Researcher Data steward research
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
ECPGR Hub for the identification of plant genetic resources in Europe Plant sciences Researcher Data steward research
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
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 COVID-19 Data Portal FAIRsharing TeSS
ELIXIR Deposition Databases for Biomolecular Data List of discipline-specific deposition databases recommended by ELIXIR. Data publication Researcher Data steward research Data steward infrastructure COVID-19 Data Portal NeLS IFB CSC FAIRsharing
ELIXIR-AAI The ELIXIR Authentication and Authorisation Infrastructure (AAI) Sensitive data NeLS TSD TransMed TeSS
EMBL-EBI Ontology Lookup Service EMBL-EBI’s web portal for finding ontologies Documentation and metadata Data steward research Researcher TeSS
EMBL-EBI's data submission wizard EMBL-EBI's wizard for finding the right EMBL-EBI repository for your data. Data publication Researcher Data steward research
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 Data publication OMERO
Ensembl Genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. bio.tools FAIRsharing TeSS
Ensembl Genomes Comparative analysis, data mining and visualisation for the genomes of non-vertebrate species bio.tools FAIRsharing TeSS
Ensembl Plants Open-access database of full genomes of plant species. Plant Genomics FAIRsharing TeSS
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 Data steward policy Human data TSD
EUDAT licence selector wizard EUDAT's wizard for finding the right licence for your data or code. Licensing Researcher Data steward research Data steward policy
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. Data steward infrastructure Data steward policy Human data
EURISCO European Search Catalogue for Plant Genetic Resources Plant sciences Researcher Data steward research bio.tools
Europe PMC Europe PMC is a repository, providing access to worldwide life sciences articles, books, patents and clinical guidelines. Researcher bio.tools FAIRsharing TeSS
European Nucleotide Archive (ENA) A record of sequence information scaling from raw sequcning reads to assemblies and functional annotation Microbial biotechnology Plant Genomics bio.tools FAIRsharing TeSS
European Variation Archive (EVA) Open-access database of all types of genetic variation data from all species. Plant Genomics bio.tools FAIRsharing
Evidence and Conclusion Ontology (ECO) Controlled vocabulary that describes types of evidence and assertion methods Existing data Documentation and metadata FAIRsharing
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 bio.tools
FAIDARE FAIDARE is a tool allowing to search data across dinstinct databases that implemented BrAPI. Researcher Data steward research Plant sciences IFB bio.tools
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) Compliance monitoring & measurement Data steward research TransMed
FAIR Evaluation Services Resources and guidelines to assess the FAIRness of digital resources. Compliance monitoring & measurement Data steward research Data steward policy
FAIRassist.org Help you discover resources to measure and improve FAIRness. Compliance monitoring & measurement Data steward research Data steward policy
FAIRDOM-SEEK Data, model and SOPs management for projects, from preliminary data to publication, support for running SBML models etc. Data storage Data steward infrastructure NeLS Microbial biotechnology IFB bio.tools TeSS
FAIRDOMHub Data, model and SOPs management for projects, from preliminary data to publication, support for running SBML models etc. (public SEEK instance) Data storage Researcher NeLS Documentation and metadata Microbial biotechnology FAIRsharing
fairsharing A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies. Documentation and metadata Data publication Data steward policy Data steward research Researcher Microbial biotechnology Existing data FAIRsharing TeSS
Feide Feide is the national solution for secure login and data exchange in education and research. Feide can be linked with ELIXIR-AAI through eduGAIN. Marine Metagenomics TSD NeLS
FigShare Data publishing platform Data publication Biomolecular simulation data FAIRsharing TeSS
FileZilla A free FTP solution Data transfer Data steward infrastructure
Free-IPA FreeIPA is an integrated Identity and Authentication solution for Linux/UNIX networked environments. Data steward infrastructure 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. Data publication Data steward policy Data steward research Data steward infrastructure Human data
GA4GH regular and ethical toolkit Framework for Responsible Sharing of Genomic and Health-Related Data Data protection Sensitive data Data steward policy Data steward research Data steward infrastructure 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 Marine Metagenomics Data analysis Researcher Data steward infrastructure IFB bio.tools TeSS
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 bio.tools FAIRsharing TeSS
Gene Expression Omnibus (GEO) A repository of MIAME-compliant genomics data from arrays and high-throughput sequencing Microbial biotechnology
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 bio.tools
GEO A public repository that stores microarray, next-generation sequencing, and other forms of high-throughput functional genomics data submitted by the research community. Toxicology data TeSS
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
Git Distributed version control system designed to handle everything from small to very large projects Data organisation Data steward research Data steward infrastructure TeSS
GitHub Versioning system, used for sharing code, as well as for sharing of small data Data publication Data organisation Data steward infrastructure Data steward research FAIRsharing TeSS
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 Data steward infrastructure Data steward research TeSS
Globus Globus lets you efficiently, securely, and reliably transfer data directly between systems separated by an office wall or an ocean. Focus on your research and offload your data transfer headaches to Globus Data transfer Data steward infrastructure
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 sciences bio.tools FAIRsharing
Google Dataset Search Search engine for datasets Existing data TeSS
Google Drive Cloud Storage for Work and Home Data storage Data transfer
GPCRmd Repository of GPCR protein simulations Biomolecular simulation data bio.tools
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 bio.tools
Harvard Medical School – ELN Comparison Grid ELN Comparison Grid by Hardvard Medical School Documentation and metadata Identifiers Researcher Data steward research
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
How to License Research Data - DCC Guidelines about how to license research data from Digital Curation Centre Licensing Researcher Data steward research Data steward policy
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 FAIRsharing TeSS
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 steward research Researcher Human data Data analysis bio.tools FAIRsharing TeSS
iCloud Data sharing Data storage Data analysis Data transfer
Identifiers.org The Identifiers.org 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). Identifiers Data steward infrastructure Data steward research bio.tools FAIRsharing
Intrinsically disordered proteins ontology (IDPO) Intrinsically disordered proteins ontology Intrinsically disordered proteins Documentation and metadata
iGEM Parts Registry A collection of standard biological parts to which all entrants in the iGEM competition must submit their parts Microbial biotechnology
Image Data Resource (IDR) A repository of image datasets from scientific publications Microbial biotechnology Data publication Documentation and metadata Data transfer OMERO bio.tools FAIRsharing
Informed Consent Ontology The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. Data steward infrastructure Data steward policy Human data FAIRsharing
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 Microbial biotechnology bio.tools
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 bio.tools FAIRsharing TeSS
IntoGen IntoGen collects and analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes. Data analysis Human data bio.tools
IRIS The Integrated Risk Information System (IRIS) resource evaluates information on health that might arise after exposure to environmental contaminants. Toxicology data bio.tools TeSS
iRODS Integrated Rule-Oriented Data System (iRODS) is open source data management software for a cancer genome analysis workflow. Data storage Data steward infrastructure TransMed bio.tools
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 Data steward infrastructure Data steward research Microbial biotechnology FAIRsharing
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 sciences bio.tools
ISO/IEC 27001 International information security standard Data protection Data steward policy Human data
ITER The International Toxicity Estimates for Risk (ITER) is a free online resource of human health risk values and cancer classifications for over 680 chemicals of environmental concern. ITER shows tabular risk data from several sources in a tabular format for easy comparison, a synopsis explaining discrepancies in data, and a link to each organization for further details. Toxicology data TeSS
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
Jupyter Jupyter notebooks allow to share code, documentation Data steward infrastructure Data analysis TeSS
Keycloak Keycloak is an open source identity and data access management solution. Data steward infrastructure TransMed TeSS
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 bio.tools
Linked Open Vocabularies (LOV) Web portal for finding ontologies Documentation and metadata Data steward research Researcher
List of Prokaryotic names with Standing in Nomenclature (LPSN) A database of prokaryote specific biodiversity information Microbial biotechnology
LUMI EuroHPC world-class supercomputer Data analysis Researcher Data steward infrastructure CSC bio.tools
maDMP - Research Bridge Machine-Actionable Data Management Plan | Webinar (2016) on making a good data management plan. Data management plan Data steward infrastructure
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 bio.tools
MarFun MarFun is a manually curated marine fungi genome database. Marine Metagenomics
Marine metagenomics portal High-quality curated and freely accessible microbial genomics and metagenomics resources for the marine scientific community Marine Metagenomics bio.tools
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 bio.tools
Multi-Crop Passport Descriptor (MCPD) The Multi-Crop Passport Descriptor is the metadata standard for plant genetic resources maintained ex situ by genbanks. Documentation and metadata Researcher Data steward infrastructure Data steward policy Plant sciences Plant sciences FAIRsharing
MemProtMD Database of over 5000 intrinsic membrane protein structures Biomolecular simulation data
Mendeley data Multidisciplinary, free-to-use open repository specialized for research data Data publication Biomolecular simulation data FAIRsharing
Meta-pipe META-pipe is a pipeline for annotation and analysis of marine metagenomics samples, which provides insight into phylogenetic diversity, metabolic and functional potential of environmental communities. Marine Metagenomics Data analysis bio.tools TeSS
MetabolomeXchange A repository of genomics data relating to the study of the metabolome Microbial biotechnology bio.tools
MIADE Minimum Information About Disorder Experiments (MIADE) standard Documentation and metadata Researcher Data steward research Intrinsically disordered proteins
MIAPPE Minimum Information About a Plant Phenotyping Experiment Documentation and metadata Researcher Data steward research Plant sciences Plant Genomics FAIRsharing TeSS
Microsoft Azure Cloud storage and file sharing service from Microsoft Data storage Data steward infrastructure Data transfer
Microsoft OneDrive Cloud storage and file sharing service from Microsoft Data storage Data steward infrastructure
MIGS/MIMS Minimum Information about a (Meta)Genome Sequence Documentation and metadata Researcher Data steward research Marine metagenomics Microbial biotechnology FAIRsharing
MINT MINT, the Molecular INTeraction database, focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators bio.tools FAIRsharing
MIxS Minimum Information about any (x) Sequence Documentation and metadata Researcher Data steward research Marine metagenomics Plant Genomics FAIRsharing TeSS
MobiDB A database of protein disorder and mobility annotations Intrinsically disordered proteins Researcher bio.tools FAIRsharing
MoDEL Database of Protein Molecular Dynamics simulations representing different structural clusters of the PDB Biomolecular simulation data bio.tools FAIRsharing TeSS
MoDEL Covid19 Database of COVID-19 related atomistic Molecular Dynamic Trajectories Biomolecular simulation data
MoDEL-CNS Repository for Central Nervous System-related mainly membrane protein MD simulations Biomolecular simulation data
ModelArchive Repository for molecular models - providing doi of models Biomolecular simulation data FAIRsharing
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. Identifiers Data steward infrastructure Data steward research bio.tools
MolMeDB Database about interactions of molecules with membranes Biomolecular simulation data bio.tools FAIRsharing
MONARC A risk assessment tool that can be used to do Data Protection Impact Assessments Data protection Data steward policy Human data TransMed FAIRsharing
MRI2DICOM a Magnetic Resonance Imaging (MRI) converter from ParaVision® (Bruker, Inc. Billerica, MA) file format to DICOM standard Researcher Data steward research XNAT-PIC
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. Microbial biotechnology
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 FAIRsharing
NCIMB Hosts information relating to strains, cultures and more Microbial biotechnology
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 Marine Metagenomics bio.tools TeSS
Nettskjema Form and survey tool, also for sensitive data Sensitive data TSD
NextCloud As fully on-premises solution, Nextcloud Hub provides the benefits of online collaboration without the compliance and security risks. Data storage Data steward infrastructure Data transfer
Nextflow Nextflow is a framework for data analysis workflow execution Data steward infrastructure Data analysis bio.tools TeSS
NMRlipids Repository for lipid MD simulations to validate force fields with NMR data Biomolecular simulation data
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. Researcher Data steward research Data analysis Data storage TransMed Toxicology data bio.tools
OMERO OMERO is an open-source client-server platform for managing, visualizing and analyzing microscopy images and associated metadata Documentation and metadata Data steward research Data steward infrastructure Data storage OMERO bio.tools TeSS
OmicsDI Omics Discovery Index (OmicsDI) provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics) Existing data Proteomics bio.tools FAIRsharing TeSS
OMOP-CDM OMOP is a common data model for the harmonisation for of observational health data. TransMed
Ontobee A web portal to search and visualise ontologies Documentation and metadata Data steward research Researcher FAIRsharing
ONTOMATON OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets. Researcher Data steward research Data steward infrastructure Documentation and metadata Identifiers
Open Definition Conformant Licenses Licenses that are conformant with the principles laid out in the Open Definition. Licensing Researcher Data steward research Data steward policy
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 Data steward research Data steward infrastructure bio.tools
OpenRefine Data curation tool for working with messy data Data quality TeSS
OpenScienceFramework free and open source project management tool that supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery Data publication Biomolecular simulation data FAIRsharing
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 storage Data analysis TransMed IFB TeSS
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 bio.tools FAIRsharing
OSF OSF (Open Science Framework) is a free, open platform to support your research and enable collaboration. Data storage Researcher Data steward research
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 Documentation and metadata Data management plan Data analysis bio.tools
OwnCloud Cloud storage and file sharing service Data storage Data steward infrastructure Data transfer Data analysis
PAA PAA is an R/Bioconductor tool for protein microarray data analysis aimed at biomarker discovery. Data analysis Researcher Human data Proteomics bio.tools
PANGAEA Data Publisher for Earth and Environmental Science Data publication bio.tools FAIRsharing
PCDDB The Protein Circular Dichroism Data Bank Intrinsically disordered proteins Researcher bio.tools
PDB The Protein Data Bank (PDB) Researcher Intrinsically disordered proteins bio.tools TeSS
PDB-Dev Prototype archiving system for structural models obtained using integrative or hybrid modeling Biomolecular simulation data
PharmGKB A resource that curates knowledge about the impact of genetic variation on drug response. Toxicology data bio.tools
Pharos Pharos provides hazard, use, and exposure information on 140,872 chemicals and 180 different kinds of building products. Toxicology data bio.tools
PIA - Protein Inference Algorithms PIA is a toolbox for mass spectrometrey based protein inference and identification analysis. Data analysis Researcher Proteomics bio.tools
PLAZA Access point for plant comparative genomics, centralizing genomic data produced by different genome sequencing initiatives. Plant sciences Plant Genomics Researcher FAIRsharing TeSS
PMut Platform for the study of the impact of pathological mutations in protein stuctures. Data analysis Human data bio.tools
PRIDE PRoteomics IDEntifications (PRIDE) Archive database Proteomics bio.tools FAIRsharing TeSS
Privacy Impact Assessment Tool Privacy Impact Assessment Tool is a software, that allows you to carry out Privacy Impact Assessment (PIA) independently. Data protection Data steward policy Human data
ProteomeXchange ProteomeXchange provides globally coordinated standard data submission and dissemination pipelines Proteomics bio.tools FAIRsharing TeSS
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. Proteomics
protocols.io A secure platform for developing and sharing reproducible methods. Microbial biotechnology
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 TeSS
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 TeSS
RDA Standards Directory of standard metadata, divided into different research areas Documentation and metadata Researcher Data steward research
re3data Registry of Research Data Repositories Existing data TeSS
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
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. Identifiers Data steward infrastructure Data steward research Data quality bio.tools
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 bio.tools
REDItools Python scripts to detect RNA editing events in RNAseq experiments Epitranscriptome data bio.tools
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. Data steward infrastructure TransMed bio.tools
Renamer4Mac File renaming software for Mac Data organisation Data steward research 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 steward research
Research Data Management Platform (RDMP) Data management platform for automated loading, storage, linkage and provision of data sets Data storage Data steward infrastructure bio.tools
Research Management Plan Machine actionable DMPs. Data management plan Researcher Data steward research TeSS
Research Object Crate (RO-Crate) RO-Crate is a lightweight approach to packaging research data with their metadata, using schema.org. An RO-Crate is a structured archive of all the items that contributed to the research outcome, including their identifiers, provenance, relations and annotations. Documentation and metadata Data storage Data organisation Data steward research Researcher Microbial biotechnology FAIRsharing
RETTE System for Risk and compliance. Processing of personal data in research and student projects at UiB. Data protection Sensitive data Data steward policy Data steward research Human data
Reva Reva connects cloud storages and application providers Data analysis Data transfer bio.tools
Rightfield RightField is an open-source tool for adding ontology term selection to Excel spreadsheets Researcher Documentation and metadata Data steward research Microbial biotechnology Identifiers bio.tools
Rstudio Rstudio notebooks allow to share code, documentation Data analysis Data steward infrastructure Researcher bio.tools TeSS
Rucio Rucio - Scientific Data Management Data storage Data analysis Data transfer
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. Toxicology data bio.tools FAIRsharing
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 disordered proteins Researcher
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
Schemapedia Web portal for finding ontologies Documentation and metadata Data steward research Researcher
ScienceMesh ScienceMesh - frictionless scientific collaboration and access to research services Data storage Data analysis Data transfer
Scientific Data's Recommended Repositories List of respositories recommended by Scientific Data, contains both discipline-specific and general repositories. Data publication Researcher Data steward research Data steward infrastructure
SeaFile SeaFile File Synchronization and Share Solution Data storage Data transfer
semares All-in-one platform for life science data management, semantic data integration, data analysis and visualization Researcher Data steward research Documentation and metadata Data analysis Data steward infrastructure Data storage
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 Researcher Intrinsically disordered proteins
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). bio.tools FAIRsharing TeSS
Singularity Singularity is a container platform. Data steward infrastructure Data analysis TSD TeSS
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. Data organisation TransMed
Snakemake Snakemake is a framework for data analysis workflow execution Data steward infrastructure Data analysis bio.tools TeSS
Standards for Reporting Enzyme Data (STRENDA) Resource of standards for reporting enzyme data Microbial biotechnology
STRING Known and predicted protein-protein interactions. Proteomics bio.tools FAIRsharing TeSS
SynBioHub A searchable design repository for biological constructs Microbial biotechnology bio.tools FAIRsharing
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 bio.tools
Systems Biology Markup Language (SBML) An open format for computational models of biological processes Microbial biotechnology bio.tools
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 bio.tools
Talend Talend is an open source data integration platform. Data steward research Researcher TransMed
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 bio.tools
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 Data publication Human data Data steward policy CSC TSD bio.tools FAIRsharing
The Genomic Standards Consortium (GSC) Minimum Information about any (x) Sequence Documentation and metadata Researcher Data steward infrastructure Data steward policy Human data FAIRsharing
The Open Biological and Biomedical Ontology (OBO) Foundry Collaborative effort to develob interoperable ontologies for the biological sciences Documentation and metadata Data steward research Researcher FAIRsharing
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
TOXNET The Toxicology Data Network (TOXNET) was a portal that allowed access to several relevant sources in the toxicological field. Nowadays, these sources have been integrated into other NLM resources. Toxicology data
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. Researcher Data steward research Data analysis Data storage TransMed bio.tools
Tryggve ELSI Checklist A list of Ethical, Legal, and Societal Implications (ELSI) to consider for research projects on human subjects Sensitive data Data steward policy Data steward research Human data NeLS CSC TSD
TSD Norwegian Services for sensitive data Sensitive data TSD Data storage TeSS
TXG-MAPr A tool that contains weighted gene co-expression networks obtained from the Primary Human Hepatocytes, rat kidney, and liver TG-GATEs dataset. Data analysis Researcher Toxicology data bio.tools
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
UniProt Comprehensive resource for protein sequence and annotation data Documentation and metadata Researcher Intrinsically disordered proteins Microbial biotechnology Proteomics bio.tools FAIRsharing TeSS
University of Cambridge - Electronic Research Notebook Products List of Electronic Research Notebook Products by University of Cambridge Documentation and metadata Identifiers Researcher Data steward research
VisBOL A JavaScript library for the visualisation of SBOL. Microbial biotechnology
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 steward research
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 Data steward infrastructure
XNAT Open source imaging informatics platform. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data. Researcher Data analysis TransMed XNAT-PIC
XNAT-PIC Pipelines Analysing of single or multiple subjects within the same project in XNAT Researcher Data steward research Data analysis XNAT-PIC
XNAT-PIC Uploader Import tool for multimodal DICOM image datasets to XNAT Researcher Data steward research XNAT-PIC
Zenodo Generalist research data repository built and developed by OpenAIRE and CERN Data publication Biomolecular simulation data FAIRsharing TeSS