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 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.
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 bio.tools registry
| Tool or resource | Description | Related pages | Registry |
|---|---|---|---|
| 3D-Beacons | Network providing unified programmatic access to experimentally determined and predicted structure models | Structural Bioinformatics | |
| Access to Biological Collection Data Schema (ABCD) | A standard schema for primary biodiversity data | Microbial biotechnology | |
| 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 | Standards/Databases |
| Amazon Web Services | Amazon Web Services | Data storage Data analysis Data transfer | Training |
| 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 | 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) | Intrinsically disordered proteins | 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 Researcher Data Steward: research | |
| ArrayExpress | A repository of array based genomics data | Microbial biotechnology 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 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 | 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. | Data Steward: research Researcher TransMed | Tool info Training |
| b2share | Store and publish your research data. Can be used to bridge between domains | Data storage Data publication Bioimaging data | Standards/Databases |
| BacDive | A searchable database for bacteria specific information | Microbial biotechnology | Tool info |
| Bacillus Genetic Stock Center (BGSC) | A repository specific to Bacillus strains | Microbial biotechnology | |
| BASE | A search engine for academic web resources | Existing data | Tool info Training |
| 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 | Tool info Training |
| 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 | Tool info |
| BigNASim | Repository for Nucleic Acids MD simulations | Biomolecular simulation data Data publication | Tool info |
| 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 | Tool info |
| BindingDB | Public, web-accessible database of measured binding affinities | Biomolecular simulation data | Tool info Standards/Databases |
| Bio-Formats | Bio-Formats is a software tool for reading and writing image data using standardized, open formats | OMERO Bioimaging data | Tool info Training |
| Bioactive Conformational Ensemble | Platform designed to efficiently generate bioactive conformers and speed up the drug discovery process. | Biomolecular simulation data | Tool info |
| Bioconda | Bioconda is a bioinformatics channel for the Conda package manager | Data Steward: infrastructure 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 simulation data | |
| BioImageArchive | The BioImage Archive stores and distributes biological images that are useful to life-science researchers. | Data publication Bioimaging data | Standards/Databases |
| BioModels | A repository of mathematical models for application in biological sciences | Microbial biotechnology Data publication | Tool info Standards/Databases Training |
| 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 | Tool info |
| 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 | Tool info Standards/Databases Training |
| Bioschemas.org | Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials | Machine actionability Data Steward: infrastructure | Training |
| 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 Data publication | Tool info Standards/Databases Training |
| BisQue | Resource for management and analysis of 5D biological images | Data organisation Data Steward: research Data analysis Bioimaging data | Tool info |
| Bitbucket | Git based code hosting and collaboration tool, built for teams. | Data organisation Data Steward: research Data Steward: infrastructure | Standards/Databases |
| BMRB | Biological Magnetic Resonance Data Bank | Intrinsically disordered proteins Researcher | 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. | Data analysis Human data | Tool info |
| Box | Cloud storage and file sharing service | Data storage Data Steward: infrastructure Data transfer | Training |
| BrAPI | Specification for a standard API for plant data: plant material, plant phenotyping data | Data Steward: infrastructure Plant sciences | Training |
| 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 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 | Tool info |
| 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. | Data analysis 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 |
| 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 | Tool info |
| CATH | A hierarchical domain classification of protein structures in the Protein Data Bank. | Tool info Standards/Databases Training | |
| CEDAR | CEDAR is making data submission smarter and faster, so that scientific researchers and analysts can create and use better metadata. | Documentation and metadata Machine actionability Researcher Data Steward: research | Tool info Standards/Databases |
| 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. | Data analysis Researcher Toxicology data | Tool info Standards/Databases Training |
| ChIPSummitDB | ChIPSummitDB is a database of transcription factor binding sites and the distances of the binding sites relative to the peak summits. | Human data | Tool info |
| Choose a license | Choose an open source license | Licensing Researcher Data Steward: research Data Steward: policy | |
| 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 | Standards/Databases |
| Common Workflow Language (CWL) | An open standard for describing workflows that are build from command line tools | Data Steward: infrastructure Researcher 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 Steward: infrastructure 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 | |
| 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 Data Steward: infrastructure Data Steward: research | |
| COPO | Portal for scientists to broker more easily rich metadata alongside data to public repos. | Documentation and metadata Researcher Plant sciences Machine actionability | Tool info Standards/Databases |
| 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 | Standards/Databases Training |
| Crypt4GH | A Python tool to encrypt, decrypt or re-encrypt files, according to the GA4GH encryption file format. | Human data | |
| 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 |
| cURL | command line tool and library for transferring data with URLs | Data transfer Data Steward: infrastructure | |
| Cytomine-IMS | Image Data management | Data Steward: research Bioimaging data | |
| 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 | Tool info |
| 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 | |
| Data Catalog Vocabulary (DCAT) | DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. | Machine actionability Data Steward: infrastructure | |
| 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 | Standards/Databases |
| 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 | Tool info Training |
| Data Use Ontology | DUO allows to semantically tag datasets with restriction about their usage. | Data Steward: research Researcher Human data | Standards/Databases Training |
| 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 | Standards/Databases |
| DATAVERSE | Open source research data respository software. | Data storage Researcher Data Steward: research Data Steward: infrastructure IFB | Training |
| 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 | Tool info Standards/Databases Training |
| DisGeNET | A discovery platform containing collections of genes and variants associated to human diseases. | Data analysis Human data Researcher Toxicology data | Tool info Standards/Databases |
| DisProt | A database of intrinsically disordered proteins | Intrinsically disordered proteins Researcher | Tool info |
| DMP Canvas Generator | Questionnaire, which generates a pre-filled a DMP | Data management plan Researcher Data Steward: research | |
| 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 | Training |
| DMPRoadmap | DMP Roadmap is a Data Management Planning tool. | Data management plan Researcher Data Steward: research | |
| DMPTool | Build your Data Management Plan | Data management plan Researcher Data Steward: research | |
| 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 | Data Steward: infrastructure Data analysis | Standards/Databases Training |
| 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 Bioimaging data | Standards/Databases |
| 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 | Tool info |
| e!DAL-PGP | Plant Genomics and Phenomics Research Data Repository | Plant sciences Plant Genomics Researcher Data Steward: research Data Steward: infrastructure Data publication | Standards/Databases |
| 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 | Standards/Databases |
| 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 | Standards/Databases |
| ELIXIR-AAI | The ELIXIR Authentication and Authorisation Infrastructure (AAI) | Sensitive data NeLS TSD TransMed | Training |
| EMBL-EBI Ontology Lookup Service | EMBL-EBI’s web portal for finding ontologies | Documentation and metadata Data Steward: research Researcher | |
| EMBL-EBI's data submission wizard | EMBL-EBI's wizard for finding the right EMBL-EBI repository for your data. | Data publication Researcher Data 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 Bioimaging data | |
| Ensembl | Genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. | Tool info Standards/Databases Training | |
| Ensembl Genomes | Comparative analysis, data mining and visualisation for the genomes of non-vertebrate species | Tool info Standards/Databases Training | |
| Ensembl Plants | Open-access database of full genomes of plant species. | Plant Genomics | Standards/Databases |
| 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 | Tool info |
| Europe PMC | Europe PMC is a repository, providing access to worldwide life sciences articles, books, patents and clinical guidelines. | Researcher | Tool info Standards/Databases Training |
| European Nucleotide Archive (ENA) | A record of sequence information scaling from raw sequcning reads to assemblies and functional annotation | Microbial biotechnology Plant Genomics | Tool info Standards/Databases Training |
| European Variation Archive (EVA) | Open-access database of all types of genetic variation data from all species. | Plant Genomics | Tool info Standards/Databases |
| Evidence and Conclusion Ontology (ECO) | Controlled vocabulary that describes types of evidence and assertion methods | Existing data Documentation and metadata | Standards/Databases |
| 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. | Researcher Data Steward: research Plant sciences IFB | Tool info |
| 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 Machine actionability | Tool info Training |
| 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 Machine actionability | Standards/Databases |
| 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 | Standards/Databases Training |
| FigShare | Data publishing platform | Data publication Biomolecular simulation data Bioimaging data | Standards/Databases Training |
| 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 Sensitive data | |
| GA4GH Genomic Data Toolkit | Open standards for genomic data sharing. | Data Steward: research Data Steward: infrastructure Human data | |
| GA4GH Regulatory and Ethics 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 | 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 Data publication Documentation and metadata Data transfer OMERO Bioimaging data Toxicology data | |
| 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 | Tool info |
| 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 | Training |
| 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 | 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 Data publication Data Steward: infrastructure Data Steward: research | Standards/Databases Training |
| 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 | Tool info Standards/Databases |
| Google Dataset Search | Search engine for datasets | Existing data | |
| Google Drive | Cloud Storage for Work and Home | Data storage Data transfer | |
| GPCRmd | Repository of GPCR protein simulations | Biomolecular simulation data Data publication | Tool info |
| 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 | Tool info |
| 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 | 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. | Data organisation Data Steward: research Researcher Human data Data analysis | Tool info Standards/Databases Training |
| 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 | Tool info Standards/Databases |
| 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 Bioimaging data | Tool info Standards/Databases |
| 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 | Standards/Databases |
| 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 | 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 | Tool info Standards/Databases Training | |
| IntoGen | IntoGen collects and analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes. | Data analysis Human data | Tool info |
| Intrinsically disordered proteins ontology (IDPO) | Intrinsically disordered proteins ontology | Intrinsically disordered proteins Documentation and metadata | 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. | Data storage Data Steward: infrastructure TransMed Bioimaging data | Tool info |
| 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 Machine actionability | 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 sciences Machine actionability | Tool info |
| 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 | 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 | |
| Jupyter | Jupyter notebooks allow to share code, documentation | Data Steward: infrastructure Data analysis | Training |
| Keycloak | Keycloak is an open source identity and data access management solution. | Data Steward: infrastructure TransMed | 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 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 | Tool info |
| 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 | Tool info |
| 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 | 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 |
| 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 | Standards/Databases |
| MetabolomeXchange | A repository of genomics data relating to the study of the metabolome | Microbial biotechnology Data publication | Tool info |
| 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 | Standards/Databases Training |
| 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 | Standards/Databases |
| MINT | MINT, the Molecular INTeraction database, focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators | Tool info Standards/Databases | |
| MIxS | Minimum Information about any (x) Sequence | Documentation and metadata Researcher Data Steward: research Marine metagenomics Plant Genomics | Standards/Databases Training |
| MobiDB | A database of protein disorder and mobility annotations | Intrinsically disordered proteins Researcher | Tool info Standards/Databases |
| MoDEL | Database of Protein Molecular Dynamics simulations representing different structural clusters of the PDB | Biomolecular simulation data | Tool info Standards/Databases Training |
| 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 Data publication | |
| ModelArchive | Repository for theoretical models of macromolecular structures with DOIs for models | Biomolecular simulation data Structural Bioinformatics Data publication | 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. | Identifiers Data Steward: infrastructure Data Steward: research | Tool info |
| MolMeDB | Database about interactions of molecules with membranes | Biomolecular simulation data | Tool info Standards/Databases |
| MONARC | A risk assessment tool that can be used to do Data Protection Impact Assessments | Data protection Data Steward: policy Human data TransMed | Standards/Databases |
| MRI2DICOM | a Magnetic Resonance Imaging (MRI) converter from ParaVision® (Bruker, Inc. Billerica, MA) file format to DICOM standard | Researcher Data Steward: research XNAT-PIC | |
| 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 | Standards/Databases |
| MyTardis | A file-system based platform handling the transfer of data | Data Steward: research Data transfer 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. | 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 | Standards/Databases |
| NCIMB | Hosts information relating to strains, cultures and more | Microbial biotechnology | |
| 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 | Tool info Training |
| NMRlipids | Repository for lipid MD simulations to validate force fields with NMR data | Biomolecular simulation data Data publication | |
| 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 | Tool info |
| 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 Bioimaging data | Tool info Training |
| OmicsDI | Omics Discovery Index (OmicsDI) provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics) | Existing data Proteomics | Tool info Standards/Databases Training |
| 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 | Standards/Databases |
| 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 | Tool info |
| OpenRefine | Data curation tool for working with messy data | Data quality | Training |
| 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 | Standards/Databases |
| 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 | Training |
| 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 | Tool info Standards/Databases Standards/Databases | |
| OSF | OSF (Open Science Framework) is a free, open platform to support your research and enable collaboration. | Data storage Researcher Data Steward: research | 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 Documentation and metadata Data management plan Data analysis | Tool info |
| 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 | Tool info |
| PANGAEA | Data Publisher for Earth and Environmental Science | Data publication | Tool info Standards/Databases |
| PCDDB | The Protein Circular Dichroism Data Bank | Intrinsically disordered proteins Researcher | Tool info |
| PDB | The Protein Data Bank (PDB) | Researcher Intrinsically disordered proteins Structural Bioinformatics | Tool info Training |
| PDB-Dev | Prototype archiving system for structural models obtained using integrative or hybrid modeling | Biomolecular simulation data Structural Bioinformatics | |
| 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 | |
| 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 |
| PIA - Protein Inference Algorithms | PIA is a toolbox for mass spectrometrey based protein inference and identification analysis. | Data analysis Researcher Proteomics | Tool info |
| PLAZA | Access point for plant comparative genomics, centralizing genomic data produced by different genome sequencing initiatives. | Plant sciences Plant Genomics Researcher | Standards/Databases Training |
| PMut | Platform for the study of the impact of pathological mutations in protein stuctures. | Data analysis Human data | Tool info |
| PRIDE | PRoteomics IDEntifications (PRIDE) Archive database | Proteomics | Tool info Standards/Databases Training |
| 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 | Tool info Standards/Databases Training |
| 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 | Standards/Databases |
| 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 | Training |
| 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 | Training |
| 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 | 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 | |
| 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 | Tool info |
| 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. | Data Steward: infrastructure TransMed | Tool info Training |
| 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 | Tool info |
| Research Management Plan | Machine actionable DMPs. | Data management plan Researcher Data Steward: research | |
| 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 Machine actionability | Standards/Databases |
| Reva | Reva connects cloud storages and application providers | Data analysis Data transfer | Tool info |
| 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 Machine actionability | Tool info |
| Rstudio | Rstudio notebooks allow to share code, documentation | Data analysis Data Steward: infrastructure Researcher | Tool info Training |
| 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 | 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 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 | |
| Schema.org | Schema.org 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 actionability Data Steward: infrastructure | Standards/Databases Training |
| 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). | Tool info Standards/Databases Training | |
| Singularity | Singularity is a container platform. | Data Steward: infrastructure Data analysis TSD | Training |
| 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 | Tool info Training |
| SSBD:database | Added-value database for biological dynamics images | Bioimaging data Data publication | |
| SSBD:repository | An open data archive that stores and publishes bioimaging and biological quantitative datasets | Bioimaging data Data publication | |
| Standards for Reporting Enzyme Data (STRENDA) | Resource of standards for reporting enzyme data | Microbial biotechnology | |
| STRING | Known and predicted protein-protein interactions. | Proteomics | Tool info Standards/Databases Training |
| 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 |
| 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. | 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 | 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 | Data publication Human data Data Steward: policy CSC TSD | Tool info Standards/Databases |
| The Genomic Standards Consortium (GSC) | Minimum Information about any (x) Sequence | Documentation and metadata Researcher Data Steward: infrastructure Data Steward: policy Human data | Standards/Databases |
| 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 | 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 | |
| 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 | Tool info |
| 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 | Training |
| 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 | Tool info |
| 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 Structural Bioinformatics | Tool info Standards/Databases Training |
| 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 | |
| WorkflowHub | WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows. | Data publication Data Steward: research Researcher | Tool info Standards/Databases |
| 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 Bioimaging data | |
| 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 Bioimaging data | Standards/Databases Training |
| Zooma | Find possible ontology mappings for free text terms in the ZOOMA repository. | Documentation and metadata Data Steward: research Researcher | Tool info Training |
| RDM Guide | RDM Guide describes Belgian data management guidelines, resources, tools and services available for researchers in Life Sciences. |
Researcher Data Steward: research | |
| Galaxy Belgium | Galaxy Belgium is a Galaxy instance managed by the Belgian ELIXIR node, funded by the Flemish government, which utilizing infrastructure provided by the Flemish Supercomputer Center (VSC).
Galaxy
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Researcher Data analysis | |
| ENA upload tool | The program submits experimental data and respective metadata to the European Nucleotide Archive (ENA). |
Data Steward: infrastructure Data Steward: research Researcher | |
| DMPonline.be | This instance of DMPonline is provided by the DMPbelgium Consortium. We can help you write and maintain data management plans for your research.
DMPRoadmap
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Data Steward: research Researcher Data management plan | |
| PIPPA | PIPPA, the PSB Interface for Plant Phenotype Analysis, is the central web interface and database that provides the tools for the management of the plant imaging robots on the one hand, and the analysis of images and data on the other hand. |
Plant sciences Data Steward: research Researcher Data Steward: infrastructure | |
| Belnet | Belnet is the privileged partner of higher education, research and administration for connectivity. We provide high-bandwidth internet access and related services for our specific target groups. |
Data Steward: research Researcher Data Steward: infrastructure Data transfer | |
| Flemish Supercomputing Center (VSC) | VSC is the Flanders’ most highly integrated high-performance research computing environment, providing world-class services to government, industry, and researchers. |
Data Steward: research Data Steward: infrastructure Data analysis Data storage | |
| e!DAL-PGP | Plant Genomics and Phenomics Research Data Repository |
Data storage Documentation and metadata Researcher Data Steward: research Data Steward: infrastructure Plant sciences Plant Genomics | |
| GFBio Data Management Plan Tool | Data management plan | ||
| GHGA | The German Human Genome-Phenome Archive |
Data storage Documentation and metadata Researcher Data Steward: research | |
| FAIRDOM-SEEK | Data management platform for organising, sharing and publishing research datasets, models, protocols, samples, publications and other research outcomes. |
Data storage Documentation and metadata Researcher Data Steward: research Data Steward: infrastructure | |
| PANGAEA | Data Publisher for Earth & Environmental Science |
Data storage Documentation and metadata Researcher Data Steward: research | |
| PUBLISSO | Open access publishing platform for life sciences |
Data publication Researcher Data Steward: research | |
| RDMO | Research Data Management Organiser |
Data management plan | |
| Galaxy Estonia | This is the Estonian instance of Galaxy, which is an open source, web-based platform for data intensive biomedical research.
Galaxy
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Researcher Data analysis | |
| REDCap Estonia | This is the Estonian instance of REDCap, which is a secure web platform for building and managing online databases and surveys.
REDCap
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Data Steward: research Data quality | |
| Red Española de Supercomputación | The Spanish Supercomputing Network’s mission is to offer the resources and services of supercomputing and data management necessary for the development of innovative and high-quality scientific and technological projects, through competitive calls based on the scientific excellence of the projects to be developed. |
Researcher Data Steward: research Data Steward: infrastructure | |
| RedIRIS | Spanish academic and research network that provides advanced communication services to the scientific community and national universities. |
Researcher Data Steward: research Data Steward: infrastructure | |
| Recolecta | The national aggregator of open access repositories. This platform brings together all the Spanish digital infrastructures in which open access research results are published and / or deposited. |
Researcher Data Steward: research Data Steward: infrastructure | |
| Datos.gob.es | Open data portal of the spanish government. A meeting point for the various actors that make up the open data ecosystem. |
Researcher Data Steward: research Data Steward: infrastructure | |
| 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 Researcher Data Steward: infrastructure Data analysis | |
| DMPTuuli | Data management planning tool (Finland)
DMPRoadmap
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CSC Researcher Data Steward: research Data management plan | |
| Fairdata.fi | With the Fairdata Services you can store, share and publish your research data with easy-to-use web tools. |
CSC Researcher Data Steward: research Data storage Data publication Existing data | |
| Federated EGA Finland | FEGA allows you to store and shaare sensitive data in Finland in a way that fulfils all the requirements of the General Data Protection Regulation (GDPR). |
CSC Researcher Data Steward: research Sensitive data Data publication Existing data Human data | |
| Findata | The Health and Social Data Permit Authority. Findata offers services and enables secure and efficient utilisation of data materials containing health and social data. |
CSC Researcher Data Steward: research Sensitive data Existing data Human data | |
| Fingenious | Finnish Biobank Cooperative (FINBB) connects researchers to Finnish biomedical research. Via Fingenious® services the researcher can connect to all Finnish public bio banks. |
CSC Researcher Data Steward: research Sensitive data Human data | |
| Sensitive Data Services for Research | CSC Sensitive Data Services for Research are designed to support secure sensitive data management through web-user interfaces accessible from the user’s own computer |
CSC Researcher Data Steward: research Sensitive data Data analysis Data storage Data publication Human data | |
| High performance computing | CSC Supercomputers Puhti, Mahti and LUMI performance ranges from medium scale simulations to one of the most competitive supercomputers in the world. |
CSC Researcher Data Steward: research Data analysis | |
| Cloud computing | CSC offers a variety of cloud computing services: the Pouta IaaS services and the Rahti container cloud service. |
CSC Researcher Data Steward: research Data analysis | |
| DMP OPIDoR | Online questionnaire for the development of data management plans - repository of DMPs
DMPRoadmap
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IFB Researcher Data Steward: research Data management plan | |
| 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. |
TSD Marine Metagenomics | |
| DS-Wizard ELIXIR-Norway | DS-Wizard is a tool to aid the creation, organisaton and sharing of data management plans. It provides scientists with guidance, facilitating the understanding of the key components of FAIR-oriented Data Stewardship. The template in this instance provides additional guidance on resources, laws and regulations in Norway.
Data Stewardship Wizard
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TSD NeLS Marine Metagenomics Data management plan | |
| EasyDMP | DMP tool from UNINETT Sigma2
EasyDMP
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Data management plan | |
| 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. |
Data analysis Marine Metagenomics | |
| 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. |
Data analysis Marine Metagenomics | |
| MarFun | MarFun is a manually curated marine fungi genome database. |
Data analysis Marine Metagenomics | |
| Norwegian COVID-19 Data Portal | The Norwegian COVID-19 Data Portal aims to bundle the Norwegian research efforts and offers guidelines, tools, databases and services to support Norwegian COVID-19 researchers. |
Human data Sensitive data Existing data Data publication | |
| Norwegian Federated EGA | Federated instance collects metadata of -omics data collections stored in national or regional archives and makes them available for search through the main EGA portal. With this solution, sensitive data will not physically leave the country, but will reside on TSD.
The European Genome-phenome Archive (EGA)
|
Human data Sensitive data Existing data Data publication TSD | |
| usegalaxy.no | Galaxy is an open source, web-based platform for data intensive biomedical research. This instance of Galaxy is coupled with NeLS for easy data transfer.
Galaxy
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Data analysis Sensitive data Existing data Data publication NeLS | |
| 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 | |
| NIRD | The National Infrastructure for Research Data (NIRD) infrastructure offers storage services, archiving services, and processing capacity for computing on the stored data. It offers services and capacities to any scientific discipline that requires access to advanced, large-scale, or high-end resources for storing, processing, publishing research data or searching digital databases and collections. This service is owned and operatedby Sigma2 NRIS, which is a joint collaboration between UiO, UiB, NTNU, UiT, and UNINETT Sigma2 |
Data transfer Data storage NeLS | |
| Sigma2 HPC systems | The current Norwegian academic HPC infrastructure consists of three systems for different purposes. The Norwegian academic high-performance computing and storage infrastructure is maintained by Sigma2 NRIS, which is a joint collaboration between UiO, UiB, NTNU, UiT, and UNINETT Sigma2. |
Data analysis | |
| Norwegian Research and Education Cloud (NREC) | NREC is an Infrastructure-as-a-Service (IaaS) project between the University of Bergen and the University of Oslo, with additional contributions from NeIC (Nordic e-Infrastructure Collaboration) and Uninett., commonly referred to as a cloud infrastructure An IaaS is a self-service infrastructure where you spawn standardized servers and storage instantly, as needed, from a given resource quota.
OpenStack
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Data analysis Data storage | |
| Educloud Research | Educloud Research is a platform provided by the Centre for information Technology (USIT) at the University of Oslo (UiO). This platform provides access to a work environment accessible to collaborators from other institutions or countries. This service provides a storage solution and a low threshold HPC system that offers batch job submission (SLURM) and interactive nodes. Data up to the red classification level can be stored/analysed. |
Data analysis Sensitive data Data storage | |
| TSD | The TSD – Service for Sensitive Data, is a platform for collecting, storing, analysing and sharing sensitive data in compliance with the Norwegian privacy regulation. TSD is developed and operated by UiO. |
Human data Data analysis Sensitive data Data storage TSD | |
| HUNTCloud | The HUNT Cloud, established in 2013, aims to improve and develop the collection, accessibility and exploration of large scale information. HUNT Cloud offers cloud services, lab management, and is a key service that has established a framework for data protection, data security, and data management. HUNT Cloud is owned by NTNU and operated by HUNT Research Centre at the Department of Public Health and Nursing at the Faculty of Medicine and Health Sciences. |
Human data Data analysis Sensitive data Data storage | |
| SAFE | SAFE (secure access to research data and e-infrastructure) is solution for secure processing of sensitive personal data in research at the University of Bergen. SAFE is based on “Norwegian Code of conduct for information security in the health and care sector” (Normen) and ensures confidentiality, integrity, and availability are preserved when processing sensitive personal data. Through SAFE, the IT-department offers a service where employees, students and external partners get access to dedicated resources for processing of sensitive personal data. |
Human data Data analysis Sensitive data Data storage | |
| RETTE | System for Risk and compliance. Processing of personal data in research and student projects at UiB. |
Human data Data protection Sensitive data Data Steward: policy Data Steward: research | |
| DataverseNO | DataverseNO is a national, generic repository for open research data. Various Norwegian research institutions have established a partner agreements about using DataverseNO as institutional repositories for open research data.
DATAVERSE
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Data publication | |
| BioData.pt Service Hub | BioData.pt Service Hub includes several data management resources, tools and services available for researchers in Life Sciences. |
Researcher Data Steward: research Data analysis Data storage | |
| BioData.pt Data Management Portal (DMPortal) | This instance of DataVerse is provided by the BioData.pt. We can help you write and maintain data management plans for your research.
DATAVERSE
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Researcher Data Steward: research Data storage | |
| BioData.pt Data Stewardship Wizard | Local instance of Data Stewardship Wizard. You can use this tool to create your own Data Management Plans.
Data Stewardship Wizard
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Researcher Data Steward: research Data management plan | |
| Ready for BioData Management | Capacity building program in data management for the life sciences to empower researchers and institutions in managing their data more effectively and efficiently.
Data Stewardship Wizard
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Researcher Data management plan | |
| DS-Wizard ELIXIR-SE | Data Stewardship Wizard is a tool to be used when planning for data management, including generating a data management plan (DMP). This instance provides guidance with focus towards Swedish life science researchers, including national resources.
Data Stewardship Wizard
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Data management plan | |
| SciLifeLab Data Repository (Figshare) | A repository for publishing any kind of research-related data, e.g. documents, figures, or presentations.
FigShare
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Existing data Data publication | |
| NBIS Data Management Consultation | Free consultation service regarding data management questions in life science research. |
Data management plan Data publication Sensitive data | |
| Swedish COVID-19 Data Portal | The Swedish COVID-19 Data Portal provides information, guidelines, tools and services to support researchers to utilise Swedish and European infrastructures for data sharing. |
COVID-19 Data Portal Human data Sensitive data Existing data Data publication | |
| SNIC | The Swedish National Infrastructure for Computing (SNIC) is a national research infrastructure that makes available large-scale high-performance computing resources, storage capacity, and advanced user support, for Swedish research. |
Data analysis Data storage | |
| SciLifeLab Data Guidelines | A data type centric resource that provides guidance on good data management practices during the data life cycle, including available infrastructures. |
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| Human Data Guidelines | Guidelines as well as further information on legal considerations when working with human biomedical data. |
Human data Sensitive data | |
| FAIRDOM-SEEK | A data Management Platform for organising, sharing and publishing research datasets, models, protocols, samples, publications and other research outcomes. |
Data storage Documentation and metadata | |
| DMPonline | DMPonline is a web-based tool that supports researchers to develop data management and sharing plans. It contains the latest funder templates and best practice guidelines to support users to create good quality DMPs.
DMPRoadmap
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Data Steward: research Researcher Data management plan | |
| COPO | COPO is an open source data brokering platform that helps researchers annotate their data with metadata conforming to repository standards, and supports submission of data to a number of these public repositories |
Data Steward: research Researcher Documentation and metadata |