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 | Tool info |
| 3DBioNotes | 3DBIONOTES-WS is a web application designed to automatically annotate biochemical and biomedical information onto structural models. | Structural Bioinformatics Machine actionability | Tool info Training |
| 4DN-BINA-OME-QUAREP (NBO-Q) | Rigorous record-keeping and quality control are required to ensure the quality, reproducibility and value of imaging data. The 4DN Initiative and BINA have published light Microscopy Metadata Specifications that extend the OME Data Model, scale with experimental intent and complexity, and make it possible for scientists to create comprehensive records of imaging experiments. The Microscopy Metadata Specifications have been adopted by QUAREP-LiMi and are being revised in QUAREP-LiMi in collaboration with instrument manufacturers | OMERO Bioimaging data | Standards/Databases |
| AACR-GENIE | Real-world cancer genomic dataset aggregated from multiple institutions. | Cancer data | |
| Access to Biological Collection Data Schema (ABCD) | A standard schema for primary biodiversity data | Microbial biotechnology | |
| Access to Research Infrastructure Administration (ARIA) | Access and data management platform that allows facilities to manage outputs and associate them with proposal information and other research outputs. | Structural Bioinformatics | Tool info |
| Ada Discovery Analytics (Ada) | Ada is a performant and highly configurable system for secured integration, visualization, and collaborative analysis of heterogeneous data sets, primarily targeting clinical and experimental sources. | TransMed | |
| Addgene | A searchable repository with a focus on plasmids | Microbial biotechnology | Tool info Standards/Databases Training |
| Agronomic Linked Data | The RDF Knowledge-based Database for plant molecular networks | Machine actionability | Standards/Databases |
| AgroPortal | Browser for ontologies for agricultural science based on NBCO BioPortal. | Plant Phenomics Documentation and meta... | Tool info Standards/Databases |
| AICSImageIO | Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python | Bioimaging data | |
| Alchemer | Commercial online survey tool. | Health data | |
| All of Us | NIH research program with diverse patient health, genetic, and lifestyle data. | Cancer data | Training |
| Amazon Web Services | Amazon Web Services | Data transfer | Training |
| Analysis Data Model for data and metadata of clinical trial statistical analysis (ADaM) | A CDISC Foundational Standard that defines dataset and metadata standards. | Health data | Tool info |
| AnnData | Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray. | Single-cell sequencing | Tool info Training |
| Annotare | Annotare is a tool for submitting functional genomics data to the ArrayExpress collection in BioStudies. | Single-cell sequencing | Training |
| AOP4EUpest | AOP4EUpest web server is devoted to the identification of pesticides involved in an Adverse Outcome Pathway via text mining approaches. | Toxicology data | Tool info |
| APID Interactomes | APID (Agile Protein Interactomes DataServer) is a server that provides a comprehensive collection of protein interactomes for more than 400 organisms based in the integration of known experimentally validated protein-protein physical interactions (PPIs) | Proteomics | Tool info |
| Apple HealthKit | A framework for health and fitness data integration on Apple devices. | Cancer data | |
| Argos | Plan and follow your data. Bring your Data Management Plans closer to where data are generated, analysed and stored. | Data management plan | Training |
| ArrayExpress | A collection in BioStudies for archiving and publishing data from high-throughput functional genomics experiments. | Microbial biotechnology Single-cell sequencing Data publication | Tool info Standards/Databases Training |
| Arvados | With Arvados, bioinformaticians run and scale compute-intensive workflows, developers create biomedical applications, and IT administrators manage large compute and storage resources. | Data analysis | |
| ATCC | Biological materials resource including cell-lines, strains and genomics tools | Microbial biotechnology | Tool info |
| Atlas | Free, publicly available web-based, open-source software application developed by the OHDSI community to support the design and execution of observational analyses to generate real world evidence from patient level observational data. | TransMed | Tool info Training |
| b2share | Store and publish your research data. Can be used to bridge between domains | Bioimaging data | Standards/Databases |
| BacDive | A searchable database for bacteria specific information | Microbial biotechnology | Tool info Standards/Databases Training |
| Bacillus Genetic Stock Center (BGSC) | A repository specific to Bacillus strains | Microbial biotechnology | |
| BBMRI-ERIC's ELSI Knowledge Base | The ELSI Knowledge Base is an open-access resource platform that aims at providing practical know-how for responsible research. | Human data Ethical aspects GDPR compliance | |
| Beacon | The Beacon protocol defines an open standard for genomics data discovery. | Human data Data discoverability | Tool info Standards/Databases Training |
| Beacon for OMOP (B4OMOP) | Beacon for OMOP (B4OMOP) software allows for the integration of a Beacon onto any OMOP Common Data Model (CDM) database. | Data discoverability | |
| Beacon v2 | Developed through the Global Alliance for Genomics and Health (GA4GH) Discovery workstream with support from ELIXIR, Beacon is a data discovery protocol defining an open standard for discovering genomic and phenoclinic data in research and clinical applications. | Data discoverability | Training |
| Beacon v2 Reference Implementation (B2RI) | An open-source out-of-the-box toolkit to initiate a Beacon v2. B2RI includes tools for loading metadata, such as phenotypic data and genomic variants into a MongoDB database, and features a Beacon query engine (REST API). | Data discoverability | |
| Benchling | R&D Platform for Life Sciences | Microbial biotechnology | Training |
| Better BibTeX (BBT) | A plugin for Zotero and Juris-M that makes it easier to manage bibliographic data. | ||
| bfconvert | The bfconvert command line tool can be used to convert files between supported formats. | Bioimaging data | |
| BIAFLOWS | BIAFLOWS is an open-soure web framework to reproducibly deploy and benchmark bioimage analysis workflows | Data analysis | Tool info |
| BigNASim | Repository for Nucleic Acids MD simulations | Biomolecular simulatio... | Tool info |
| BIII | The BioImage Informatics Index is a registry of software tools, image databases for benchmarking, and training materials for bioimage analysis | Bioimaging data | Tool info |
| BindingDB | Public, web-accessible database of measured binding affinities | Biomolecular simulatio... | Tool info Standards/Databases |
| Bio-Formats | Bio-Formats is a software tool for reading and writing image data using standardized, open formats. | OMERO | Tool info Training |
| Bio-Formats | Bio-Formats is a software tool for reading and writing image data using standardized, open formats | Bioimaging data | Tool info Training |
| bio.tools | Essential scientific and technical information about software tools, databases and services for bioinformatics and the life sciences. | Human pathogen genomics Data analysis | Tool info Standards/Databases Training |
| Bioactive Conformational Ensemble | Platform designed to efficiently generate bioactive conformers and speed up the drug discovery process. | Biomolecular simulatio... | Tool info |
| Bioassay Ontology | The BioAssay Ontology (BAO) describes chemical biology screening assays and their results, including high-throughput screening (HTS) data, to categorise assays and data analysis. | Enzymology and biocata... | Standards/Databases |
| Bioconda | Bioconda is a bioinformatics channel for the Conda package manager | Data analysis | Tool info Standards/Databases Training |
| BioContainers | BioContainers Flow | Single-cell sequencing Data analysis | Tool info Training |
| Biodiversity Information Standards (TDWG) | Biodiversity Information Standards (TDWG), historically the Taxonomic Databases Working Group, work to develop biodiversity information standards | Microbial biotechnology | |
| BioExcel COVID-19 | Platform designed to provide web-access to atomistic-MD trajectories for macromolecules involved in the COVID-19 disease. | Biomolecular simulatio... | |
| bioformats2raw | Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification. | Bioimaging data | |
| BioImage Model Zoo | BioImage is a collaborative effort to bring AI models to the bioimaging community. | Machine learning | Standards/Databases Training |
| BioImageArchive | The BioImage Archive stores and distributes biological images that are useful to life-science researchers. | Bioimaging data Data publication | Standards/Databases |
| BioModels | A repository of mathematical models for application in biological sciences | Enzymology and biocata... Microbial biotechnology Data publication | Tool info Standards/Databases Training |
| BioPortal | A comprehensive repository of biomedical ontologies | Bioimaging data Health data Documentation and meta... | Tool info Standards/Databases Training |
| BioSamples | BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. | Plant Genomics Plant sciences Virology | Tool info Standards/Databases Training |
| Bioschemas | Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials | Enzymology and biocata... Intrinsically disorder... Virology Machine actionability | Standards/Databases Training |
| BioStudies | A database hosting datasets from biological studies. Useful for storing or accessing life sciences data without community-accepted repositories, and for linking components of data from multi-omics studies. | Microbial biotechnology Plant sciences Single-cell sequencing Data publication Project data managemen... | Tool info Standards/Databases Training |
| BisQue | Resource for management and analysis of 5D biological images | Bioimaging data | Tool info |
| Bitbucket | Git-based code hosting and collaboration tool, built for teams. | Data organisation | Standards/Databases |
| BMDS | EPA's Benchmark Dose Software (BMDS) collects and provides easy access to numerous mathematical models that help risk assessors estimate the quantitative relationship between a chemical dose and the test subject’s response. | Toxicology data | |
| BMRB | Biological Magnetic Resonance Data Bank | Intrinsically disorder... Structural Bioinformatics | Tool info |
| BoostDM | BoostDM is a method to score all possible point mutations (single base substitutions) in cancer genes for their potential to be involved in tumorigenesis. | Human data | Tool info |
| Box | Cloud storage and file sharing service | Data transfer Data storage | Training |
| BrAPI | Specification for a standard API for plant data: plant material, plant phenotyping data | Plant Phenomics Plant sciences | Training |
| BrAPI compatible server | Submit a new BrAPI compatible server | Plant sciences | |
| BRAVA | BRAVA is a tool designed to help developers test servers that comply with the BrAPI specifications. | Plant Phenomics | |
| BRENDA | Database of enzyme and enzyme-ligand information, across all taxonomic groups, manually extracted from primary literature and extended by text mining procedures | Enzymology and biocata... Microbial biotechnology | Tool info Standards/Databases Training |
| BRENDA Tissue Ontology | A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. | Enzymology and biocata... | Standards/Databases |
| Bulk Rename Utility | File renaming software for Windows | Data organisation | |
| CAMEO | Continuous evaluation of the accuracy and reliability of protein structure prediction methods in a fully automated manner | Structural Bioinformatics | Tool info Standards/Databases |
| Cancer Genome Interpreter | Cancer Genome Interpreter (CGI) is designed to support the identification of tumor alterations that drive the disease and detect those that may be therapeutically actionable. | Cancer data Human data | Tool info |
| Cancer Pharmacogenomics | Pharmacogenomics knowledge base including cancer pharmacogenomic information. | Cancer data | |
| Cancer Therapeutics Response Portal (CTRP) | Resource to explore relationships between cancer cell line genotypes and drug response. | Cancer data | |
| CAPRI | Critical assessment of structure prediction methods for protein-protein interactions | Structural Bioinformatics | |
| CAS Registry | The CAS Registry (Chemical Abstracts Service Registry) includes more than 188 million unique chemicals. CAS Registry Numbers are broadly used as a unique identifier for chemical substances. The Registry is maintained by CAS, a subdivision of the American Chemical Society. | Toxicology data | Standards/Databases |
| CASP | Biennial critical assessment of techniques for protein structure prediction | Structural Bioinformatics | Tool info Training |
| Castor | Castor is an EDC system for researchers and institutions. With Castor, you can create and customize your own database in no time. Without any prior technical knowledge, you can build a study in just a few clicks using our intuitive Form Builder. Simply define your data points and start collecting high quality data, all you need is a web browser. | Health data Identifiers | Tool info |
| CatBoost | CatBoost is a high-performance open source library for gradient boosting on decision trees. | Machine learning | |
| CATH | A hierarchical domain classification of protein structures in the Protein Data Bank. | Proteomics | Tool info Standards/Databases Training |
| cBioPortal | A platform for exploring, analysing, and visualising cancer genomics data. | Cancer data | Tool info Standards/Databases Training |
| CDISC/SEND | CDISC SEND Controlled Terminology | Toxicology data | |
| CEDAR | CEDAR is making data submission smarter and faster, so that scientific researchers and analysts can create and use better metadata. | Data discoverability Documentation and meta... | Tool info Standards/Databases |
| Cell Ontology | The Cell Ontology (CL) is a candidate OBO Foundry ontology for the representation of cell types. | Enzymology and biocata... | Standards/Databases |
| CellDataSet | The main class used by Monocle to hold single cell expression data. CellDataSet extends the basic Bioconductor ExpressionSet class. | Single-cell sequencing | |
| CellMarker | A database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data. | Single-cell sequencing | Tool info |
| CellProfiler | Image analysis software | OMERO | Tool info Training |
| CellRanger | A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data. | Single-cell sequencing | |
| CellRepo | A version management tool for modifying strains | Microbial biotechnology | |
| Cellular Microscopy Phenotype Ontology (CMPO) | An ontology for expressing cellular (or multi-cellular) terms with applications in microscopy | Microbial biotechnology | Training |
| CERNBox | CERNBox cloud data storage, sharing and synchronization | Data storage | |
| ChEBI | Dictionary of molecular entities focused on 'small' chemical compounds | Enzymology and biocata... Human pathogen genomics 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. | Enzymology and biocata... Toxicology data | Tool info Standards/Databases Training |
| Chemical Entities of Biological Interest (ChEBI) | ChEBI) is a dictionary describing small chemical compounds including distinct synthetic or natural atoms, molecules, ions, ion pairs, radicals, radical ions, complexes, and conformers. | Enzymology and biocata... Human pathogen genomics Microbial biotechnology | Tool info Standards/Databases Training |
| Chemotion | Chemotion is a repository for chemistry research data that provides solutions for current challenges to store research data in a feasible manner, allowing the conservation of domain specific information in a machine readable format. | Enzymology and biocata... | Tool info Standards/Databases |
| Chocolatey | The Package Manager for Windows | Data analysis | |
| Choose a license | Choose an open source license | Licensing | |
| Clinical Data Interchange Standards Consortium (CDISC) | Consortium which defines several open standards for regulatory approval and case report forms in particular in the context of clinical trials meant for submission to FDA and EMA. | Health data | |
| Clinical Data Interoperability Services (CDIS) | REDCap feature which allows a REDCap project to interact with an EHR system and pull EHR data into REDCap. | Health data | |
| Clinical Interpretations of Variants in Cancer (CIViC) | A community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer | Cancer data | Tool info |
| Clinical Trial Registry-XML (CTR-XML) | A CDISC Data Exchange Standard that lets technology vendors implement tools that support a “write once, use many times” solution based on XML. | Health data | |
| ClinicalTrials.gov | ClinicalTrials.gov is a resource depending on the National Library of medicine which makes available private and public-funded clinical trials. | Cancer data Toxicology data | Standards/Databases |
| Comet | Open source tandem mass spectrometry (MS/MS) sequence database search tool. | Proteomics | Tool info |
| Common Data Elements (CDE) in a box | A collection of software applications which enables creation, storing and publishing of Common Data Elements according to the CDE semantic model. | Rare disease data | Tool info |
| Common Workflow Language (CWL) | An open standard for describing workflows that are build from command line tools | Data analysis | Standards/Databases Training |
| Comptox | The CompTox Chemicals Dashboard provides toxicological information for over 800.000 chemical compounds. It is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks. | Toxicology data | Tool info Standards/Databases |
| COmputational Modeling in BIology NEtwork (COMBINE) | An initiative to bring together various formats and standard for computational models in biology | Microbial biotechnology | |
| Conda | Open source package management system | Data analysis | Training |
| Consent Clauses for Genomic Research | A resource for researchers when drafting consent forms so they can use language matching cutting-edge GA4GH international standards | Human data | |
| Convenient And Reusable Rapid OMOP Transformer (CaRROT-Mapper) | Open-source tool to map datasets to the OMOP CDM. | Health data | |
| Cookiecutter | A command-line utility that creates projects from cookiecutters (project templates), e.g. creating a Python package project from a Python package project template. | Data organisation | |
| Copasi | COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. | Enzymology and biocata... | Tool info |
| COPO | Portal for scientists to broker more easily rich metadata alongside data to public repos. | Plant Phenomics Plant sciences Data discoverability Documentation and meta... | Tool info Standards/Databases |
| COVID-19 Data Portal | The COVID-19 Data Portal enables researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. The portal includes relevant datasets submitted to EMBL-EBI as well as other major centres for biomedical data. The COVID-19 Data Portal is the primary entry point into the functions of a wider project, the European COVID-19 Data Platform. | Human pathogen genomics | Tool info Standards/Databases Training |
| COVID-19 Structural Hub | Structural information organiser, collecting structures deposited in public repositories together with computationally predicted models from SARS-CoV-2, as well as their interactions with host proteins. | Structural Bioinformatics | Training |
| Create a Codebook | Examples and tools to create a codebook by the Data Documentation Initiative (DDI) | Documentation and meta... | |
| Creative Commons License Chooser | It helps you choose the right Creative Commons license for your needs. | Licensing | |
| Cromwell | Cromwell is a Workflow Management System geared towards scientific workflows. | Data analysis | |
| Crop Ontology | The Crop Ontology compiles concepts to curate phenotyping assays on crop plants, including anatomy, structure and phenotype. | Plant sciences | Standards/Databases Training |
| Crypt4GH | A Python tool to encrypt, decrypt or re-encrypt files, according to the GA4GH encryption file format. | Human data | Training |
| CS3 | Cloud Storage Services for Synchronization and Sharing (CS3) | Data storage | |
| CTD | A database that aims to advance understanding about how environmental exposures affect human health. | Toxicology data | Tool info Training |
| CUDA toolkit | The CUDA Toolkit from NVIDIA provides everything you need to develop GPU-accelerated applications | Machine learning | |
| cURL | Command line tool and library for transferring data with URLs | Data transfer | Training |
| CWL in Toil | The Common Workflow Language CWL is an emerging standard for writing workflows that are portable across multiple workflow engines and platforms. Toil has full support for the CWL v1.0, v1.1, and v1.2 standards. | Data analysis | |
| cwltool | This is the reference implementation of the Common Workflow Language open standards. It is intended to be feature complete and provide comprehensive validation of CWL files as well as provide other tools related to working with CWL. | Data analysis | |
| Cytomine-IMS | Image Data management | Bioimaging data | |
| DAISY | Data Information System to keep sensitive data inventory and meet GDPR accountability requirement. | TransMed Human data GDPR compliance | Tool info Training |
| DAMAP | It guides you step by step through a DMP and lets you export a pre-filled DMP as a Word document that you can customize and use for submission to funders. Also, DAMAP is compatible with the RDA recommendation for machine-actionable DMPs and offers an export of JSON DMPs. DAMAP is open source and to be self deployed. | Data management plan | |
| Data Agreement Wizard (DAWID) | The Data Agreement Wizard is a tool developed by ELIXIR-Luxembourg to facilitate data sharing agreements. | Human data GDPR compliance | |
| Data Catalog | Unique collection of project-level metadata from large research initiatives in a diverse range of fields, including clinical, molecular and observational studies. Its aim is to improve the findability of these projects following FAIR data principles. | TransMed | Training |
| Data Catalog Vocabulary (DCAT) | DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. | Rare disease data Virology Machine actionability | |
| Data Curation Centre Metadata list | List of metadata standards | Data discoverability Documentation and meta... | |
| Data Stewardship Wizard | Publicly available online tool for composing smart data management plans | CSC FAIRtracks Plant Genomics Plant Phenomics Plant sciences Data management plan GDPR compliance | Tool info Training |
| Data Stewardship Wizard Storage Costs Evaluator | This service provides simple estimation of storage costs based on desired properties and local/actual configuration. | Costs of data management | |
| Data Use Ontology (DUO) | DUO allows to semantically tag datasets with restriction about their usage. | Cancer data Human data Ethical aspects | Standards/Databases Training |
| data.world Data License list | Overview of typical licenses used for data resources | Licensing | |
| DataCite | A search engine for the complete collection of publicly available DataCite DOIs | Existing data | Standards/Databases |
| DataPLAN | Data Management Plan (DMP) generator that focuses on plant science. | Plant sciences | Tool info |
| DATAVERSE | Open source research data respository software. | Plant Phenomics Enzymology and biocata... Plant sciences Machine actionability Data storage | Training |
| dbGAP | The database of Genotypes and Phenotypes (dbGaP) archives and distributes data from studies investigating the interaction of genotype and phenotype in Humans | Cancer data Human data | Tool info Standards/Databases Training |
| DESEq2 | Differential gene expression analysis based on the negative binomial distribution | Toxicology data | Tool info Training |
| Digital Imaging and Communications in Medicine (DICOM) | A standard for medical imaging data storage and transmission. | Cancer data | |
| Disease Ontology (DOID) | The Disease Ontology has been developed as a standardised ontology for human disease to provide the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics, underlying mechanisms and related medical vocabulary disease concepts. | Human pathogen genomics | Standards/Databases |
| DisGeNET | A discovery platform containing collections of genes and variants associated to human diseases. | Human data Toxicology data | Tool info Standards/Databases Training |
| DisProt | A database of intrinsically disordered proteins | Intrinsically disorder... | Tool info Standards/Databases Training |
| DMP Canvas Generator | Questionnaire, which generates a pre-filled a DMP | Data management plan | |
| DMPlanner | Semi-automatically generated, searchable catalogue of resources that are relevant to data management plans. | Data management plan | |
| DMPonline | Data Management Plans that meet institutional funder requirements. | CSC Plant sciences Data management plan | Training |
| DMPRoadmap | DMP Roadmap is a Data Management Planning tool | Data management plan | |
| DMPTool | Build your Data Management Plan | Data management plan | Training |
| DNA Data Bank of Japan (DDBJ) | A database of DNA sequences | Microbial biotechnology | Tool info |
| Docker | Docker is a software for the execution of applications in virtualized environments called containers. It is linked to DockerHub, a library for sharing container images | Single-cell sequencing Data analysis | Training |
| Docker Compose overview | Compose is a tool for defining and running multi-container Docker applications. | Data analysis | |
| Docker Hub | Docker Hub is the world's easiest way to create, manage, and deliver your team's container applications. | Data analysis | Standards/Databases Training |
| Dockerfile reference | Docker can build images automatically by reading the instructions from a Dockerfile | Data analysis | |
| Dockstore | Dockstore is a free and open source platform for sharing reusable and scalable analytical tools and workflows. It’s developed by the Cancer Genome Collaboratory and used by the GA4GH. | Data analysis | Tool info Training |
| DOME-ML | Data, Optimisation, Model and Evaluation in Machine Learning (DOME-ML) is a set of community guidelines, recommendations and checklists for supervised ML validation in biology. | Cancer data Machine learning | Standards/Databases |
| DPIA Knowledge Model | A DSW knowledge model guiding users through a set of questions to collect information necessary for a research project Data Protection Impact Assessment (DPIA). | Human data GDPR compliance | |
| draw.io | draw.io is a free online diagram software for making flowcharts, process diagrams, org charts, UML, ER and network diagrams. | Creating a data-flow d... | |
| Dropbox | Cloud storage and file sharing service | Data transfer Documentation and meta... Data storage | |
| Drug Matrix | A toxicogenomic resource that provides access to the gene expression profiles of over 600 different compounds in several cell types from rats and primary rat hepatocytes. | Toxicology data | |
| Drug-Gene Interaction Database (DGIdb) | Drug-Gene Interaction Database linking drugs to their target genes. | Cancer data | Tool info |
| DrugBank | Comprehensive database containing information on drugs and drug targets. | Cancer data | Tool info Standards/Databases Training |
| DrugMap | Database for drug mechanisms, targets, pathways, and indications. | Cancer data | Tool info |
| Dryad | Open-source, community-led data curation, publishing, and preservation platform for CC0 publicly available research data | Bioimaging data Biomolecular simulatio... Data publication | Standards/Databases |
| Dublin Core Metadata Terms | A metadata standard for describing resources of any kind. | Virology | Standards/Databases |
| Dynameomics | Database of folding / unfolding pathway of representatives from all known protein folds by MD simulation | Biomolecular simulatio... | |
| e!DAL | Electronic data archive library is a framework for publishing and sharing research data | Plant Phenomics Plant sciences | Tool info Training |
| e!DAL-PGP | Plant Genomics and Phenomics Research Data Repository | Plant Genomics Plant Phenomics | Standards/Databases Training |
| Eastern Cooperative Oncology Group (ECOG) | A scale for assessing patient functional status. | Cancer data | |
| easy.DMP | Data Management Plan Generator | Data management plan | |
| ECOTOX | The ECOTOXicology Knowledgebase (ECOTOX) is a comprehensive, publicly available Knowledgebase providing single chemical environmental toxicity data on aquatic life, terrestrial plants, and wildlife. | Toxicology data | Standards/Databases |
| ECPGR | Hub for the identification of plant genetic resources in Europe | Plant sciences | |
| ECPGR Central Crop Databases and other Crop Databases | A number of ECPGR Central Crop Databases have been established through the initiative of individual institutes and of ECPGR Working Groups. The databases hold passport data and, to varying degrees, characterization and primary evaluation data of the major collections of the respective crops in Europe. | Plant sciences | |
| EDKB | Endocrine Disruptor Knowledge Base is a platform designed to foster the development of computational predictive toxicology. This platform allows direct access to ten libraries containing the following resources: a biological activity database, QSAR training sets, in vitro and in vivo experimental data for more than 3,000 chemicals, literature citations, chemical-structure search capabilities. | Toxicology data | |
| eLabFTW | A free and open source electronic lab notebook. | Documentation and meta... | Training |
| Electron Microscopy Data Bank (EMDB) | A public repository for electron cryo-microscopy maps and tomograms of macromolecular complexes and subcellular structures. | Structural Bioinformatics | Tool info |
| ELIXIR Core Data Resources | Set of European data resources of fundamental importance to the wider life-science community and the long-term preservation of biological data | COVID-19 Data Portal Existing data | Standards/Databases |
| ELIXIR Deposition Databases for Biomolecular Data | List of discipline-specific deposition databases recommended by ELIXIR. | CSC IFB Marine Metagenomics NeLS Data discoverability Data publication Documentation and meta... | Standards/Databases |
| ELN Finder | A tool to aid in choosing the most suitable Electronic Lab Notebook (ELN) for a specific purpose. | Documentation and meta... | |
| EMBL-EBI's data submission wizard | EMBL-EBI's wizard for finding the right EMBL-EBI repository for your data. | Data publication | |
| EMPIAR | Electron Microscopy Public Image Archive is a public resource for raw, 2D electron microscopy images. You can browse, upload and download the raw images used to build a 3D structure | OMERO Bioimaging data Structural Bioinformatics Data publication | Tool info Standards/Databases Training |
| ENA COMPARE Data Hubs | This tool carries out data hub set up at the European Nucleotide Archive (ENA). | Project data managemen... | |
| ENA upload tool | The program submits experimental data and respective metadata to the European Nucleotide Archive (ENA). | Data brokering | Training |
| Ensembl | Genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. | Identifiers | Tool info Standards/Databases Training |
| Ensembl Plants | Open-access database of full genomes of plant species. | Plant Genomics | Standards/Databases Training |
| EnzymeML | EnzymeML is a standardised data format for catalytic reaction data, designed to ensure consistency and interoperability. It enables researchers to store, share, and enrich reaction data with detailed metadata in JSON or XML formats. | Enzymology and biocata... | Tool info |
| ERN Registries Generic Informed Consent Forms | EJP RD - European Joint Programme on Rare Diseases - ERN Registries Generic Informed Consent Forms | Rare disease data | |
| ERPA | Web-based tool allowing users to create and manage a register of personal data processing activities (ROPA). | Human data GDPR compliance | |
| EU General Data Protection Regulation | Regulation (eu) 2016/679 of the european parliament and of the council on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing directive 95/46/ec (general data protection regulation). | TSD Human data Data sensitivity | |
| EU Survey | European Commission's official multilingual online survey-management system built for the creation and publishing of globally accessible forms. | Health data | |
| EUDAT licence selector wizard | EUDAT's wizard for finding the right licence for your data or code. | Licensing | |
| EudraVigilance | The European database of suspected adverse drug reaction reports is a public resource aimed to provide access to reported suspected side-effects of drugs. Side-effects are defined according to the MedDRA ontology. | Toxicology data | |
| EUPID | EUPID provides a method for identity management, pseudonymisation and record linkage to bridge the gap between multiple contexts. | Human data | |
| EURISCO | European Search Catalogue for Plant Genetic Resources | Plant sciences | Tool info |
| Europe PMC | Europe PMC is a repository, providing access to worldwide life sciences articles, books, patents and clinical guidelines. | Machine actionability | Tool info Standards/Databases Training |
| European Cancer Imaging Initiative (EUCAIM) | A federated platform for cancer imaging data. | Cancer data | |
| European Electronic Health Record Exchange Format (EEHRxF) | Recommended by the European Commission as the format to be used for the exchange of EHR data for cross-border healthcare. | Health data | |
| European Joint Programme on Rare Diseases (EJP RD) | A programme aiming to create an effective rare diseases research ecosystem for progress, innovation and for the benefit of everyone with a rare disease. | Rare disease data | |
| European Joint Programme on Rare Diseases Metadata Model | This core model is designed to represent data about a rare disease patient and biosample registries. The model is based on and builds on existing standards, such as the European Rare Disease Registry Infrastructure and the Common Data Elements from the rare disease community and other more generalised standards for data sharing such as the W3C DCAT vocabulary. | Rare disease data | |
| European Joint Programme on Rare Diseases Virtual Platform (EJP RD) | The Virtual Platform is a federated ecosystem, in which resources are enhanced to be amenable to rare disease research, and made Findable, Accessible, Interoperable and Reusable: data stays at the source level but can be queyrable at distance from an EJP RD query point. | Rare disease data | |
| European Medicines Agency's (EMA) medicine finder | European Medicines Agency's (EMA) portal for authorised medicines in the EU. | Cancer data | |
| European Nucleotide Archive (ENA) | A record of sequence information scaling from raw sequcning reads to assemblies and functional annotation | Galaxy Plant Genomics Human pathogen genomics Microbial biotechnology Single-cell sequencing Virology Data brokering Data publication Project data managemen... | Tool info Standards/Databases Training |
| European Organisation for Research and Treatment of Cancer (EORTC) Quality of Life Questionnaires (QLQ) | A set of questionnaires developed to assess the quality of life of cancer patients. | Cancer data | |
| European Rare Disease Registry Infrastructure directory of registries (ERDRI.dor) | ERDRI.dor provides an overview of participating rare disease registries with their main characteristics and description. | Rare disease data | |
| European Rare Disease Registry Infrastructure metadata repository (ERDRI.mdr) | ERDRI.mdr serves to ease the integration of heterogeneous data from different rare disease registries. For this purpose, it contains a collection of metadata which specifies the used data elements of a registry including the designation of the used data elements, their definition and units of measurement. | Rare disease data | |
| European Reference Networks (ERNs) | Virtual networks involving healthcare providers across Europe. They aim to facilitate discussion on complex or rare diseases and conditions that require highly specialised treatment, and concentrated knowledge and resources. | Rare disease data | Training |
| European Variation Archive (EVA) | Open-access database of all types of genetic variation data from all species. | Plant Genomics Plant sciences | Tool info Standards/Databases Training |
| Evidence and Conclusion Ontology (ECO) | Controlled vocabulary that describes types of evidence and assertion methods | Existing data Documentation and meta... | Standards/Databases |
| EVORA Ontology | European Viral Outbreak Response Alliance Ontology | Virology | |
| Expression Atlas | Gene expression across species and biological conditions | Machine actionability | Tool info Standards/Databases Training |
| EzCatDB | EzCatDB is a database of enzyme catalytic mechanisms. | Enzymology and biocata... | |
| FAERS | The FDA Adverse Event Reporting System (FAERS) is an american resource that contains adverse event reports, medication error reports and product quality complaints submitted by healthcare professionals, consumers, and manufacturers. MedDRA ontology is used for coding adverse effects. Note that reports available in FAERS do not require a causal relationship between a product and an adverse event and further evaluations are conducted by FDA to monitor the safety of products. | Toxicology data | Tool info |
| FAIDARE | FAIDARE is a tool allowing to search data across dinstinct databases that implemented BrAPI. | Plant Phenomics Plant sciences | Tool info Training |
| FAIR Cookbook | FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable and Reusable (FAIR) | TransMed Health data Human pathogen genomics Compliance monitoring ... | Tool info Training |
| FAIR Data Point (FDP) | A FAIR Data Point stores metadata in a standardized and sharable way. | Rare disease data | Standards/Databases Training |
| FAIR Data Points | Metadata for machines | Rare disease data | Training |
| FAIR Evaluation Services | Resources and guidelines to assess the FAIRness of digital resources. | Compliance monitoring ... | |
| FAIR Implementation Profile | The FIP is a collection of FAIR implementation choices made by a community of practice for each of the FAIR Principles. | Data management plan Project data managemen... | Standards/Databases |
| FAIR-Wizard | The FAIR wizard utilizes FAIRification resources developed by the FAIRplus project and other platforms, suggests FAIRification materials based on the FAIRification requirements, and designs FAIRification solutions for data owners, data stewards, and other people involved in FAIRification. | Compliance monitoring ... | Training |
| FAIRassist.org | Help you discover resources to measure and improve FAIRness. | Compliance monitoring ... | |
| FAIRDOM-SEEK | A data Management Platform for organising, sharing and publishing research datasets, models, protocols, samples, publications and other research outcomes. | NeLS Plant Phenomics Microbial biotechnology Plant sciences Data discoverability Documentation and meta... Data storage | Tool info |
| FAIRDOMHub | Data, model and SOPs management for projects, from preliminary data to publication, support for running SBML models, etc. (public SEEK instance) | NeLS Plant Genomics Plant Phenomics Microbial biotechnology Plant sciences Data discoverability Documentation and meta... | Standards/Databases Training |
| FAIRshake | A System to Evaluate the FAIRness of Digital Objects | Compliance monitoring ... | |
| FAIRsharing | A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies. | FAIRtracks Health data Microbial biotechnology Plant sciences Virology Data discoverability Data provenance Data publication Existing data Machine actionability Documentation and meta... | Standards/Databases Training |
| FDA-approved tools | Various digital health tools approved by the FDA for medical use (e.g., wearables, software, diagnostics). | Cancer data | |
| Federated EGA | The Federated EGA is an infrastructure built upon the European Genome-phenome Archive (EGA), an EMBL-EBI and CRG data resource for secure archiving and sharing of human sensitive biomolecular and phenotypic data resulting from biomedical research projects. | Cancer data | Training |
| Federated Health Information Model (FHIM) | A UML-based logical health information model defined by the Open Group, intended to achieve interoperability between multiple healthcare standards and protocols. | Health data | |
| FHIR4FAIR | Guidance on how FHIR can be used for supporting FAIR health data. | Health data | |
| FigShare | Data publishing platform | Biomolecular simulatio... Enzymology and biocata... Data publication Identifiers Documentation and meta... | Standards/Databases Training |
| Fiji | Fiji is an image processing package | OMERO | Tool info Training |
| FileZilla | A free FTP (FTPS and SFTP) solution with graphical interface | Data transfer | Training |
| FIP Wizard | FIP Wizard is a toolset to facilitate the capture of data in FAIR Convergence Matrix questionnaire prompting communities to explicitly declare their FAIR Implementation Profiles. These profiles can be then stored and published as nanopublications. | Data management plan Project data managemen... | |
| Flame | Flame is a flexible framework supporting predictive modeling and similarity search within the eTRANSAFE project. | Toxicology data | Tool info |
| Free-IPA | FreeIPA is an integrated Identity and Authentication solution for Linux/UNIX networked environments. | TransMed | |
| Freegenes | Repository of IP-free synthetic biological parts | Microbial biotechnology | |
| GA4GH Data Security Toolkit | Principled and practical framework for the responsible sharing of genomic and health-related data. | Human data | |
| GA4GH Genomic Data Toolkit | Open standards for genomic data sharing. | Human data | |
| GA4GH Regulatory and Ethics toolkit | Framework for Responsible Sharing of Genomic and Health-Related Data | Human data Ethical aspects | |
| Galaxy | Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. | Marine Metagenomics Single-cell sequencing Data analysis Data provenance Data storage | Tool info Training |
| GenBank | A database of genetic sequence information. GenBank may also refer to the data format used for storing information around genetic sequence data. | Microbial biotechnology Virology | Tool info Standards/Databases Training |
| Gene Expression Omnibus (GEO) | A repository of MIAME-compliant genomics data from arrays and high-throughput sequencing | Microbial biotechnology Single-cell sequencing Data publication | Standards/Databases |
| Gene Ontology | The Gene Ontology Consortium continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. | Single-cell sequencing | Tool info Standards/Databases Training |
| Genesys | Genesys is an online platform where you can find information about Plant Genetic Resources for Food and Agriculture PGRFA conserved in genebanks worldwide. | Plant sciences | |
| Genomic Epidemiology Ontology (GenEpiO) | The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research food-borne pathogens, infectious disease surveillance and outbreak investigations. | Human pathogen genomics | Standards/Databases |
| Genomic Standards Consortium (GSC) | The Genomic Standards Consortium (GSC) is an open-membership working body enabling genomic data integration, discovery and comparison through international community-driven standards. | Marine metagenomics | Standards/Databases |
| Genomics of Drug Sensitivity in Cancer (GDSC) | Database of drug sensitivity and genomic data from cancer cell lines. | Cancer data | |
| 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 | Single-cell sequencing Data organisation | Training |
| GitHub | Versioning system, used for sharing code, as well as for sharing of small data | Machine learning Creating a data-flow d... Data organisation Documentation and meta... | Standards/Databases Training |
| GitLab | GitLab is an open source end-to-end software development platform with built-in version control, issue tracking, code review, CI/CD, and more. Self-host GitLab on your own servers, in a container, or on a cloud provider. | Data organisation | Standards/Databases Training |
| Global Initiative on Sharing All Influenza Data (GISAID) | A web-based platform for sharing viral sequence data, initially for influenza data, and now for other pathogens (including SARS-CoV-2). | Human pathogen genomics Virology Machine actionability | Standards/Databases |
| Globus | High-performance data transfers between systems within and across organizations | Data transfer | |
| GnpIS | A multispecies integrative information system dedicated to plant and fungi pests. It allows researchers to access genetic, phenotypic and genomic data. It is used by both large international projects and the French National Research Institute for Agriculture, Food and Environment. | Plant Phenomics | Tool info Standards/Databases |
| Google Dataset Search | Search engine for datasets | Existing data | |
| Google Drive | Cloud Storage for Work and Home | Data transfer | |
| Google Fit | A health-tracking platform by Google for collecting and accessing fitness data. | Cancer data | |
| GotEnzymes | GotEnzymes: an extensive database of enzyme parameter predictions. | Enzymology and biocata... | |
| GPCRmd | Repository of GPCR protein simulations | Biomolecular simulatio... | Tool info |
| Harmony | Fast, sensitive and accurate integration of single-cell data. | Single-cell sequencing | Tool info Training |
| Hartwig Medical Foundation (HMF) | Multi-omic cancer dataset of >7000 patients, including whole genome sequencing and clinical outcomes. | Cancer data | |
| Harvard Medical School - Electronic Lab Notebooks | ELN Comparison Grid by Hardvard Medical School | Identifiers Documentation and meta... | |
| Haz-Map | Haz-Map is an occupational health database that makes available information about the adverse effects of exposures to chemical and biological agents at the workplace. These associations have been established using current scientific evidence. | Toxicology data | |
| Hierarchical Data Format | HDF5 consists of a file format for storing HDF5 data, a data model for logically organizing and accessing HDF5 data from an application, and the software (libraries, language interfaces, and tools) for working with this format. | Single-cell sequencing | Standards/Databases |
| HL7 FHIR | A standard used for health care data exchange. | Cancer data Health data | |
| Homebrew | The Missing Package Manager for macOS or Linux | Data analysis | |
| How to License Research Data - DCC | Guidelines about how to license research data from Digital Curation Centre | Licensing | |
| HuggingFace | The platform where the machine learning community collaborates on models, datasets, and applications. | Machine learning | Training |
| Human Phenotype Ontology (HPO) | Standardised vocabulary of phenotypic abnormalities encountered in human disease. | Health data | Tool info |
| Human Protein Atlas | The Human Protein Atlas contains information for a large majority of all human protein-coding genes regarding the expression and localization of the corresponding proteins based on both RNA and protein data. | Proteomics | Standards/Databases Training |
| HumanMine | HumanMine integrates many types of human data and provides a powerful query engine, export for results, analysis for lists of data and FAIR access via web services. | Human data | Tool info Standards/Databases Training |
| HUPO Proteomics Standards Initiative | The HUPO Proteomics Standards Initiative defines community standards for data representation in proteomics and interactomics to facilitate data comparison, exchange and verification. | Microbial biotechnology Proteomics | |
| IBM Aspera | With fast file transfer and streaming solutions built on the award-winning IBM FASP protocol, IBM Aspera software moves data of any size across any distance | Data transfer | |
| ICD-O-3 Coding Materials | A classification system for oncology, used in cancer registries and pathology reporting. | Cancer data | |
| ICGC-ARGO | Integrated clinical and genomic data for over 100,000 cancer patients from the International Cancer Genome Consortium. | Cancer data | |
| ICTV | The International Committee on Taxonomy of Viruses (ICTV) taxonomic database is a maintained resource comprised of a universal taxonomic scheme for all the viruses infecting animals (vertebrates, invertebrates and protozoa), plants (higher plants and algae), fungi, bacteria and archaea. | Virology | Standards/Databases |
| 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). | FAIRtracks Identifiers | Tool info Standards/Databases Training |
| iGEM Parts Registry | A collection of standard biological parts to which all entrants in the iGEM competition must submit their parts | Microbial biotechnology | |
| ilastik | ilastik is a user-friendly tool for interactive image classification, segmentation and analysis | OMERO | Tool info |
| Image Data Resource (IDR) | A repository of image datasets from scientific publications | OMERO Bioimaging data Microbial biotechnology | Tool info Standards/Databases |
| Infectious Diseases Toolkit (IDTk) | Discover tools and best practices for working with infectious disease data. IDTk provides general guidance as well as specific information for pathogen characterisation, socioeconomic data, human biomolecular data, and human clinical and health data. | COVID-19 Data Portal Human pathogen genomics Virology | |
| Informatics for Integrating Biology & the Bedside (i2b2) | An open-source data warehouse for clinical and translational research. | Cancer data | Training |
| Informed Consent Ontology (ICO) | The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. | Human data Ethical aspects | Standards/Databases |
| Inkscape | Inkscape is a versatile and free graphic design editor suitable for both personal and professional use. It offers a comprehensive suite of design tools, enabling users to create and edit vector graphics, primarily in the SVG format. Additionally, Inkscape supports working with rasterized images (bitmaps), making it a powerful tool for diverse design projects. | Creating a data-flow d... | Training |
| Integrated Database of Small Molecules (IDSM) | Increasing interoperability of small molecules by agregating many different sources of information into a single, logically coherent and semantically interconnected information source. | Machine actionability | Tool info Standards/Databases |
| International Classification of Diseases 10th Revision (ICD-10) | Codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases. Replaced by ICD-11 on 1/1/2022. | Health data | Tool info |
| International Classification of Diseases 11th Revision (ICD-11) | Replaces the ICD-10 as the global standard for recording health information and causes of death. It is developed by the World Health Organization and is annually updated. | Health data | Tool info |
| International Compilation of Human Research Standards | The International Compilation of Human Research Standards enumerates over 1,000 laws, regulations, and guidelines (collectively referred to as standards) that govern human subject protections in 133 countries, as well as standards from a number of international and regional organizations | Human data | |
| International Multicrop Databases | A catalogue of relevant International Multicrop Databases | Plant sciences | |
| International Nucleotide Sequence Database Collaboration | The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, through alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations. | Galaxy Microbial biotechnology Plant sciences Data publication | |
| International Nucleotide Sequence Database Collaboration (INSDC) | A collaborative database of genetic sequence datasets from DDBJ, EMBL-EBI and NCBI | Galaxy Microbial biotechnology Plant sciences Data publication | Tool info |
| International Society for the Advancement of Cytometry (ISAC) | Data standards and formats for reporting flow cytometry data | Microbial biotechnology | |
| International Union of Biochemistry and Molecular Biology (IUBMB) | Resource for naming standards in biochemistry and molecular biology | Microbial biotechnology | |
| InterPro | Functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites | Proteomics | Tool info Standards/Databases Training |
| IntoGen | IntoGen collects and analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes. | Human data | Tool info |
| Intrinsically disordered proteins ontology (IDPO) | Intrinsically disordered proteins ontology | Intrinsically disorder... | Tool info |
| IRIS | The Integrated Risk Information System (IRIS) resource evaluates information on health that might arise after exposure to environmental contaminants. | Toxicology data | Tool info Training |
| iRODS | Integrated Rule-Oriented Data System (iRODS) is open source data management software for a cancer genome analysis workflow. | TransMed Bioimaging data Data storage | Tool info |
| IRRMC | Integrated Resource for Reproducibility in Macromolecular Crystallography. Repository of diffraction experiments used to determine protein structures in the PDB, contributed by the CSGID, SSGCID, JCSG, MCSG, SGC, and other large-scale projects, as well as individual research laboratories. | Structural Bioinformatics | |
| ISA-tools | Open source framework and tools helping to manage a diverse set of life science, environmental and biomedical experiments using the Investigation Study Assay (ISA) standard | Plant sciences | Standards/Databases |
| ISA4J | Open source software library that can be used to generate a ISA-TAB export from in-house data sets. These comprises e.g. local database or local file system based experimental. | Plant Phenomics | Tool info |
| ISO 13606 | A standard designed by the European Committee for Standardization to define a information architecture for communicating part or all of the EHR of a single patient between EHR systems or between EHR systems and a centralised EHR data repository. | Health data | |
| ISO 13972:2022 | Defines data elements, the relationships between such data elements and terminologies for detailed small, reusable clinical models. | Health data | |
| ISO/DIS 14199 | Domain model for data interchange that enables semantic interoperability and intends to integrate biomedical, clinical research and routine healthcare data. | Health data | |
| ISO/IEC 27001 | International information security standard | Human data Compliance monitoring ... | |
| ITER | ITER is an Internet database of human health risk values and cancer classifications for over 680 chemicals of environmental concern from multiple organizations worldwide. | Toxicology data | Training |
| IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN) | A collaborative resource from IUPAC and IUBMB for naming standards in biochemistry | Microbial biotechnology | |
| JBEI-ICE | A registry platform for biological parts | Microbial biotechnology | |
| JGA | The Japanese Genotype-phenotype Archive (JGA) is a service for permanent archiving and sharing of all types of individual-level genetic and de-identified phenotypic data resulting from biomedical research projects. | Human data | |
| Jotform | Commercial online survey tool. | Health data | |
| Jupyter | Jupyter notebooks allow to share code, documentation | Data analysis | Training |
| Jupyter kernels | Kernel Zero is IPython, which you can get through ipykernel, and is still a dependency of jupyter. The IPython kernel can be thought of as a reference implementation, as CPython is for Python. | Data analysis | |
| JWS Online | JWS-Online is a systems biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models. | NeLS Enzymology and biocata... | Standards/Databases |
| Keras | Keras is an open-source library that provides a Python interface for artificial neural networks. | Machine learning | Training |
| Keycloak | Keycloak is an open source identity and data access management solution. | TransMed | Training |
| KnetMiner | A software to make biological search more integrated, intuitive and intelligent, enabling a better way to discover and share new insights. | Machine actionability | Tool info Standards/Databases Training |
| Kubernetes | Kubernetes, also known as K8s, is an open-source system for automating deployment, scaling, and management of containerized applications. | Data analysis | Training |
| LeafNet | LeafNet is a convenient tool that can robustly localise stomata and segment pavement cells for light-microscope images of leaves | Plant Phenomics | Tool info |
| Libre Office Draw | LibreOffice Draw is a free, open-source vector graphics editor that is part of the LibreOffice suite, developed by The Document Foundation. This tool allows users to create designs with ease, offering a variety of features such as shape tools, straight and curved line tools, polygon tools, and more. It provides a robust platform for crafting illustrations and diagrams. | Creating a data-flow d... | |
| Life Science Login (LS Login) | An authentication service from EOSC-Life | IFB NeLS TransMed TSD | |
| Life-Monitor | LifeMonitor is a service to support the sustainability and reusability of published computational workflows. | Data analysis | Training |
| LimeSurvey | A free and open source platform to develop and publish online surveys. | Health data | |
| limma | Linear Models for Microarray Data | Toxicology data | Tool info Training |
| LimTox | The LiMTox system is a text mining approach that tries to extract associations between compounds and a particular toxicological endpoint at various levels of granularity and evidence types, all inspired by the content of toxicology reports. It integrates direct ranking of associations between compounds and hepatotoxicity through combination of heterogeneous complementary strategies from term co-mention, rules, and patterns to machine learning-based text classification. It also provides indirect associations to hepatotoxicity through the extraction of relations reflecting the effect of compounds at the level of metabolism and liver enzymes. | Toxicology data | Tool info |
| Linked Open Vocabularies (LOV) | Web portal for finding ontologies | Documentation and meta... | |
| List of Prokaryotic names with Standing in Nomenclature (LPSN) | A database of prokaryote specific biodiversity information | Microbial biotechnology | Tool info |
| Logical Observation Identifiers Names and Codes (LOINC) | Terminology standard for health measurements, observations, and documents. | Health data | |
| Loom | Loom is an efficient file format for large omics datasets. | Single-cell sequencing | |
| LUMI | EuroHPC world-class supercomputer | Data analysis | Tool info |
| M-CSA (Mechanism and Catalytic Site Atlas) | M-CSA is a database of enzyme reaction mechanisms. | Enzymology and biocata... | Standards/Databases |
| MacPorts | The MacPorts Project is an open-source community initiative to design an easy-to-use system for compiling, installing, and upgrading either command-line, X11 or Aqua based open-source software on the Mac operating system. | Data analysis | |
| MarDB | MarDB includes all non-complete marine microbial genomes regardless of level of completeness. Each entry contains 120 metadata fields including information about sampling environment or host, organism and taxonomy, phenotype, pathogenicity, assembly and annotation. | Marine Metagenomics | Tool info |
| MarFun | MarFun is a manually curated marine fungi genome database. | Marine Metagenomics | |
| Marine Metagenomics Portal (MMP) | High-quality curated and freely accessible microbial genomics and metagenomics resources for the marine scientific community | Marine Metagenomics | Tool info |
| MarRef | MarRef is a manually curated marine microbial reference genome database that equenced genomes. Each entry contains 120 metadata fields including information about sampling environment or host, organism and taxonomy, phenotype, pathogenicity, assembly and annotation information | Marine Metagenomics | Tool info |
| Mascot | Powerful search engine which uses mass spectrometry data to identify proteins from DNA, RNA and protein sequence databases as well as spectral libraries. | Proteomics | Tool info Standards/Databases Training |
| Mass Centric Peptide Database (MaCPepDB) | A database to quickly access all tryptic peptides of the UniProtKB | Proteomics | Standards/Databases |
| MassIVE | Powerful search engine which uses mass spectrometry data to identify proteins from DNA, RNA and protein sequence databases as well as spectral libraries. | Proteomics | Standards/Databases Training |
| Medical Dictionary for Regulatory Activities (MedDRA) | A single standardised international medical terminology. | Cancer data | |
| MemProtMD | Database of over 5000 intrinsic membrane protein structures | Biomolecular simulatio... | Tool info |
| Mendeley data | Multidisciplinary, free-to-use open repository specialized for research data | Biomolecular simulatio... Data publication Existing data | Standards/Databases |
| Metabolome Exchange | A repository of genomics data relating to the study of the metabolome | Microbial biotechnology | |
| MetaCyc | The MetaCyc database is a comprehensive resource for metabolic pathways and enzymes from all domains of life. | Enzymology and biocata... | Tool info Standards/Databases |
| Metagen-FastQC | Cleans metagenomic reads to remove adapters, low-quality bases and host (e.g. human) contamination | Data publication | |
| MIADE | Minimum Information About Disorder Experiments (MIADE) standard | Intrinsically disorder... | Training |
| MIAME | Minimum Information About a Microarray Experiment | Documentation and meta... | Standards/Databases Training |
| MIAPPE | Minimum Information About a Plant Phenotyping Experiment | Plant Genomics Plant Phenomics Plant sciences Documentation and meta... | Standards/Databases Training |
| MIAPPE-compliant spreadsheet template | MIAPPE-compliant spreadsheet template | Plant sciences | |
| MIAPPE_Checklist-Data-Model | This document describes the MIAPPE Checklist and Data Model | Plant sciences | |
| Microsoft Azure | Cloud storage and file sharing service from Microsoft | Data transfer | |
| Microsoft OneDrive | Cloud storage and file sharing service from Microsoft | Data transfer Data storage | |
| MineProt | A stand-alone server for structural proteome curation | Structural Bioinformatics | Tool info |
| Minimum Information about a (Meta)Genome Sequence (MIxS - MIGS/MIMS) | a conceptual structure for extending the core INSDC information to describe genomic and metagenomic sequences. | Human pathogen genomics Marine metagenomics | Standards/Databases |
| Minimum Information about a Single-Cell Experiment (minSCe) | MinSCe is a minimum set of metadata categories used to describe a single-cell assay in sufficient detail to enable the analysis of transcriptomic data. | Single-cell sequencing | Standards/Databases |
| Minimum Information about an Uncultivated Virus Genome (MIOViG) | MIxS - MIUViG (Minimum Information about an Uncultivated Virus Genome) is a checklist that is a part of the larger MIxS standard. | Virology | Standards/Databases |
| Minimum Information about any (x) Sequence (MIxS) | An overarching framework of standard metadata that includes sequence-type and technology-specific checklists. | Human pathogen genomics Marine metagenomics Virology | Standards/Databases |
| Minimum information standards in life sciences | List of minimum information standards on Wikipedia | Documentation and meta... | |
| MINSEQE | Minimum Information about a high-throughput SEQuencing Experiment | Documentation and meta... | Standards/Databases Training |
| MobiDB | A database of protein disorder and mobility annotations | Intrinsically disorder... | Tool info Standards/Databases Training |
| MoDEL | Database of Protein Molecular Dynamics simulations representing different structural clusters of the PDB | Biomolecular simulatio... | Tool info Training |
| MoDEL-CNS | Repository for Central Nervous System-related mainly membrane protein MD simulations | Biomolecular simulatio... | |
| ModelArchive | Repository for theoretical models of macromolecular structures with DOIs for models | Biomolecular simulatio... Structural Bioinformatics | Tool info Standards/Databases |
| MOLGENIS | Molgenis is a modular web application for scientific data. Molgenis provides researchers with user friendly and scalable software infrastructures to capture, exchange, and exploit the large amounts of data that is being produced by scientific organisations all around the world. | MOLGENIS Identifiers | Tool info |
| MolMeDB | Database about interactions of molecules with membranes | Biomolecular simulatio... | Tool info Standards/Databases |
| MolSSI - BioExcel COVID-19 therapeutics hub | Aggregating critical information to accelerate COVID-19 drug discovery for the molecular modeling and simulation community. | Biomolecular simulatio... | |
| MONARC | A risk assessment tool that can be used to do Data Protection Impact Assessments | TransMed Human data | |
| Monocle | The Monocle 3 package provides a toolkit for analyzing single-cell gene expression experiments. | Single-cell sequencing | Tool info Training |
| MRI2DICOM | a Magnetic Resonance Imaging (MRI) converter from ParaVision® (Bruker, Inc. Billerica, MA) file format to DICOM standard | XNAT-PIC | |
| msconvert | Provides a set of open-source, cross-platform software libraries and tools that facilitate proteomics data analysis. | Proteomics | Tool info Training |
| MSK-CHORD | Platform from Memorial Sloan Kettering providing molecular and clinical data to support precision oncology. | Cancer data | |
| MTB Portal | Provides a general framework to interpret the functional and predictive relevance of a list of gene variants through interactive reports. | Cancer data | |
| Multi-Crop Passport Descriptor (MCPD) | The Multi-Crop Passport Descriptor is the metadata standard for plant genetic resources maintained ex situ by genbanks. | Plant sciences | Standards/Databases Training |
| MyTARDIS | A file-system based platform handling the transfer of data | Bioimaging data | |
| National Cancer Institute (NCI) treatment drugs | A database of cancer-related drugs, including descriptions, uses, and approvals. | Cancer data | |
| National Center for Biotechnology Information (NCBI) | Online database hosting a vast amount of biotechnological information including nucleic acids, proteins, genomes and publications. Also boasts integrated tools for analysis. | Identifiers | Training |
| 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 | Human pathogen genomics Microbial biotechnology | Standards/Databases |
| NCIMB | Hosts information relating to strains, cultures and more | Microbial biotechnology | |
| Nextcloud | As fully on-premises solution, Nextcloud Hub provides the benefits of online collaboration without the compliance and security risks | Data storage | |
| Nextflow | Nextflow is a framework for data analysis workflow execution | Data analysis | Tool info Training |
| Nextstrain | Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. | Virology | Tool info Standards/Databases Training |
| NMRlipids | Repository for lipid MD simulations to validate force fields with NMR data | Biomolecular simulatio... | Standards/Databases |
| NPDS | The National Poison Data System (NPDS) is a resource that provides poisson exposure occurring in the US and some freely associated states. | Toxicology data | |
| OHDSI | Multi-stakeholder, interdisciplinary collaborative to bring out the value of health data through large-scale analytics. All our solutions are open-source. | TransMed Toxicology data Data quality | Tool info |
| OHDSI Athena | Repository of ontologies for use with the OMOP CDM. | Health data | |
| OME Data Model and File Formats | The OME Model is a specification for storing data on biological imaging. | Machine actionability | |
| OMERO | OMERO is an open-source client-server platform for managing, visualizing and analyzing microscopy images and associated metadata | Galaxy OMERO Bioimaging data | Tool info Training |
| OmicsDI | Omics Discovery Index (OmicsDI) provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics) | Galaxy Existing data Machine actionability | Tool info Standards/Databases Training |
| Omnipy | Omnipy is a high level Python library for type-driven data wrangling and scalable workflow orchestration. | FAIRtracks | Tool info Training |
| OMOP Common Data Model | Open community standard for observational health care data obtained from health records. | Health data | Training |
| OMOP-CDM | OMOP is a common data model for the harmonisation for of observational health data. | TransMed Cancer data Data quality | |
| OncoKB | Precision oncology knowledge base that annotates the effects and treatment implications of somatic mutations in cancer. | Cancer data | |
| OnotoMaton | OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets. | Plant sciences Identifiers | |
| Ontobee | A web portal to search and visualise ontologies | Documentation and meta... | Standards/Databases Training |
| ONTOBROWSER | The OntoBrowser tool was developed to manage ontologies and code lists. | Toxicology data | Tool info |
| Ontology Lookup Service | EMBL-EBI's web portal for finding ontologies | FAIRtracks Bioimaging data Enzymology and biocata... Health data Documentation and meta... | Tool info Standards/Databases Training |
| Open Definition Conformant Licenses | Licenses that are conformant with the principles laid out in the Open Definition. | Licensing | |
| Open Funder Registry (OFR) | The Open Funder Registry (OFR) is a registry of persistent identifiers for grant-giving organisations. | Identifiers | Standards/Databases |
| Open mHealth | An open-source Clinical Interpretations platform for integrating mobile health data to improve healthcare insights. | Cancer data | Standards/Databases |
| Open Neural Network Exchange (ONNX) | ONNX is an open format built to represent machine learning models. | Machine learning | |
| Open Researcher and Contributor ID Registry (ORCID) | ORCID is an open, non-profit, community-driven registry of unique researcher identifiers and offers a transparent method of attributing outputs. | Identifiers | Tool info Standards/Databases |
| OpenAIRE Explore | Explore Open Access research outcomes from OpenAIRE network | Existing data | |
| openBIS | openBIS (open Biology Information System) is an Electronic Laboratory Notebook and a Laboratory Information Management System (ELN-LIMS) solution suitable for life science laboratories. | Enzymology and biocata... | |
| OpenEBench | ELIXIR benchmarking platform to support community-led scientific benchmarking efforts and the technical monitoring of bioinformatics reosurces | Data analysis | Tool info |
| OpenEHR | Non-profit organisation that publishes technical standards for an EHR platform along with domain‑developed clinical models to define content. | Health data | Standards/Databases |
| OpenMS | OpenMS offers an open-source C++ library (+ Python bindings) for LC/MS data management, analysis and visualization. | Proteomics | Tool info Training |
| OpenRefine | Data curation tool for working with messy data | TransMed Data quality Machine actionability | Training |
| OpenScienceFramework | free and open source project management tool that supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery | Biomolecular simulatio... Documentation and meta... | Standards/Databases |
| OpenSlide | C library that provides a simple interface to read whole-slide images (also known as virtual slides) | Bioimaging data | |
| OpenStack | OpenStack is an open source cloud computing infrastructure software project and is one of the three most active open source projects in the world | Data analysis Data storage | Training |
| Operational Data Model-XML (ODM-XML) | A CDISC Data Exchange Standard that is a vendor-neutral, platform-independent format for exchanging and archiving clinical and translational research data, along with their associated metadata, administrative data, reference data, and audit information. | Health data | |
| OSF | OSF (Open Science Framework) is a free, open platform to support your research and enable collaboration. | Data storage | Training |
| OTP | One Touch Pipeline (OTP) is a data management platform for running bioinformatics pipelines in a high-throughput setting, and for organising the resulting data and metadata. | Human data | Tool info |
| ownCloud | Cloud storage and file sharing service | Data transfer Data storage | |
| PAA | PAA is an R/Bioconductor tool for protein microarray data analysis aimed at biomarker discovery. | Proteomics | Tool info |
| Paige AI | AI solutions for digital pathology in cancer detection. | Cancer data | |
| PanDrugs | Platform to prioritise cancer drug treatments based on individual multi-omics data including SNVs, CNVs, and gene expression. | Cancer data | Tool info Standards/Databases Training |
| PANGAEA | Data Publisher for Earth and Environmental Science | Data publication | Tool info Standards/Databases Training |
| PathAI | AI-powered pathology tools for cancer diagnosis and research. | Cancer data | |
| Pathogen Detection | NCBI Pathogen Detection integrates bacterial and fungal pathogen genomic sequences from numerous ongoing surveillance and research efforts whose sources include food, environmental sources such as water or production facilities, and patient samples. Foodborne, hospital-acquired, and other clinically infectious pathogens are included. | Human pathogen genomics | Training |
| Pathogens Portal | The Pathogens Portal aims to provide access to data and tools relating to pathogens, their human and animal hosts and their vectors. Current content spans bacterial, viral and eukaryotic parasite lineages alongside human host data. | Human pathogen genomics | Standards/Databases Training |
| Pathoplexus | Pathoplexus is an open-source database designed to enhance the sharing and analysis of human viral pathogen genomic data. | Virology | Standards/Databases |
| Patient-Reported Outcomes Measurement Information System (PROMIS) | A set of person-centred measures that evaluates and monitors physical, mental, and social health in adults and children. | Cancer data | |
| PCDDB | The Protein Circular Dichroism Data Bank | Intrinsically disorder... | Tool info |
| PDB | The Protein Data Bank (PDB) | Galaxy Intrinsically disorder... Structural Bioinformatics Data publication | Tool info Training |
| PDB-Dev | Prototype archiving system for structural models obtained using integrative or hybrid modeling | Biomolecular simulatio... Structural Bioinformatics | |
| PDBe-KB | Protein Data Bank in Europe Knowledge Base | Machine actionability | Tool info Training |
| PDBx/mmCIF format and tools | Information about the standard PDB archive format PDBx/mmCIF, its dictionaries and related software tools | Structural Bioinformatics | Standards/Databases |
| PDBx/mmCIF ModelCIF Extension Dictionary | Extension of the PDBx/mmCIF dictionary for theoretical models of macromolecular structures | Structural Bioinformatics | |
| PeptideAtlas | Database of multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. | Proteomics | Tool info Standards/Databases |
| PET Response Criteria in Solid Tumors (PERCIST) | A standardised method for assessing tumor response via PET imaging. | Cancer data | |
| 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 Standards/Databases |
| Phenomenal 3D | Phenomenal-3D is an automatic open-source library for 3D shoot architecture reconstruction and analysis for image-based plant phenotyping | Plant Phenomics | Tool info |
| Phenotypic QualiTy Ontology (PATO) | PATO is an ontology of phenotypic qualities, intended for use primarily in phenotype annotation. | Human pathogen genomics | Tool info Standards/Databases |
| PHIS | The open-source Phenotyping Hybrid Information System (PHIS) manages and collects data from plants phenotyping and high throughput phenotyping experiments on a day to day basis. | Plant Phenomics | Training |
| PIA - Protein Inference Algorithms | PIA is a toolbox for mass spectrometrey based protein inference and identification analysis. | Proteomics | Tool info |
| pISA-tree | A data management solution for intra-institutional organization and structured storage of life science project-associated research data, with emphasis on the generation of adequate metadata. | Plant Phenomics | Tool info |
| Plant 3D | Plant 3D is a plant phenotyping toolkit for 3D point clouds. Plant 3D (P3D) automatically extracts common phenotyping features of interest from high-resolution 3D scans of plant architectures. | Plant Phenomics | Tool info |
| plant-miappe.json | BioSamples Plant MIAPPE checklist in JSON format | Plant sciences | |
| PlantCV | Plant Computer Vision (PlantCV)is an image processing toolkit for plant phenotyping analysis. | Plant Phenomics | Tool info |
| PLAZA | Access point for plant comparative genomics, centralizing genomic data produced by different genome sequencing initiatives. | Plant Genomics | Standards/Databases Training |
| PMut | Platform for the study of the impact of pathological mutations in protein stuctures. | Human data | Tool info |
| Podman | Manage containers, pods, and images with Podman. Seamlessly work with containers and Kubernetes from your local environment. | Data analysis | |
| Prefect | Prefect is a workflow orchestration tool empowering developers to build, observe, and react to data pipelines. | FAIRtracks | |
| PRIDE | PRoteomics IDEntifications (PRIDE) Archive database | Proteomics Data publication | Tool info Standards/Databases Training |
| PRIDE Submission Tool | Main tool used to submit proteomics datasets to PRIDE Archive | Proteomics | |
| Privacy Impact Assessment Tool (PIA) | The open source PIA software helps to carry out data protection impact assessment | Human data | Tool info |
| PROAST | PROAST (copyright RIVM National Institute for Public Health and the Environment) is a software package for the statistical analysis of dose-response data. | Toxicology data | |
| Protein MODification (PSI-MOD) | PSI-MOD is an ontology consisting of terms that describe protein chemical modifications. | Enzymology and biocata... | Standards/Databases |
| PRotein Ontology (PRO) | Protein Ontology (PRO) provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. | Enzymology and biocata... | Standards/Databases |
| ProteomeXchange | ProteomeXchange provides globally coordinated standard data submission and dissemination pipelines | Proteomics | Tool info Standards/Databases Training |
| protocols.io | A secure platform for developing and sharing reproducible methods. | Microbial biotechnology | Standards/Databases |
| PROV-DM: The PROV Data Model | PROV-DM is the conceptual data model that forms a basis for the W3C provenance (PROV) family of specifications. | Data provenance | |
| PUBLISSO | Documenting research data: Electronic Lab(oratory) Notebooks. | Documentation and meta... | |
| Pydantic | Pydantic is the most widely used data validation library for Python. | FAIRtracks | |
| PyEnzyme | PyEnzyme is a comprehensive software solution for manipulating EnzymeML files. | Enzymology and biocata... | |
| PySCeS | The Python Simulator for Cellular Systems (PySCeS) is a a flexible, user friendly tool for the analysis of cellular systems. | Enzymology and biocata... | Tool info |
| Qure.ai | AI-based medical imaging analysis for radiology and oncology. | Cancer data | Tool info |
| R Markdown | R Markdown documents are fully reproducible. Use a productive notebook interface to weave together narrative text and code to produce elegantly formatted output. Use multiple languages including R, Python, and SQL. | Data storage | Training |
| raw2ometiff | Java application to convert a directory of tiles to an OME-TIFF pyramid. This is the second half of iSyntax/.mrxs => OME-TIFF conversion. | Bioimaging data | |
| RD-Connect Genome Phenome Analysis Platform | The RD-Connect GPAP is an online tool for diagnosis and gene discovery in rare disease research. | Human data | Tool info Training |
| RDA Standards | Directory of standard metadata, divided into different research areas | Data discoverability Data provenance Documentation and meta... | |
| re3data | Registry of Research Data Repositories | Data discoverability Data publication Existing data Licensing | Training |
| REACH registered substances | Portal with public data submitted to ECHA in REACH registration dossiers by substance manufacturers, importers, or their representatives, as laid out by the REACH Regulation (see Understanding REACH regulation). | Toxicology data | |
| Real World Data for Clinical Research (Vulcan) | A minimal set of clinical research FHIR resources and elements in an EHR that can be utilised in an interoperable and consistent manner for clinical research. | Health data | Tool info |
| Recherche Data Gouv | An ecosystem for sharing and opening research data | Plant sciences | Standards/Databases |
| REDCap | REDCap is a secure web application for building and managing online surveys and databases. While REDCap can be used to collect virtually any type of data in any environment, it is specifically geared to support online and offline data capture for research studies and operations. | TransMed Cancer data Health data Data quality Identifiers | Tool info Training |
| REDCap Cloud | A fully managed REDCap system based in the cloud, provided by nPhase. | Health data | |
| REDIportal | Database of A-to-I (deamination of adenosines to inosines) events that enables to search RNA editing sites by genomic region, gene name and other relevant features as the tissue of origin. | Epitranscriptome data | Tool info |
| REDItools | Python scripts to detect RNA editing events in RNAseq experiments | Epitranscriptome data | Tool info |
| REDItools2 | REDItools2 is the optimized, parallel multi-node version of REDItools. | Epitranscriptome data | |
| REMS | REMS (Resource Entitlement Management System), developed by CSC, is a tool that can be used to manage researchers’ access rights to datasets. | TransMed | Tool info Training |
| Renamer4Mac | File renaming software for Mac | Data organisation | |
| Repository Finder | Repository Finder can help you find an appropriate repository to deposit your research data. The tool is hosted by DataCite and queries the re3data registry of research data repositories. | Data publication | |
| Research Data Management Organiser | Supports the systematic planning, organisation and implementation of research data management throughout the course of a project | Data management plan | |
| Research Data Management Platform (RDMP) | Data management platform for automated loading, storage, linkage and provision of data sets | Data storage | Tool info |
| Research Management Plan | Machine actionable DMPs. | Data management plan | |
| Research Object Crate (RO-Crate) | RO-Crate is a lightweight approach to packaging research data with their metadata, using 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. | Galaxy Microbial biotechnology Data provenance | Standards/Databases |
| Research Organization Registry (ROR) | The Research Organization Registry (ROR) is a project developing open unique identifiers for research organisations. | Identifiers | Standards/Databases |
| Reva | Reva connects cloud storages and application providers | Data transfer | Tool info Training |
| Rightfield | RightField is an open-source tool for adding ontology term selection to Excel spreadsheets | Microbial biotechnology Plant sciences Identifiers | Tool info |
| RRI self reflection tool | The Self-Reflection Tool provides questions and statements addressing all stakeholder groups (policy makers, education representatives, civil society organisations, industry and business, and the research community). | Ethical aspects | |
| RRI Toolkit | The RRI Toolkit helps stakeholders across Europe put Responsible Research and Innovation into practice. | Ethical aspects | |
| Rstudio | Rstudio notebooks allow to share code, documentation | Data analysis | Tool info Training |
| Rucio | Rucio - Scientific Data Management | Data transfer Data storage | |
| RxNorm | RxNorm is a normalized naming system for medications that is maintained by the National Library of Medicine. Rxnorm provides unique identifiers and allows unambiguous communication of drug-related information across the American health computer systems. | Health data Toxicology data | Tool info Standards/Databases |
| SABIO-RK | SABIO-RK is a curated database that contains information about biochemical reactions, their kinetic rate equations with parameters and experimental conditions. | Enzymology and biocata... | Tool info Standards/Databases |
| salDB | SalDB is a salmon specific database of genome sequenced prokaryotes representing the microbiota of fishes found in the taxonomic family of Salmonidae. | Marine Metagenomics | |
| SASBDB | Small Angle Scattering Biological Data Bank | Intrinsically disorder... | |
| SBGrid Data Bank | Repository of X-ray diffraction, MicroED, LLSM datasets, as well as structural models. | Structural Bioinformatics | |
| SBOL Visual | A standard library of visual glyphs used to represent SBOL designs and interactions. | Microbial biotechnology | |
| SBOLDesigner | A CAD tool to create SBOL designs through the use of SBOL Visual glyphs. | Microbial biotechnology | |
| Scanpy | Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. | Single-cell sequencing | Tool info Training |
| Scater | Scater offers a collection of tools for analysis (such as quality control) for single-cell gene expression data. | Single-cell sequencing | Tool info Training |
| SCEasy | sceasy is a package that helps easy conversion of different single-cell data formats to each other. | Single-cell sequencing | Tool info |
| 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. | Enzymology and biocata... Machine learning Machine actionability | Standards/Databases Training |
| ScienceMesh | ScienceMesh - frictionless scientific collaboration and access to research services | Data transfer Data storage | |
| Scientific Data's Recommended Repositories | List of respositories recommended by Scientific Data, contains both discipline-specific and general repositories. | Existing data | |
| scikit-learn | scikit-learn is a free software machine learning library for the Python programming language. | Machine learning | Tool info Training |
| Scipion | Cryo em image processing framework. Integration, traceability and analysis. | Structural Bioinformatics | Tool info Standards/Databases |
| ScipionCloud | Cloud virtual machine with the Scipion software to process EM imaging data either in a single server or in a cluster. | Structural Bioinformatics | |
| SDRF | Information about a proposed standard for sample metadata annotations in public repositories called Sample and Data Relationship File (SDRF)-Proteomics format. | Proteomics | |
| SeaFile | SeaFile File Synchronization and Share Solution | Data transfer Data storage | |
| Semantic data model of the set of common data elements for rare diseases registration | A semantic data model describing the common data elements for rare diseases registration. | Rare disease data | |
| Semares | All-in-one platform for life science data management, semantic data integration, data analysis and visualization | Data discoverability Documentation and meta... Data storage | |
| Sequence Read Archive | Sequence Read Archive (SRA) data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequencing data. | Cancer data Single-cell sequencing | Standards/Databases Training |
| Set of common data elements for rare diseases registration | Contains 16 data elements to be registered by each rare disease registry across Europe, which are considered to be essential for further research. | Rare disease data | |
| Seurat | Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. | Single-cell sequencing | Tool info Training |
| ShortBOL | A scripting language for creating Synthetic Biology Open Language (SBOL) in a more abstract way. | Microbial biotechnology | |
| SIDER | Side Effect Resource containing information on marketed medicines and their recorded adverse drug reactions. | Cancer data | Tool info |
| SIFTS | Structure integration with function, taxonomy and sequence | Intrinsically disorder... | |
| Single Cell Portal | Interactive portal for single-cell genomics data. | Single-cell sequencing | |
| Single-cell best pratices | An entry point for novices in the field of single-cell (multi-)omic analysis and guides advanced users to the most recent best practices. | Single-cell sequencing | |
| SingleCellExperiment | The SingleCellExperiment class is a lightweight Bioconductor container for storing and manipulating single-cell genomics data. | Single-cell sequencing | Tool info |
| Singularity | Singularity is a container platform. | Data analysis | Training |
| Skyline | Freely-available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), DIA/SWATH and targeted DDA quantitative methods and analyzing the resulting mass spectrometer data. | Proteomics | Tool info |
| SMASCH | SMASCH (Smart Scheduling) system, is a web-based tooldesigned for longitudinal clinical studies requiring recurrent follow-upvisits of the participants. SMASCH controls and simplifies the scheduling of big database of patients. Smasch is also used to organize the daily plannings (delegation of tasks) for the different medical professionals such as doctors, nurses and neuropsychologists. | TransMed Health data | |
| Snakemake | Snakemake is a framework for data analysis workflow execution | Data analysis | Tool info Training |
| SPIDER pseudonymisation tool | ERDRI.spider (Secure Privacy-preserving Identity management in Distributed Environments for Research) pseudonymisation tool generates pseudonyms for RD patients. | Rare disease data | |
| SSBD:database | Added-value database for biological dynamics images | Bioimaging data | Standards/Databases |
| SSBD:repository | An open data archive that stores and publishes bioimaging and biological quantitative datasets | Bioimaging data | |
| Standards for Reporting Enzyme Data (STRENDA) | Resource of standards for reporting enzyme data | Enzymology and biocata... Microbial biotechnology | Standards/Databases |
| STARsolo | A comprehensive turnkey solution for quantifying gene expression in single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR. | Single-cell sequencing | Training |
| STRENDA DB | STRENDA DB is a storage and search platform that incorporates the STRENDA Guidelines in a user-friendly, web-based system. | Enzymology and biocata... | Standards/Databases |
| STRING | Known and predicted protein-protein interactions. | Proteomics | Tool info Standards/Databases Training |
| Study Data Tabulation Model (SDTM) | A CDISC Foundational Standard that provides a standard for organizing and formatting data to streamline processes in collection, management, analysis and reporting. | Health data | |
| SynBioHub | A searchable design repository for biological constructs | Microbial biotechnology | Tool info Standards/Databases |
| Synthetic Biology Open Language (SBOL) | An open standard for the representation of in silico biological designs and their place in the Design-Build-Test-Learn cycle of synthetic biology. | Microbial biotechnology | Tool info |
| Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT) | Terminology standard consisting of codes, terms, synonyms and definitions used in clinical documentation and reporting. | Cancer data Health data | |
| Systems Biology Markup Language (SBML) | An open format for computational models of biological processes | Enzymology and biocata... Microbial biotechnology | Tool info |
| T3DB | The Toxin and Toxin Target Database is a bioinformatics resource that combines exhaustive toxin data with toxin target information. Currently it presents more than 42,000 toxin-target associations extracted from other databases, government documents, books and scientific literature. Each toxin record includes data on chemical properties and descriptors, toxicity values and medical information. | Toxicology data | Tool info |
| Talend | Talend is an open source data integration platform. | TransMed | |
| Tensorflow | A free and open-source software library for machine learning and artificial intelligence. | Machine learning | Tool info Training |
| TG-GATES | A toxicogenomics database that stores gene expression data and biochemistry, hematology, and histopathology findings derived from in vivo (rat) and in vitro (primary rat hepatocytes, primary human hepatocytes) exposure to 170 compounds at multiple dosages and time points. | Toxicology data | Tool info |
| The Cancer Imaging Archive (TCIA) | A repository of medical images related to cancer. | Cancer data | Standards/Databases |
| The Environment Ontology (EnvO) | An ontology for expressing environmental terms | Microbial biotechnology | |
| The European Genome-phenome Archive (EGA) | EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects | CSC TSD Cancer data Human data Virology Data publication | Tool info Standards/Databases Training |
| The Open Biological and Biomedical Ontology (OBO) Foundry | Collaborative effort to develob interoperable ontologies for the biological sciences | Documentation and meta... | Standards/Databases |
| Therapeutic Target Database (TTD) | Database of known and explored therapeutic targets and their related drugs. | Cancer data | Tool info |
| TopEnzyme | TopEnzyme is a framework and database for structural coverage of the functional enzyme space. | Enzymology and biocata... | Tool info |
| Tox21_Toolbox | The Toxicology in the 21st Century program, or Tox21, is a unique collaboration between several federal agencies to develop new ways to rapidly test whether substances adversely affect human health. The Tox21 Toolbox contains data-analysis tools for accessing and visualizing Tox21 quantitative high-throughput screening (qHTS) 10K library data, as well as integrating with other publicly available data. | Toxicology data | |
| ToxCast_data | The Toxicology in the 21st Century program, or Tox21, is a unique collaboration between several federal agencies to develop new ways to rapidly test whether substances adversely affect human health. This portal contains diverse downloadable results of the ToxCast project. | Toxicology data | |
| Track Hub Registry | A global centralised collection of publicly accessible track hubs | FAIRtracks | Standards/Databases |
| TrackFind | TrackFind is a search and curation engine for metadata of geneomic tracks. It supports crawling of the TrackHub Registry and other portals. | FAIRtracks | Tool info |
| tranSMART | Knowledge management and high-content analysis platform enabling analysis of integrated data for the purposes of hypothesis generation, hypothesis validation, and cohort discovery in translational research. | TransMed Data storage | Tool info |
| Transparent Reporting of a Multivariable Prediction Model | Guidelines for reporting predictive model studies in medicine. | Cancer data | Standards/Databases |
| Tryggve ELSI Checklist | A list of Ethical, Legal, and Societal Implications (ELSI) to consider for research projects on human subjects | NeLS TSD Human data GDPR compliance | |
| TU Delft data management costing tool | TU Delft costing tool helps to budget for data management personnel costs in proposals. | Costs of data management | |
| Tumour, Nodes, Metastases (TNM) cancer staging system | A cancer staging system that describes the size of the tumor (T), lymph node involvement (N), and metastasis (M). | Cancer data | |
| TXG-MAPr | A tool that contains weighted gene co-expression networks obtained from the Primary Human Hepatocytes, rat kidney, and liver TG-GATEs dataset. | Toxicology data | Tool info |
| UBER anatomy ONtology (UBERON) | Uberon is an integrated cross-species anatomy ontology covering animals and bridging multiple species-specific ontologies. | Human pathogen genomics | Standards/Databases |
| udocker | udocker is a basic user tool to execute simple docker containers in user space without requiring root privileges. | Data analysis | |
| UK Biobank | Large-scale biomedical database with genetic, clinical, and lifestyle data from UK participants. | Cancer data | Tool info Training |
| UK Data Service Data Management costing Tool | UK Data Service activity-based costing tool. | Costs of data management | |
| UMLS | The Unified Medical Language System (UMLS) is a set of tools that establishes a mapping structure among different vocabularies in the biomedical sciences field to enable interoperativity between computer systems. | Toxicology data | |
| UniChem | UniChem is a very simple, large-scale non-redundant database of pointers between chemical structures and EMBL-EBI chemistry resources. Primarily, this service has been designed to maintain cross references between EBI chemistry resources. These include primary chemistry resources (ChEMBL and ChEBI), and other resources where the main focus is not small molecules, but which may nevertheless contain some small molecule information (eg: Gene Expression Atlas, PDBe). | Toxicology data | Training |
| Unimod | Protein modification for mass spectrometry | Proteomics | Tool info Standards/Databases |
| UniProt | Comprehensive resource for protein sequence and annotation data | Galaxy Enzymology and biocata... Intrinsically disorder... Proteomics Single-cell sequencing Structural Bioinformatics Machine actionability | Tool info Standards/Databases Training |
| University of Cambridge - Electronic Research Notebook Products | List of Electronic Research Notebook Products by University of Cambridge | Identifiers Documentation and meta... | |
| Variant Call Format (VCF) | A common file format that contains information about variants found at specific positions in a reference genome. | Cancer data | Standards/Databases |
| VisBOL | A JavaScript library for the visualisation of SBOL. | Microbial biotechnology | |
| Volumes | Volumes are the preferred mechanism for persisting data generated by and used by Docker containers. | Data analysis | Training |
| WAYFIND-R | A federated real-world evidence platform containing clinical and genomic data from patients with solid tumours. | Cancer data | |
| Wellcome Open Research - Data Guidelines | Wellcome Open Research requires that the source data underlying the results are made available as soon as an article is published. This page provides information about data you need to include, where your data can be stored, and how your data should be presented. | Data publication | Standards/Databases |
| WHO Classification of Tumours | The standard for diagnostic oncology, defining tumor types and classifications. | Cancer data | |
| Windows Package Manager | Windows Package Manager is a comprehensive package manager solution that consists of a command line tool and set of services for installing applications on Windows 10 and Windows 11. | Data analysis | |
| WinSCP | WinSCP is a popular SFTP client and FTP client for Microsoft Windows! Copy file between a local computer and remote servers using FTP, FTPS, SCP, SFTP, WebDAV or S3 file transfer protocols. | Data transfer | |
| WorkflowHub | WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows. | Galaxy Data analysis Data provenance | Tool info Standards/Databases Training |
| XNAT | Open source imaging informatics platform. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data. | TransMed XNAT-PIC Bioimaging data Cancer data | |
| XNAT-PIC Pipelines | Analysing of single or multiple subjects within the same project in XNAT | XNAT-PIC | |
| XNAT-PIC Uploader | Import tool for multimodal DICOM image datasets to XNAT | XNAT-PIC | |
| Zenodo | Generalist research data repository built and developed by OpenAIRE and CERN | FAIRtracks Plant Phenomics Bioimaging data Biomolecular simulatio... Enzymology and biocata... Plant sciences Single-cell sequencing Data publication Identifiers | Standards/Databases Training |
| Zooma | Find possible ontology mappings for free text terms in the ZOOMA repository. | Bioimaging data | Tool info Training |
| Zotero | Free and open-source reference management software to manage bibliographic data and related research materials. | ||
| RDM Guide | RDM Guide describes Belgian data management guidelines, resources, tools and services available for researchers in Life Sciences. |
Researcher Data Steward | |
| 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 | |
| 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 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 Phenomics Plant sciences Data Steward Researcher Research Software Engi... | Tool info |
| 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 Researcher Research Software Engi... 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 Software Engi... Data analysis Data storage | |
| OLOS | OLOS is a Swiss-based data management portal, to help Swiss researchers safely manage, publish and preserve their data. |
Data storage Data publication | |
| SWISSUbase | SWISSUbase is a national cross-disciplinary solution for Swiss universities and other research organizations in need of local institutional data repositories for their researchers. The platform relies on international archiving standards and processes to ensure that data are preserved and accessible in the long-term. |
Data storage Data publication | |
| OpenRDM.swiss | openRDM.swiss offers research data management as a service to the scientific community, based on the powerful openBIS platform. |
Data analysis | |
| Renku | An open-source knowledge infrastructure for collaborative and reproducible data science. |
Data analysis | |
| BioMedIT | A secure IT network for the responsible processing of health-related data. |
Human data Data analysis Data sensitivity | |
| Swiss Pathogen Surveillance Platform (SPSP) | A secure One-health online platform that enables near real-time sharing under controlled access of pathogen whole genome sequences (WGS) and their associated clinical/epidemiological metadata. Since 20221 it has centralized and processed all SARS-CoV-2 sequencing data within the national genomic surveillance program. |
COVID-19 Data Portal Existing data | |
| DORA | Digit Object Repository at the Libr4RI (4 ETH Domain Research Institutes, that are EAWAG, EMPA, PSI, WSL). |
Data publication | |
| UNIL DMP Online | This instance of DMPonline is provided by the Service des ressources informationnelles et archives (UNIRIS) of the University of Lausanne (UNIL) to help its community of researchers to write a Data Management Plan (DMP).
DMPonline
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Data management plan | |
| SIB/Vital-IT Canvas Generator | This is a tool to help scientists generate data management plans for SNSF -unded projects. The Word document produced complies with the SNSF instructions for creating DMPs. |
Data management plan | |
| Galaxy MetaCentrum | Galaxy MetaCentrum is a Galaxy instance managed by the Czech ELIXIR node and e-INFRA. It provides extra support for RepeatExplorer tool for plant genomic analysis.
Galaxy
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Researcher Data analysis | Tool info |
| e-INFRA CZ (Supercomputing and Data Services) | e-INFRA CZ provides integrated high-performance research computing/data storage environment, providing world-class services to government, industry, and researchers. It also cooperates with European Open Science Cloud (EOSC) implementation in the Czech Republic. |
Data Steward Research Software Engi... Data analysis Data storage | |
| ownCloud@CESNET | CESNET-hosted ownCloud is a 100 GB cloud storage freely available for Czech scientists to manage their data from any research projects.
ownCloud
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Researcher Research Software Engi... Data storage Data organisation | |
| Czech National Repository | National Repository (NR) is a service provided to the scientific and research communities in the Czech Republic to store their generated research data together with persistent DOI identifier. NR service is currently under the pilot program. |
Researcher Data Steward Research Software Engi... Data storage Existing data Identifiers Data management plan | |
| ELN Finder | Electronic Laboratory Notebook (ELN) selection service. |
Documentation and meta... Researcher Research Software Engi... | |
| ELN Guide | Guide for Electronic Laboratory Notebooks (ELN). |
Documentation and meta... Researcher Research Software Engi... | |
| ELN Video Tutorials | Video Tutorials for Electronic Laboratory Notebooks (ELN). |
Documentation and meta... Researcher Research Software Engi... | |
| GFBio Data Management Plan Tool | DMP creation and support by German Federation for Biological Data (GFBio). |
Data management plan | |
| GHGA | The German Human Genome-Phenome Archive. |
Data storage Documentation and meta... Researcher Data Steward | |
| PUBLISSO | Open access publishing platform for life sciences. |
Data publication Researcher Data Steward | |
| 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 | |
| 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 Software Engi... | |
| RedIRIS | Spanish academic and research network that provides advanced communication services to the scientific community and national universities. |
Researcher Data Steward Research Software Engi... | |
| 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 Software Engi... | |
| 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 Software Engi... | |
| 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 Research Software Engi... Data analysis | |
| DMPTuuli | Data management planning tool (Finland).
DMPRoadmap
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CSC Researcher Data Steward 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 Data storage Data publication Existing data | |
| Federated EGA Finland | FEGA allows you to store and share sensitive data in Finland in a way that fulfils all the requirements of the General Data Protection Regulation (GDPR).
The European Genome-phenome Archive (EGA)
|
CSC Researcher Data Steward Data sensitivity 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 Data sensitivity 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 Data sensitivity 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 Data sensitivity 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 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 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 Data management plan | |
| HYPATIA - Cloud Infrastructure for ELIXIR Greece | HYPATIA is a cloud-based infrastructure that has been developed to support the computational needs of the ELIXIR Greece community and the wider life sciences community including researchers and institutions in Greece and internationally. |
Data analysis Data storage Data transfer | |
| National instance of Genomic Data Infrastructure for ELIXIR Greece | An instance of the Genomic Data Infrastructure GDI on ELIXIR Greece, for secure genomic data management, including storage, discovery, access, and reception. This is a pilot instance based on the GDI Starter Kit. |
Human data Data sensitivity Data publication Existing data | |
| Greek COVID-19 Portal | Provides information, guidelines, tools and services to support researchers to utilise Greek and European infrastructures for data sharing. The portal is a national node of the European COVID-19 Data Portal.
COVID-19 Data Portal
|
COVID-19 Data Portal | |
| Open-science.it | Italian portal dedicated to the field of open science. |
Data Steward Researcher Data management plan | |
| learning.DSW | A training instance of Data Steward Wizard (DSW), which has the FNR and the DPIA templates.
Data Stewardship Wizard
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Data management plan | |
| DPMRoadmap @ ELIXIR Luxembourg | This instance of DMPOnline is provided by ELIXIR Luxembourg and has FNR template for Data Management Plan (DMP).
DMPRoadmap
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Data management plan | |
| Luxembourg Covid-19 data portal | The Luxembourgish COVID-19 Data Portal acts as a collection of links and provides information to support researchers to utilise Luxembourgish and European infrastructures for data sharing. |
COVID-19 Data Portal Data sensitivity | |
| Health-RI Service Catalogue | Health-RI provides a set of tools and services available to the biomedical research community. |
Human data Researcher Data analysis Existing data Data storage | |
| BBMRI catalogue | Biobanking Netherlands makes biosamples, images and data findable, accessible and usable for health research. |
Human data Researcher Data analysis Existing data Data storage | |
| cBioPortal for Cancer Genomics | cBioPortal provides a web-based resource for researchers to explore, visualize, analyze, and share multidimensional cancer genomic datasets, as well as other studies involving multidimensional genomic data. |
Human data Researcher Data analysis Existing data Data storage | |
| CBS, Statistics Netherlands | The national statistical office, Statistics Netherlands (CBS), provides reliable statistical information and data in the life sciences and health domain. |
Human data Researcher Existing data | |
| Technology Hotels | More than 130 Technology Hotels offer access to high-end technology and expertise in the field of bioimaging, bioinformatics, genomics, medical imaging, metabolomics, phenotyping, proteomics, structural biology, and/or systems biology. |
Human data Bioimaging data Proteomics Researcher Compliance monitoring ... | |
| Dutch COVID-19 Data Support Programme | To support investigators and health care professionals with tools and services in their search for ways to overcome the pandemic and its health consequences. |
Human data Researcher Existing data | |
| RIVM Health and Healthcare Data | The Dutch National Institute for Public Health and the Environment (RIVM), together with other organisations, provides numbers and explanation on relevant topics, to prevent duplication of data collection. |
Human data Researcher Existing data | |
| Handbook for Adequate Natural Data Stewardship | Guidelines on data stewardship and practical toolbox for researchers at Dutch University Medical Centres (UMCs). |
Human data Researcher Data management plan Compliance monitoring ... | |
| 23 Things for Research Data Management tool | Shared reference tool for knowledge on data management. |
Human data Data management plan Compliance monitoring ... | |
| FAIR-Aware | Online tool which helps researchers and data managers assess how much they know about the requirements for making datasets findable, accessible, interoperable, and reusable (FAIR) before uploading them into a data repository. |
Researcher Data management plan Compliance monitoring ... Data publication | |
| Feide | Feide is the national solution for secure login and data exchange in education and research. Feide can be linked with Life Science Login (LS Login) through eduGAIN. |
TSD NeLS Marine Metagenomics | |
| DS-Wizard ELIXIR-Norway | DS-Wizard is a tool to aid the creation, organisation 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 (SIKT). |
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 | |
| 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 Data sensitivity Existing data Data publication COVID-19 Data Portal | |
| Federated EGA Norway node | 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 Data sensitivity 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 Data sensitivity 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 operated by Sigma2 NRIS, which is a joint collaboration between UiO, UiB, NTNU, UiT, and UNINETT Sigma2. |
Data transfer Data storage NeLS FAIRtracks | |
| 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 (SIKT). |
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 Data sensitivity 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 Data sensitivity 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 and lab management. It 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 Data sensitivity Data storage | |
| SAFE | SAFE (secure access to research data and e-infrastructure) is the solution for the secure processing of sensitive personal data in research at the University of Bergen. SAFE is based on the “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 Data sensitivity Data storage | |
| RETTE | System for Risk and compliance. Processing of personal data in research and student projects at UiB. |
Human data Data security GDPR compliance Data sensitivity Policy maker Data Steward | |
| DataverseNO | DataverseNO is a national, generic repository for open research data. Various Norwegian research institutions have established partner agreements about using DataverseNO as institutional repositories for open research data.
DATAVERSE
|
Data publication | |
| openscience.no | General information about open research, especially open access and guidance for researchers and institutions. |
||
| Nettskjema | Nettskjema is a solution for designing and managing data collections using online forms and surveys. It can be used for collecting sensitive data and offers a high degree of security and privacy. |
Data sensitivity TSD | |
| 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
|
Researcher Data Steward Data storage | Tool info Standards/Databases |
| BioData.pt Data Stewardship Wizard | This tool guides users through generating Data Management Plans.
Data Stewardship Wizard
|
Researcher Data Steward Data management plan | Tool info |
| 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. |
Researcher Data management plan Project data managemen... | |
| eLab BioData.pt | An electronic lab notebook (ELN) for BioData.pt training programmes (data wiped periodically). |
Researcher Data Steward Principal Investigator... Documentation and meta... Data quality Project data managemen... Data provenance Machine actionability | |
| INDEXAR | National directory of repositories and digital scientific journals, in the fields of science and culture. |
Researcher Data Steward Data publication Existing data | |
| dados.gov.pt | Open data portal of the Portuguese Public Administration. |
Researcher Data Steward Data publication Existing data | |
| 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
|
Data management plan | |
| SciLifeLab Data Repository (Figshare) | A repository for publishing any kind of research-related data, e.g. documents, figures, or presentations.
FigShare
|
Existing data Data publication | |
| NBIS Data Management Consultation | Free consultation service regarding data management questions in life science research. |
Data management plan Data publication Data sensitivity | |
| Swedish Pathogens Portal | The Swedish Pathogens 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 Data sensitivity Existing data Data publication | |
| NAISS | The National Academic Infrastructure for Supercomputing in Sweden (NAISS) 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 RDM Guidelines | Knowledge hub for the management of life science research data in Sweden. |
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| Human Data Guidelines | Guidelines as well as further information on legal considerations when working with human biomedical data. |
Human data Data sensitivity | |
| Federated EGA Sweden node | Secure archiving and sharing of genetic and phenotypic data resulting from Swedish biomedical research projects.
The European Genome-phenome Archive (EGA)
|
Human data Data sensitivity Existing data Data publication | |
| DS Wizard ELIXIR Slovenia | Publicly available online tool for composing smart data management plans.
Data Stewardship Wizard
|
Data management plan | |
| ELIXIR eLearning Platform | Learning Management System. |
||
| 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
|
Data Steward Researcher Data management plan | |
| CyVerse UK | The CyVerse Data Store is a cloud-based storage space, accessible via the CyVerse Discovery Environment (DE), a virtual bioinformatics lab workbench, and developer APIs such as the AGAVE API. In the DE, users can share datasets and tools to analyse data with as many or as few people as they wish. |
Data Steward Researcher Documentation and meta... | |
| Jisc Research data management toolkit | Guidance on the research data lifecycle that signposts resources from a wide range of organisations and websites. |
Data Steward Researcher Documentation and meta... | |
| Agrischema | Linked data schemas for the fields of agriculture, food, agri-business, plant biology. |
Data Steward Researcher Documentation and meta... | |
| InterMine | InterMine integrates heterogenous data sources, making it easy to query and analyse data. |
Data Steward Researcher Documentation and meta... |