Resource List
List all resources, or create a new resource.
GET /api/t/?format=api&maturity=Mature
{ "count": 3560, "next": "?page=2", "previous": null, "list": [ { "name": "Genetic and Genomic Information System (GnpIS)", "description": "GnpIS is an integrative and multi-species information system dedicated to plants, including forest trees. It handles various types of data, focusing on genetic resources and phenomics. It allows researchers from the Plant community to access and cross-reference genetic data (accessions, phenotypes, polymorphisms, markers and QTLs) and genomic data (sequences, physical maps, genome annotations) for species of agronomic and forestry interest.\nAccessible via a public web portal, GnpIS enables different types of data to be managed, browsed and retrieved via specialized search tools and web services.\nGnpIS is used by the French National Research Institute for Agriculture, Food and Environment (INRAE) and its partners in major national and international projects.", "homepage": "https://urgi.versailles.inrae.fr/gnpis", "biotoolsID": "gnpis", "biotoolsCURIE": "biotools:gnpis", "version": [ "20.2.1" ], "otherID": [ { "value": "doi:10.25504/FAIRsharing.dw22y3", "type": "doi", "version": null } ], "relation": [ { "biotoolsID": "faidare", "type": "uses" }, { "biotoolsID": "wheatis", "type": "uses" }, { "biotoolsID": "wheatmine", "type": "includes" }, { "biotoolsID": "oakmine", "type": "includes" }, { "biotoolsID": "repetdb", "type": "includes" }, { "biotoolsID": "grapemine", "type": "includes" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3208", "term": "Genome visualisation" }, { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" }, { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3559", "term": "Ontology visualisation" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2353", "term": "Ontology data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0920", "term": "Genotype/phenotype report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "JavaScript", "Java" ], "license": "BSD-3-Clause", "collectionID": [ "elixir-fr-sdp-2019", "Animal and Crop Genomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://forge.inrae.fr/urgi/is/gnpis", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://urgi.versailles.inrae.fr/Data-Services/Data-Access/GnpIS", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/database/bat058", "pmid": "23959375", "pmcid": "PMC3746681", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "GnpIS: An information system to integrate genetic and genomic data from plants and fungi", "abstract": "", "date": "2013-12-01T00:00:00Z", "citationCount": 43, "authors": [], "journal": "Database" } }, { "doi": "10.1007/978-1-4939-6658-5_5", "pmid": "27987166", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Mining plant genomic and genetic data using the gnpis information system", "abstract": "", "date": "2017-01-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Methods in Molecular Biology" } }, { "doi": "10.1038/hortres.2016.56", "pmid": "27917288", "pmcid": "PMC5120350", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Towards an open grapevine information system", "abstract": "", "date": "2016-11-23T00:00:00Z", "citationCount": 38, "authors": [], "journal": "Horticulture Research" } }, { "doi": "10.3835/plantgenome2015.06.0038", "pmid": "27898761", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "TransPLANT resources for triticeae genomic data", "abstract": "", "date": "2016-03-01T00:00:00Z", "citationCount": 6, "authors": [], "journal": "Plant Genome" } }, { "doi": "10.1186/s13059-018-1491-4", "pmid": "30115101", "pmcid": "PMC6097284", "type": [], "version": null, "note": null, "metadata": { "title": "Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data", "abstract": "", "date": "2018-08-17T00:00:00Z", "citationCount": 205, "authors": [], "journal": "Genome Biology" } }, { "doi": "10.34133/2019/1671403", "pmid": "33313522", "pmcid": "PMC7718628", "type": [], "version": null, "note": null, "metadata": { "title": "Applying FAIR principles to plant phenotypic data management in GnpIS", "abstract": "", "date": "2019-01-01T00:00:00Z", "citationCount": 43, "authors": [], "journal": "Plant Phenomics" } } ], "credit": [ { "name": "URGI helpdesk", "email": "urgi-support@inrae.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "cpommier", "additionDate": "2017-03-23T14:24:24Z", "lastUpdate": "2025-12-19T17:15:16.754031Z", "editPermission": { "type": "group", "authors": [ "urgi-contact", "animalandcropgenomics", "nfrancillon", "cmichotey" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Data Integration Quality Check Tool (DIQCT)", "description": "A tool that checks the clinical metadata quality (validity, completeness), the integrity between images and clinical metadata provided as well as their accuracy, the de-identification protocol applied, and existence of annotation together with the consistency between the images and the annotation files and informs the user on corrective actions prior to data upload.", "homepage": "https://www.mdpi.com/2939712", "biotoolsID": "data_integration_quality_check_tool_diqct", "biotoolsCURIE": "biotools:data_integration_quality_check_tool_diqct", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Desktop application", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R", "Python" ], "license": "Proprietary", "collectionID": [ "eucaim" ], "maturity": "Mature", "cost": "Commercial", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/1b_5-pf94_QeOZVT2wVdG1YpWkAiTskwa/edit?usp=sharing&ouid=106267739460923945711&rtpof=true&sd=true", "type": [ "Other" ], "note": null }, { "url": "https://docs.google.com/document/d/1EnkkmFOGAo-WhPwx3OQ8vxSb3FKFn4b-/edit?usp=sharing&ouid=106267739460923945711&rtpof=true&sd=true", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.3390/info15090533", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Toward Ensuring Data Quality in Multi-Site Cancer Imaging Repositories", "abstract": "", "date": "2024-09-01T00:00:00Z", "citationCount": 7, "authors": [], "journal": "Information (Switzerland)" } }, { "doi": "10.1109/EMBC48229.2022.9871018", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Data Quality Check in Cancer Imaging Research: Deploying and Evaluating the DIQCT Tool", "abstract": "", "date": "2022-01-01T00:00:00Z", "citationCount": 5, "authors": [], "journal": "Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS" } } ], "credit": [ { "name": "Ioanna Chouvarda", "email": "ioannach@auth.gr", "url": null, "orcidid": "https://orcid.org/0000-0001-8915-6658", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "authEucaim", "additionDate": "2025-05-16T09:56:39.880752Z", "lastUpdate": "2025-12-19T16:12:53.819165Z", "editPermission": { "type": "group", "authors": [ "dimfilos" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "D-GENIES", "description": "D-GENIES – for Dot plot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualization.", "homepage": "https://dgenies.toulouse.inrae.fr/", "biotoolsID": "d-genies", "biotoolsCURIE": "biotools:d-genies", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3182", "term": "Genome alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2161", "term": "Sequence similarity plot" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0490", "term": "Dot plot plotting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2161", "term": "Sequence similarity plot" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python", "Shell" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/genotoul-bioinfo/dgenies", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://dgenies.readthedocs.io/en/latest/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.7717/peerj.4958", "pmid": "29888139", "pmcid": "PMC5991294", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "D-GENIES: Dot plot large genomes in an interactive, efficient and simple way", "abstract": "", "date": "2018-01-01T00:00:00Z", "citationCount": 493, "authors": [], "journal": "PeerJ" } } ], "credit": [ { "name": "Floréal Cabanettes", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Christophe Klopp", "email": "christophe.klopp@inrae.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-7126-5477", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Philippe Bordron", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-1975-0920", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Vincent Dominguez", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "GenoToul bioinformatics facility", "email": null, "url": "http://bioinfo.genotoul.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-07-29T10:31:55Z", "lastUpdate": "2025-12-18T10:02:18.098079Z", "editPermission": { "type": "group", "authors": [ "pbordron" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MicroMiner", "description": "MicroMiner assists in identifying single-residue substitutions in protein structure databases. It searches protein residue environments with local sequence and structural similarity based on the SIENA methodology. Users can search for structural mutation in the entire PDB, their in-house structure collection, or (subsets of) the AlphaFold Database. They can use the method to explore the mutation landscape of proteins with experimental or predicted structures. MicroMiner can be applied to single domains or even protein-protein or protein-ligand interfaces. Several filter options to simplify downstream analysis are available.", "homepage": "https://www.zbh.uni-hamburg.de/en/forschung/amd/software/microminer.html", "biotoolsID": "microminer", "biotoolsCURIE": "biotools:microminer", "version": [], "otherID": [], "relation": [ { "biotoolsID": "siena", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0360", "term": "Structural similarity search" }, { "uri": "http://edamontology.org/operation_0509", "term": "Local structure alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1479", "term": "Structure alignment (pair)" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "Other", "collectionID": [ "de.NBI", "de.NBI-biodata" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://proteins.plus", "type": [ "Service" ], "note": "A web service to run MicroMiner calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures." } ], "download": [ { "url": "https://uhh.de/naomi", "type": "Binaries", "note": "Please register to download the tool.", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1093/bib/bbad357", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Searching similar local 3D micro-environments in protein structure databases with MicroMiner", "abstract": "", "date": "2023-11-01T00:00:00Z", "citationCount": 4, "authors": [], "journal": "Briefings in Bioinformatics" } } ], "credit": [ { "name": null, "email": "proteinsplus.zbh@lists.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": "Primary Contact for Web Service Issues" }, { "name": null, "email": "software.zbh@uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": "Primary Contact for Standalone Tool Issues" }, { "name": "University of Hamburg, ZBH - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "00g30e956", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "ehrt", "additionDate": "2025-12-17T13:59:47.755840Z", "lastUpdate": "2025-12-17T14:37:27.778268Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "JAMDA", "description": "JAMDA enables the preparation of individual protein structures and the docking of small molecules in preprocessed binding sites of choice. JAMDA simplifies the process of protein-ligand docking by automatic preprocessing protocols for the protein and binding sites of interest. The JAMDAscore scoring function retrieved 75% of the native poses in the three highest-ranked solutions for high-quality protein-ligand complexes with default settings. Individual configurations for protein preparation are available, e.g., considering protein ensembles, relevant binding site water molecules, or cofactors. A user-defined number of input conformations for the ligands of interest can be generated fully automated using Conformator. Alternatively, users can also provide externally prepared ligand conformers.", "homepage": "https://www.zbh.uni-hamburg.de/en/forschung/amd/software/jamda.html", "biotoolsID": "jamda", "biotoolsCURIE": "biotools:jamda", "version": [], "otherID": [], "relation": [ { "biotoolsID": "protoss", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0482", "term": "Protein-ligand docking" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2301", "term": "SMILES string" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "Other", "collectionID": [ "de.NBI", "de.NBI-biodata" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://proteins.plus", "type": [ "Service" ], "note": "A web service to run JAMDA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures." } ], "download": [ { "url": "https://uhh.de/naomi", "type": "Binaries", "note": "Please register to download the tool.", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1021/acs.jcim.3c01573", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Redocking the PDB", "abstract": "", "date": "2024-01-08T00:00:00Z", "citationCount": 23, "authors": [], "journal": "Journal of Chemical Information and Modeling" } }, { "doi": "10.1002/jcc.26522", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "LSLOpt: An open-source implementation of the step-length controlled LSL-BFGS algorithm", "abstract": "", "date": "2021-06-05T00:00:00Z", "citationCount": 3, "authors": [], "journal": "Journal of Computational Chemistry" } }, { "doi": "10.1021/acs.jcim.0c01095", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "A Consistent Scheme for Gradient-Based Optimization of Protein - Ligand Poses", "abstract": "", "date": "2020-12-28T00:00:00Z", "citationCount": 47, "authors": [], "journal": "Journal of Chemical Information and Modeling" } } ], "credit": [ { "name": null, "email": "proteinsplus.zbh@lists.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": "Primary Contact for Web Service Issues" }, { "name": null, "email": "software.zbh@uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": "Primary Contact for Standalone Tool Issues" }, { "name": "University of Hamburg, ZBH - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "00g30e956", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "ehrt", "additionDate": "2025-12-17T13:44:30.421942Z", "lastUpdate": "2025-12-17T13:55:40.709149Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PoseEdit", "description": "PoseEdit automatically generates 2D diagrams of protein-ligand complexes, focusing on the interactions between protein and ligand. Interactions between molecules are estimated by an underlying interaction model that relies on atom types and simple geometric criteria. The structure mining tool GeoMine also uses this model to describe binding sites. In addition, users can manipulate the diagrams by translating, rotating, mirroring parts of the structure, adding additional interactions, or removing them. Furthermore, users can add individual labels or adjust available labels. Users can download the final 2D diagrams for a binding site of interest in JSON or SVG format.", "homepage": "https://www.zbh.uni-hamburg.de/en/forschung/amd/software/poseedit.html", "biotoolsID": "poseedit", "biotoolsCURIE": "biotools:poseedit", "version": [], "otherID": [], "relation": [ { "biotoolsID": "geomine", "type": "usedBy" }, { "biotoolsID": "protoss", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0248", "term": "Residue interaction calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1566", "term": "Protein-ligand interaction report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [], "license": "Other", "collectionID": [ "de.NBI", "de.NBI-biodata" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://proteins.plus/#poseedit", "type": [ "Service" ], "note": "A web service to run PoseEdit calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database." } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1007/s10822-023-00522-4", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams", "abstract": "", "date": "2023-10-01T00:00:00Z", "citationCount": 57, "authors": [], "journal": "Journal of Computer-Aided Molecular Design" } } ], "credit": [ { "name": null, "email": "proteinsplus.zbh@lists.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "University of Hamburg, ZBH - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "00g30e956", "fundrefid": null, "typeEntity": null, "typeRole": [ "Provider" ], "note": null } ], "owner": "ehrt", "additionDate": "2025-12-15T10:27:32.766629Z", "lastUpdate": "2025-12-17T13:49:34.712757Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DoGSite3", "description": "DoGSite3 was developed for predicting robust and reliable small molecule binding sites and computing their geometrical and chemical descriptors. It is based on the grid-based DoGSite algorithm for predicting pockets and their sub-pockets. The new tool is largely rotation- and translation-invariant due to a normalization procedure before binding site prediction. Known ligands in the structure can be used to bias the grid by sufficiently buried ligand fragments. The output encompasses novel chemical binding site descriptors considering solvent accessibility. Compared to its predecessor, it shows increased robustness through comprehensive parameter optimization. DoGSite3 runs finish within seconds.", "homepage": "https://www.zbh.uni-hamburg.de/en/forschung/amd/software/dogsite3.html", "biotoolsID": "dogsite3", "biotoolsCURIE": "biotools:dogsite3", "version": [], "otherID": [], "relation": [ { "biotoolsID": "geomine", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0420", "term": "Nucleic acids-binding site prediction" }, { "uri": "http://edamontology.org/operation_3897", "term": "Ligand-binding site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_3534", "term": "Protein binding sites" }, { "uri": "http://edamontology.org/topic_0749", "term": "Transcription factors and regulatory sites" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "Other", "collectionID": [ "de.NBI", "de.NBI-biodata" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://proteins.plus/", "type": [ "Service" ], "note": "A web service to run DoGSite3 calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database." } ], "download": [ { "url": "https://uhh.de/naomi", "type": "Binaries", "note": "Please register to download the tool.", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1021/acs.jcim.3c00336", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3", "abstract": "", "date": "2023-05-22T00:00:00Z", "citationCount": 81, "authors": [], "journal": "Journal of Chemical Information and Modeling" } } ], "credit": [ { "name": null, "email": "proteinsplus.zbh@lists.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": "Primary Contact for Web Service Issues" }, { "name": null, "email": "software.zbh@uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": "Primary Contact for Standalone Tool Issues" }, { "name": "University of Hamburg, ZBH - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "00g30e956", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "ehrt", "additionDate": "2025-12-15T10:10:43.359638Z", "lastUpdate": "2025-12-17T12:41:42.702839Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "LifeSoaks", "description": "LifeSoaks was designed to find solvent channels in macromolecular structures solved by X-ray crystallography. It predicts their accessibility by molecules through an automated annotation of so-called bottleneck radii. It simplifies the process of manually checking a crystal structure for solvent channels. Bottleneck radii can be calculated for solvent channels and small molecule binding sites. The tool is ideally suited for channel analyses before the actual soaking experiments to select the most promising experimental conditions and crystal forms. LifeSoaks runs fully automated and will finish within seconds to minutes for moderately sized crystals.", "homepage": "https://www.zbh.uni-hamburg.de/en/forschung/amd/software/lifesoaks.html", "biotoolsID": "lifesoaks", "biotoolsCURIE": "biotools:lifesoaks", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0250", "term": "Protein property calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_2828", "term": "X-ray diffraction" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "Other", "collectionID": [ "de.NBI", "de.NBI-biodata" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://proteins.plus", "type": [ "Service" ], "note": "A web service to run DoGSite3 calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures." } ], "download": [ { "url": "https://uhh.de/naomi", "type": "Binaries", "note": "Please register to download the tool.", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1107/S205979832300582X", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "LifeSoaks: A tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments", "abstract": "", "date": "2023-08-10T00:00:00Z", "citationCount": 7, "authors": [], "journal": "Acta Crystallographica Section D: Structural Biology" } } ], "credit": [ { "name": null, "email": "proteinsplus.zbh@lists.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": "Primary Contact for Web Service Issues" }, { "name": null, "email": "software.zbh@uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": "Primary Contact for Standalone Tool Issues" }, { "name": "University of Hamburg, ZBH - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "00g30e956", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "ehrt", "additionDate": "2025-12-15T10:42:55.566760Z", "lastUpdate": "2025-12-17T12:28:33.670677Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SAMtools", "description": "SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.", "homepage": "http://www.htslib.org/", "biotoolsID": "samtools", "biotoolsCURIE": "biotools:samtools", "version": [ "1.0", "1.1", "1.2", "1.3", "1.3.1", "1.4", "1.4.1", "1.5", "1.6", "1.7", "1.8", "1.9", "1.10", "1.11", "1.12", "1.13", "1.14", "1.15", "1.15.1", "1.16", "1.16.1", "1.17", "1.18", "1.19", "1.19.1", "1.19.2", "1.20", "1.21", "1.22", "1.23" ], "otherID": [], "relation": [ { "biotoolsID": "htslib", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_0335", "term": "Data formatting" }, { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" }, { "uri": "http://edamontology.org/operation_1812", "term": "Data parsing" }, { "uri": "http://edamontology.org/operation_3802", "term": "Data sorting" }, { "uri": "http://edamontology.org/operation_3096", "term": "Data editing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_3462", "term": "CRAM" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_3462", "term": "CRAM" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "C" ], "license": "MIT", "collectionID": [ "Rare Disease", "Animal and Crop Genomics", "SAMtools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/samtools/samtools", "type": [ "Repository" ], "note": null }, { "url": "http://www.htslib.org/support/#lists", "type": [ "Mailing list" ], "note": null }, { "url": "https://github.com/samtools/samtools/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "http://www.htslib.org/download/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.htslib.org/doc/#howtos", "type": [ "Other" ], "note": "HowTos for samtools" }, { "url": "http://www.htslib.org/doc/#manual-pages", "type": [ "User manual" ], "note": null }, { "url": "http://www.htslib.org/download/", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp352", "pmid": "19505943", "pmcid": "PMC2723002", "type": [ "Primary" ], "version": null, "note": "The Sequence Alignment/Map format and SAMtools.", "metadata": { "title": "The Sequence Alignment/Map format and SAMtools", "abstract": "", "date": "2009-08-01T00:00:00Z", "citationCount": 44891, "authors": [], "journal": "Bioinformatics" } }, { "doi": "10.1093/gigascience/giab008", "pmid": "33590861", "pmcid": "PMC7931819", "type": [ "Primary" ], "version": null, "note": "Twelve years of SAMtools and BCFtools.", "metadata": { "title": "Twelve years of SAMtools and BCFtools", "abstract": "", "date": "2021-02-01T00:00:00Z", "citationCount": 8157, "authors": [], "journal": "GigaScience" } }, { "doi": "10.1093/bioinformatics/btr509", "pmid": "21903627", "pmcid": "PMC3198575", "type": [], "version": null, "note": null, "metadata": { "title": "A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data", "abstract": "", "date": "2011-11-01T00:00:00Z", "citationCount": 4643, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Richard Durbin", "email": "rd@sanger.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Wellcome Sanger Institute", "email": "samtools@sanger.ac.uk", "url": "https://www.sanger.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider", "Primary contact" ], "note": null }, { "name": "Samtools Help mailing list", "email": null, "url": "https://lists.sourceforge.net/lists/listinfo/samtools-help", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Support" ], "note": null } ], "owner": "awhitwham", "additionDate": "2017-01-13T13:16:12Z", "lastUpdate": "2025-12-16T15:42:24.521617Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "animalandcropgenomics", "alice", "awhitwham", "sergitobara" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HTSlib", "description": "The main purpose of HTSlib is to provide access to genomic information files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools.", "homepage": "http://www.htslib.org/", "biotoolsID": "htslib", "biotoolsCURIE": "biotools:htslib", "version": [ "1.0", "1.1", "1.2", "1.2.1", "1.3", "1.3.1", "1.3.2", "1.4", "1.4.1", "1.5", "1.6", "1.7", "1.8", "1.9", "1.10", "1.10.1", "1.10.2", "1.11", "1.12", "1.13", "1.14", "1.15", "1.15.1", "1.16", "1.17", "1.18", "1.19", "1.20", "1.21", "1.22", "1.22.1", "1.23" ], "otherID": [], "relation": [ { "biotoolsID": "samtools", "type": "usedBy" }, { "biotoolsID": "bcftools", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_3462", "term": "CRAM" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3020", "term": "BCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_3462", "term": "CRAM" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3020", "term": "BCF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "C" ], "license": "MIT", "collectionID": [ "Animal and Crop Genomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/samtools/htslib", "type": [ "Repository" ], "note": null }, { "url": "http://www.htslib.org/support/#lists", "type": [ "Mailing list" ], "note": null }, { "url": "https://github.com/samtools/htslib/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "http://www.htslib.org/download/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.htslib.org/doc/#manual-pages", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/gigascience/giab007", "pmid": "33594436", "pmcid": "PMC7931820", "type": [ "Primary" ], "version": null, "note": "HTSlib: C library for reading/writing high-throughput sequencing data.", "metadata": { "title": "HTSlib: C library for reading/writing high-Throughput sequencing data", "abstract": "", "date": "2021-02-01T00:00:00Z", "citationCount": 236, "authors": [], "journal": "GigaScience" } } ], "credit": [ { "name": "Wellcome Sanger Institute", "email": "samtools@sanger.ac.uk", "url": "https://www.sanger.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider", "Primary contact" ], "note": null }, { "name": "Samtools Help mailing list", "email": null, "url": "https://lists.sourceforge.net/lists/listinfo/samtools-help", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Support" ], "note": null } ], "owner": "awhitwham", "additionDate": "2017-08-20T16:07:58Z", "lastUpdate": "2025-12-16T15:41:44.904477Z", "editPermission": { "type": "group", "authors": [ "animalandcropgenomics", "smoe" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BCFtools", "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.", "homepage": "http://www.htslib.org/", "biotoolsID": "bcftools", "biotoolsCURIE": "biotools:bcftools", "version": [ "1.0", "1.1", "1.2", "1.3", "1.3.1", "1.4", "1.4.1", "1.5", "1.6", "1.7", "1.8", "1.9", "1.10", "1.10.1", "1.10.2", "1.11", "1.12", "1.13", "1.14", "1.15", "1.15.1", "1.16", "1.17", "1.18", "1.19", "1.20", "1.21", "1.22", "1.23" ], "otherID": [], "relation": [ { "biotoolsID": "htslib", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" }, { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3020", "term": "BCF" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3020", "term": "BCF" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": "Multiple data munging operations.", "cmd": null } ], "toolType": [ "Command-line tool", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" }, { "uri": "http://edamontology.org/topic_3516", "term": "Genotyping experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "C" ], "license": "MIT", "collectionID": [ "BCFtools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/samtools/bcftools", "type": [ "Repository" ], "note": null }, { "url": "http://www.htslib.org/support/#lists", "type": [ "Mailing list" ], "note": null }, { "url": "https://github.com/samtools/bcftools/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "http://www.htslib.org/download/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.htslib.org/doc/bcftools.html", "type": [ "General" ], "note": null }, { "url": "http://www.htslib.org/workflow/#mapping_to_variant", "type": [ "Other" ], "note": "A workflow for BCFtools." } ], "publication": [ { "doi": "10.1093/bioinformatics/btp352", "pmid": "19505943", "pmcid": "PMC2723002", "type": [ "Primary" ], "version": null, "note": "The Sequence Alignment/Map format and SAMtools.", "metadata": { "title": "The Sequence Alignment/Map format and SAMtools", "abstract": "", "date": "2009-08-01T00:00:00Z", "citationCount": 44891, "authors": [], "journal": "Bioinformatics" } }, { "doi": "10.1093/gigascience/giab008", "pmid": "33590861", "pmcid": "PMC7931819", "type": [ "Primary" ], "version": null, "note": "Twelve years of SAMtools and BCFtools.", "metadata": { "title": "Twelve years of SAMtools and BCFtools", "abstract": "", "date": "2021-02-01T00:00:00Z", "citationCount": 8157, "authors": [], "journal": "GigaScience" } } ], "credit": [ { "name": "Wellcome Sanger Institute", "email": "samtools@sanger.ac.uk", "url": "https://www.sanger.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Samtools Help mailing list", "email": null, "url": "https://lists.sourceforge.net/lists/listinfo/samtools-help", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Support" ], "note": null } ], "owner": "awhitwham", "additionDate": "2015-08-24T08:35:55Z", "lastUpdate": "2025-12-16T15:40:43.213782Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "nnUNet", "description": "nnU-Net is a self-configuring method for deep learning-based biomedical image segmentation, developed by the Applied Computer Vision Lab (ACVL) of Helmholtz Imaging and the Division of Medical Image Computing at the German Cancer Research Center (DKFZ). It is designed to automatically adapt to a given dataset, analyzing the provided training cases to configure a matching U-Net-based segmentation pipeline without requiring expertise from the user.\nThe tool provides pretrained models for \nPancreas and Pancreas tumor segmentation, Colon cancer primaries segmentation, Abdominal organ segmentation, Liver and liver tumor segmentation, Kidney and kidney tumor segmentation, Brain Tumor segmentation and Hippocampus (MR data) segmentation", "homepage": "https://github.com/MIC-DKFZ/nnUNet/tree/nnunetv1", "biotoolsID": "nnunet", "biotoolsCURIE": "biotools:nnunet", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Run nnUnet pretrained on Task007_Pancreas targeting are pancras and pancreas tumor", "cmd": "docker run --rm -v /host/dataset/study_001/:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-pancreas-tumour" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Run nnUnet model pretrained on Task029_LiTS targeting are liver and liver tumor", "cmd": "docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-liver-tumour" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Run nnUnet pretrained on Task004_Hippocampus MRI data targeting posterior and anterior parts of the hippocampus", "cmd": "docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-hippocampus-segmentation" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Run nnUnet pretrained on Task010_Colon targeting are colon cancer primaries.", "cmd": "docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-colon-cancer" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Run nnUnet pretrained on Task169_BrainTumorPET targeting are brain tumor", "cmd": "docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-brain-tumour-pet" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Run nnUNet model pretrained on Task017_AbdominalOrganSegmentation targeting thirteen different abdominal organs", "cmd": "docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-abdominal-organ-segmentation" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Run nnUNet model pretrained on Task135_KiTS2021 targeting are kidney, tumor and cyst.", "cmd": "docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-kidney-tumour" } ], "toolType": [ "Command-line tool" ], "topic": [], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/MIC-DKFZ/nnUNet/tree/nnunetv1", "type": [ "General" ], "note": "GitHub Readme" }, { "url": "https://github.com/MIC-DKFZ/nnunet-eucaim-docker/", "type": [ "User manual" ], "note": "Docker containers and other relevant instructions" } ], "publication": [ { "doi": "10.1038/s41592-020-01008-z", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation", "abstract": "", "date": "2021-02-01T00:00:00Z", "citationCount": 6593, "authors": [], "journal": "Nature Methods" } } ], "credit": [ { "name": "DKFZ Heidelberg", "email": "r.floca@Dkfz-Heidelberg.de", "url": "https://www.dkfz.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider", "Contributor", "Maintainer" ], "note": "Group Lead and Board Member, Medical Image Computing department, DKFZ Heidelberg" } ], "owner": "ASHISR", "additionDate": "2025-07-21T09:36:40.711284Z", "lastUpdate": "2025-12-16T12:04:54.619598Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "globalamfungi", "description": "The GlobalAMFungi Database is an open-access, global repository of arbuscular mycorrhizal (AM) fungal occurrence data compiled from high-throughput sequencing studies. It aggregates millions of DNA sequence observations of AM fungi from thousands of geographically referenced environmental samples, together with rich metadata on sampling location and environmental context, to map the global distribution and diversity of these key plant symbionts. The resource is designed to be community-driven and FAIR (Findable, Accessible, Interoperable, Reusable), supporting research into AM fungal ecology, biogeography, and how environmental factors shape their diversity.", "homepage": "https://globalamfungi.com/", "biotoolsID": "globalamfungi", "biotoolsCURIE": "biotools:globalamfungi", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Data deposition" }, { "uri": "http://edamontology.org/operation_0226", "term": "Annotation" }, { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [ { "uri": "http://edamontology.org/format_2310", "term": "FASTA-HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3050", "term": "Biodiversity" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" } ], "operatingSystem": [], "language": [ "R" ], "license": "CC-BY-4.0", "collectionID": [ "ELIXIR-CZ", "Czech Republic" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "Plant Sciences" ], "link": [ { "url": "https://globalamfungi.com/", "type": [ "Helpdesk", "Repository", "Service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://globalamfungi.com/", "type": [ "User manual", "Citation instructions", "Quick start guide", "Contributions policy", "General" ], "note": null } ], "publication": [ { "doi": "10.1111/nph.19283", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": null, "abstract": null, "date": null, "citationCount": 0, "authors": [], "journal": null } } ], "credit": [ { "name": "Tomas Vetrovsky", "email": "vetrovsky@biomed.cas.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-0831-486X", "gridid": null, "rorid": "02p1jz666", "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Contributor" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null } ], "owner": "TomasVetrovsky", "additionDate": "2025-12-16T11:00:25.334832Z", "lastUpdate": "2025-12-16T11:00:25.337448Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MR-based DIPG tumour detection and segmentation (EUCAIM-SW-020_T-01-02-003)", "description": "The tool performs an automatic segmentation of the possible DIPG tumours on MR images. DIPG (Diffuse Intrinsic Pontine Glioma), or more recently, DMG (Diffuse Midline Glioma) is a H3 K27M–mutant pediatric brainstem cancer detected in T1W and Flair/T2-weighted magnetic resonance images. The tool includes a complete workflow from DICOM images to DICOM seg tumoral masks.", "homepage": "https://www.acim.lafe.san.gva.es/acim/?page_id=675&lang=es", "biotoolsID": "mr-based_dipg_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:mr-based_dipg_tumour_detection_and_segmentation", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input \\\n -v /path/to/output:/output \\\nharbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest \\\n --series-selector /input/config/series.csv" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input -v /path/to/output:/output harbor.eucaim.cancerimage.eu/processing-tools/mr-based_dipg_tumour_detection_and_segmentation:latest \\\n --json-args '{\"dataset_id\":\"DS1\",\"patient_id\":\"P1\",\"study_id\":\"S1\",\"sequences\":{\"T1w\":\"/input/DICOM/DS1/P1/S1/T1\",\"FLAIR\":\"/input/DICOM/DS1/P1/S1/FLAIR\"}}'" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://link.springer.com/article/10.1007/s10278-025-01557-9", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1007/s10278-025-01557-9", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Deep Learning Auto-segmentation of Diffuse Midline Glioma on Multimodal Magnetic Resonance Images", "abstract": "", "date": "2025-01-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Journal of Imaging Informatics in Medicine" } } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Matias Fernandez-Paton", "email": "matias_fernandez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0001-9374-1411", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Support" ], "note": null }, { "name": "Adrian Galiana-Bordera", "email": "adrian_galiana@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8324-8284", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor", "Support" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T09:19:51.404419Z", "lastUpdate": "2025-12-16T08:28:53.473104Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MR-based glioblastoma tumour detection and segmentation (EUCAIM-SW-021_T-01-02-004)", "description": "The tool performs an automatic segmentation of the possible glioblastoma tumours on MRI images and its subregions: necrosis (Intratumoral necrotic core), edema (Peritumoral vasogenic edema), enhancing (Contrast-enhancing tumor region), total (Total tumor including edema and necrosis by a single model) and total-fused (Total tumor fusioning of necrosis+edema+enhancing). It applies preprocessing steps as skull stripping, intra-patient registration, z-score normalization, patching, among others. It takes DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/artifacts-tab", "biotoolsID": "mr-based_glioblastoma_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:mr-based_glioblastoma_tumour_detection_and_segmentation", "version": [ "2.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input \\\n -v /path/to/output:/output \\\n harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest \\\n --series-selector /input/config/series.csv \\\n --target total \\\n --emit-config true" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input \\\n -v /path/to/output:/output \\\n harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest \\\n --series-list '[{\"dataset_id\":\"DS001\",\"patient_id\":\"PAT001\",\"study_id\":\"ST001\",\"series_path\":\"/input/DICOM/DS001/PAT001/ST001/T1_POST\"}]' \\\n --target total-fused \\\n --emit-config true" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/artifacts-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1007/s11548-024-03205-z", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Deep learning automatic semantic segmentation of glioblastoma multiforme regions on multimodal magnetic resonance images", "abstract": "", "date": "2024-09-01T00:00:00Z", "citationCount": 8, "authors": [], "journal": "International Journal of Computer Assisted Radiology and Surgery" } } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Maria Beser-Robles", "email": "maria_beser@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-0072-5525", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Support" ], "note": null }, { "name": "Adrian Galiana-Bordera", "email": "adrian_galiana@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8324-8284", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T12:09:16.704255Z", "lastUpdate": "2025-12-16T08:22:56.322315Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Profiler", "description": "Profiler is a peer-reviewed, open-source web platform and desktop version for end-to-end multi-omics data analysis, integrating statistical methods, machine learning, and artificial intelligence into a unified workflow.\n\nThe platform supports proteomics, metabolomics, lipidomics, transcriptomics, genomics, and other omics datasets from raw or tabular inputs. Profiler provides automated preprocessing, data exploration, biomarker discovery, AI-driven modeling, survival analysis, and biological interpretation using enrichment analysis.\n\nDesigned for both bioinformaticians and experimental scientists, Profiler enables reproducible, explainable, and high-performance omics analysis through an intuitive web interface.\n\nProfiler is developed by the PRISM U1192 laboratory and protected by INSERM Transfer.", "homepage": "https://prism-profiler.univ-lille.fr/", "biotoolsID": "profiler", "biotoolsCURIE": "biotools:profiler", "version": [ "1.0" ], "otherID": [ { "value": "doi:10.1093/bioinformatics/btaf644", "type": "doi", "version": "1.0" } ], "relation": [], "function": [], "toolType": [ "Desktop application", "Web application", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "Other", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Training", "Interoperability" ], "elixirNode": [ "France" ], "elixirCommunity": [ "Metabolomics", "Proteomics", "Rare Diseases" ], "link": [ { "url": "https://prism-profiler.univ-lille.fr/", "type": [ "Other" ], "note": "softeware link" }, { "url": "https://github.com/yanisZirem/Profiler_v1_requests_datatests", "type": [ "Repository" ], "note": "dataset examples" }, { "url": "https://github.com/yanisZirem/prism-profiler", "type": [ "Repository" ], "note": "Desktop version" } ], "download": [ { "url": "https://doi.org/10.5281/zenodo.17478158", "type": "Source code", "note": null, "version": null }, { "url": "https://github.com/yanisZirem/Profiler_v1_requests_datatests", "type": "Test data", "note": null, "version": "1.0" }, { "url": "https://prism-profiler.univ-lille.fr/app/", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://prism-profiler.univ-lille.fr/citation/", "type": [ "Citation instructions" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btaf644", "pmid": "41324558", "pmcid": null, "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": null } ], "credit": [ { "name": "Michel Salzet", "email": "michel.salzet@univ-lille.fr", "url": "https://www.laboratoire-prism.fr/member/michel-salzet/", "orcidid": "https://orcid.org/0000-0003-4318-0817", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": "Professor Michel Salzet known for his work in immunology, oncology and proteomic" } ], "owner": "YZirem", "additionDate": "2025-12-16T08:20:17.123908Z", "lastUpdate": "2025-12-16T08:20:49.442259Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Verdanta", "description": "Curated plant RNASeq data portal, focusing on multiple transcriptomes of Capsicum annuum. The portal currently contains about 70 high quality hand-curated studies, along with pre-computed quality charts, analysis-ready data in csv, parquet and yaml (metadata) forms and advanced search that allows to pick not just full studies but also individual samples into the dataset. \n\nFour curated Capsicum transcriptomes are currently available.\n\nThe portal is free for academic use, both for students and researchers. Working E-mail or social login is required as protection from botnet attacks. Academic email automatically unlocks full access, otherwise you can contact us to unlock it if you think you are eligible.", "homepage": "https://verdanta.info/", "biotoolsID": "verdanta", "biotoolsCURIE": "biotools:verdanta", "version": [ "1.0" ], "otherID": [], "relation": [ { "biotoolsID": "salmon", "type": "uses" }, { "biotoolsID": "fastqc", "type": "uses" }, { "biotoolsID": "fastp", "type": "uses" }, { "biotoolsID": "ncbi_resources", "type": "uses" }, { "biotoolsID": "thaf", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0339", "term": "Structure database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2589", "term": "Hierarchy" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0219", "term": "Data curation and archival" }, { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Rust" ], "license": "Other", "collectionID": [], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://verdanta.info/", "type": [ "Other" ], "note": "Project description, documentation" }, { "url": "https://verdanta.org/ca", "type": [ "Service" ], "note": "Register/login" } ], "download": [], "documentation": [ { "url": "https://verdanta.info/#data-organization", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "owner": "Bourumir", "additionDate": "2025-12-16T08:08:29.575906Z", "lastUpdate": "2025-12-16T08:15:22.926670Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MR-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-019_T-01-02-002)", "description": "This tool is specifically designed and validated for automated detection and segmentation of neuroblastic tumours in T2-weighted magnetic resonance images (T2-MR) using deep learning. It processes DICOM or NIfTI input data and outputs in NIFTI or DICOM SEG.\n\nTRAINING & VALIDATION COHORTS:\n\nInitial Development (Veiga-Canuto 2022):\n-Training: 106 patients, 5-fold CV (median DSC 0.965 ± 0.018).\n-Internal validation: 26 patients (median DSC 0.918 ± 0.067).\n-Sources: La Fe (Spain), SIOPEN HR-NBL1/LINES, St. Anna (Austria), Pisa (Italy).\n-Mean age: 37.6 ± 39.3 months.\n-Median tumor volume: 116,518 mm³.\n\nExternal Validation (Veiga-Canuto 2023):\n-300 patients, 535 independent T2 MRI scans (486 at diagnosis, 49 post-chemotherapy).\n-Performance: median DSC 0.997 (0.944–1.000), 94% successful detection.\n-Sources: 12 European countries (HR-NBL1/SIOPEN 119, LINES/SIOPEN 107, German Registry 62, others 12).\n-Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105), Canon (3).", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/artifacts-tab", "biotoolsID": "mr-based_neuroblastoma_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:mr-based_neuroblastoma_tumour_detection_and_segmentation", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n --gpus all \\\n harbor.eucaim.cancerimage.eu/processing-tools/mr_based_neuroblastoma_tumour_detection_and_segmentation:2.0.0 \\\n --mode dicom-seg \\\n --series-selector /output/config/series_to_segment.csv \\\n --seg-series-number 2302001 \\\n --seg-algorithm-name \"nnUNet_Neuroblastoma_Primage_training\" \\\n --seg-coordinating-center \"EUCAIM Consortium\" \\\n --keep-nifti false" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/artifacts-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://www.mdpi.com/2072-6694/14/15/3648", "type": [ "General" ], "note": null }, { "url": "https://drive.google.com/file/d/1xzmrPQx9LfZr6WS5OR80RkipukoO_3Gw/view?usp=drive_link", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.3390/cancers14153648", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Comparative Multicentric Evaluation of Inter-Observer Variability in Manual and Automatic Segmentation of Neuroblastic Tumors in Magnetic Resonance Images", "abstract": "", "date": "2022-08-01T00:00:00Z", "citationCount": 33, "authors": [], "journal": "Cancers" } }, { "doi": "10.3390/cancers15051622", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Independent Validation of a Deep Learning nnU-Net Tool for Neuroblastoma Detection and Segmentation in MR Images", "abstract": "", "date": "2023-03-01T00:00:00Z", "citationCount": 16, "authors": [], "journal": "Cancers" } } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Diana Veiga Canuto", "email": "dianaveigac@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0002-6048-2940", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Support", "Documentor", "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support", "Documentor" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T09:08:44.174795Z", "lastUpdate": "2025-12-16T01:53:35.476918Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ASAFind", "description": "ASAFind is a software that predicts the intracellular location of proteins in cells with four membrane-bound complex plastids of red algal origin. \nThese plastids evolved via eukaryote-eukaryote endosymbiosis and for example can be found in diatoms and cryptophytes. ASAFind uses protein sequence data and external predictions of signal peptides (by the tools SignalP and TargetP), and predicts plastid proteins, and proteins that are targeted to the periplastidic compartment from these data; optionally, a graphical output can generated.", "homepage": "https://asafind.jcu.cz/", "biotoolsID": "asafind", "biotoolsCURIE": "biotools:asafind", "version": [ "2.0" ], "otherID": [], "relation": [ { "biotoolsID": "signalp", "type": "uses" }, { "biotoolsID": "targetp", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2489", "term": "Subcellular localisation prediction" }, { "uri": "http://edamontology.org/operation_0239", "term": "Sequence motif recognition" }, { "uri": "http://edamontology.org/operation_0422", "term": "Protein cleavage site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Script", "Command-line tool", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python" ], "license": "CC-BY-SA-4.0", "collectionID": [ "ELIXIR-CZ", "Czech Republic" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "Plant Sciences", "Marine Metagenomics", "Microbial Biotechnology" ], "link": [ { "url": "https://asafind.jcu.cz", "type": [ "Service" ], "note": "Web Service" }, { "url": "https://github.com/ASAFind/ASAFind-2", "type": [ "Repository" ], "note": "Information and source code, for local installation or development" } ], "download": [ { "url": "https://asafind.jcu.cz/download-page/", "type": "Downloads page", "note": "Download page on web-service, links to repository", "version": "2.0" } ], "documentation": [ { "url": "https://asafind.jcu.cz/download-page/", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1111/tpj.70138", "pmid": "40464854", "pmcid": "PMC12136025", "type": [ "Primary" ], "version": "2.0", "note": "Publication of the current version of ASAFind (2.0)", "metadata": { "title": "ASAFind 2.0: multi-class protein targeting prediction for diatoms and algae with complex plastids", "abstract": "", "date": "2025-06-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Plant Journal" } }, { "doi": "10.1111/tpj.12734", "pmid": "25438865", "pmcid": "PMC4329603", "type": [ "Other" ], "version": "1.0", "note": "Publication of the first version of ASAFind", "metadata": { "title": "Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage", "abstract": "", "date": "2015-02-01T00:00:00Z", "citationCount": 138, "authors": [], "journal": "Plant Journal" } }, { "doi": "10.48550/arXiv.2303.02509", "pmid": null, "pmcid": null, "type": [ "Benchmarking study" ], "version": "1.0", "note": "Benchmarking of the performance of the first version of ASAFind", "metadata": null } ], "credit": [ { "name": "Marta Vohnoutová", "email": "mvohnoutova@jcu.cz", "url": "https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Vohnoutova_Marta_61699", "orcidid": "https://orcid.org/0000-0002-8915-8626", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Developer", "Maintainer" ], "note": null }, { "name": "Ansgar Gruber", "email": "agruber@prf.jcu.cz", "url": "https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gruber_Ansgar_118401", "orcidid": "https://orcid.org/0000-0002-5876-4391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor" ], "note": null } ], "owner": "martavohnoutova", "additionDate": "2025-12-15T14:17:14.627791Z", "lastUpdate": "2025-12-15T17:36:43.189214Z", "editPermission": { "type": "group", "authors": [ "agruber" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "EAPP - Extended a Priori Probability tool", "description": "The tool provides a semi-supervised metric (EAPP) for binary classification tasks that considers not only the a priori probability but also some possible bias present in the dataset, as well as other features that could provide a relatively trivial separability of the target classes. Therefore, it allows for evaluating the ease or complexity of the task or bias of the data beyond the well-established baseline for any binary classification.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/image_batch_iti-eapp", "biotoolsID": "extended_a_priori_probability_tool", "biotoolsCURIE": "biotools:extended_a_priori_probability_tool", "version": [ "v1.0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Data analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "input_data_class0_path: Input path for class 0 data; input_data_class1_path: Input path for class 1 data. In both cases it must be a CSV file, images stored in a folder or compressed into a ZIP file, or a 3D DICOM series file; output_path: directory and filename (JSON format) where the results will be saved", "cmd": "jobman submit -i image_batch_EAPP -r small gpu -- -i0 input_data_class0_path -i1 input_data_class1_path -o output_directory/results.json" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "Proprietary", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": null, "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://ieeexplore.ieee.org/document/9950248", "type": [ "Other" ], "note": "Scientific paper" }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/image_batch_iti-eapp", "type": [ "Repository" ], "note": "Harbor repository with the tool's Docker images" } ], "download": [], "documentation": [ { "url": "https://drive.eucaim.cancerimage.eu/s/Ld2AgbGZmm4qcke", "type": [ "Quick start guide" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/CAwxZaC4xDzkCA5", "type": [ "Terms of use" ], "note": "Tool License Agreement in DOCX format" }, { "url": "https://drive.eucaim.cancerimage.eu/s/Z8mYAoPk2JjZLFL", "type": [ "Terms of use" ], "note": "Tool License Summary in TXT format" } ], "publication": [ { "doi": "10.1109/ACCESS.2022.3221936", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Extended a Priori Probability (EAPP): A Data-Driven Approach for Machine Learning Binary Classification Tasks", "abstract": "", "date": "2022-01-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "IEEE Access" } } ], "credit": [ { "name": "Ana María Arias Beltrán", "email": "aarias@iti.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Instituto Tecnológico de Informática (ITI)", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "dsilveira", "additionDate": "2025-05-22T14:58:20.772120Z", "lastUpdate": "2025-12-15T12:21:49.565380Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Breast Dense Tissue Segmentation", "description": "The tool takes a digital mammogram and performs an automatic segmentation of the breast area and the dense tissue. After the mammogram segmentation, the tool returns a DICOM-SEG image with both the dense tissue and the breast tissue mask combined.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/image_batch_iti-breast", "biotoolsID": "breast_dense_tissue_segmentation", "biotoolsCURIE": "biotools:breast_dense_tissue_segmentation", "version": [ "v1.0.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "input_dcm_path: input path to the 2D DICOM image (FFDM); output_directory: output directory to store the results", "cmd": "jobman submit -i mammography-density-segmenter -r small-gpu -- -p\ninput_dcm_path -o output_directory" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "Proprietary", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": null, "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://pubmed.ncbi.nlm.nih.gov/36010173/", "type": [ "Other" ], "note": "Scientific paper" }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/image_batch_iti-breast", "type": [ "Repository" ], "note": "Harbor repository with the tool's Docker images" } ], "download": [], "documentation": [ { "url": "https://drive.eucaim.cancerimage.eu/s/agktHMkYfy5pHes", "type": [ "Quick start guide" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/gPcqYKakCDSXGjN", "type": [ "Terms of use" ], "note": "Tool License Agreement in DOCX format" }, { "url": "https://drive.eucaim.cancerimage.eu/s/7ZPfQqsJ6YRjgpe", "type": [ "Terms of use" ], "note": "Tool License Summary in TXT format" } ], "publication": [ { "doi": "10.3390/diagnostics12081822", "pmid": "36010173", "pmcid": "PMC9406546", "type": [], "version": null, "note": null, "metadata": { "title": "Breast Dense Tissue Segmentation with Noisy Labels: A Hybrid Threshold-Based and Mask-Based Approach", "abstract": "", "date": "2022-08-01T00:00:00Z", "citationCount": 7, "authors": [], "journal": "Diagnostics" } } ], "credit": [ { "name": "Ana María Arias Beltrán", "email": "aarias@iti.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Instituto Tecnológico de Informática (ITI)", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "dsilveira", "additionDate": "2025-05-22T12:06:46.866961Z", "lastUpdate": "2025-12-15T12:09:26.486490Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "metagWGS", "description": "metagWGS is a workflow dedicated to the analysis of metagenomic data. It allows assembly, taxonomic annotation, and functional annotation of predicted genes. Since release 2.3, binning step with the possibility of cross-alignment is included. It has been developed in collaboration with several CATI BIOS4biol agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest.", "homepage": "https://forgemia.inra.fr/genotoul-bioinfo/metagwgs", "biotoolsID": "metagwgs", "biotoolsCURIE": "biotools:metagwgs", "version": [ "2.3", "2.5.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3917", "term": "Count matrix" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://forge.inrae.fr/genotoul-bioinfo/metagwgs", "type": [ "Repository" ], "note": "See documentation, source code and functionnal test documentation." } ], "download": [ { "url": "https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets", "type": "Test data", "note": "Functional tests data and script", "version": null } ], "documentation": [ { "url": "https://genotoul-bioinfo.pages-forge.inrae.fr/metagwgs/master/index.html", "type": [ "User manual" ], "note": "We provide up to date installation documentation, usage documentation, output description and functionnal test datasets and procedure." } ], "publication": [], "credit": [ { "name": "Claire Hoede", "email": "claire.hoede@inrae.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-5054-7731", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "GenoToul bioinformatics facility", "email": null, "url": "http://bioinfo.genotoul.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null } ], "owner": "choede", "additionDate": "2022-04-19T09:32:41.303637Z", "lastUpdate": "2025-12-11T14:51:44.804907Z", "editPermission": { "type": "group", "authors": [ "pbordron" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "easy16S", "description": "Easy16S is designed to facilitate the exploration, visualization, and analysis of microbiome data.", "homepage": "https://easy16s.migale.inrae.fr/", "biotoolsID": "easy16s", "biotoolsCURIE": "biotools:easy16s", "version": [ "v25.07" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3744", "term": "Multiple sample visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "R" ], "license": "AGPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://forge.inrae.fr/migale/easy16s", "type": [ "Repository" ], "note": null }, { "url": "https://doi.org/10.57745/ZN1HXQ", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://easy16s.migale.inrae.fr/", "type": [ "General", "User manual" ], "note": null } ], "publication": [ { "doi": "10.21105/joss.06704", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Cédric Midoux", "email": "cedric.midoux@inrae.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-7964-0929", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "cmidoux", "additionDate": "2025-12-11T14:36:21.061830Z", "lastUpdate": "2025-12-11T14:36:21.065324Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Jalview", "description": "Jalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.", "homepage": "https://www.jalview.org/", "biotoolsID": "Jalview", "biotoolsCURIE": "biotools:Jalview", "version": [ "2.11.5.1" ], "otherID": [], "relation": [ { "biotoolsID": "jabaws", "type": "uses" }, { "biotoolsID": "chimera", "type": "uses" }, { "biotoolsID": "chimerax", "type": "uses" }, { "biotoolsID": "pymol", "type": "uses" }, { "biotoolsID": "bioconda", "type": "includedIn" }, { "biotoolsID": "3d-beacons", "type": "uses" }, { "biotoolsID": "uniprot", "type": "uses" }, { "biotoolsID": "pfam", "type": "uses" }, { "biotoolsID": "ensembl", "type": "uses" }, { "biotoolsID": "pdb", "type": "uses" }, { "biotoolsID": "rfam", "type": "uses" }, { "biotoolsID": "3d-beacons", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3081", "term": "Sequence alignment editing" }, { "uri": "http://edamontology.org/operation_0324", "term": "Phylogenetic tree analysis" }, { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" }, { "uri": "http://edamontology.org/format_1938", "term": "GFF2-seq" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_3311", "term": "RNAML" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1939", "term": "GFF3-seq" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" } ] }, { "data": { "uri": "http://edamontology.org/data_0886", "term": "Structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3466", "term": "EPS" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] } ], "note": "Other Input formats:\nAMSA (.amsa);\nJnetFile (.concise, .jnet);\nPFAM (.pfam);\nSubstitution matrix (.matrix);\nJalview Project File (.jvp);\nJalview Feature File (.features, .jvfeatures);\nJalview Annotations File (.annotations, .jvannotations);\nPredicted Aligned Error (PAE) Matrix File (.json)\n...\nOther Output formats:\nPFAM (.pfam);\nBioJS (.biojs) (interactive HTML/Javascript);\nJalview Project File (.jvp);", "cmd": null } ], "toolType": [ "Desktop application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "GPL-3.0", "collectionID": [ "ELIXIR-UK" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Interoperability" ], "elixirNode": [ "UK" ], "elixirCommunity": [], "link": [ { "url": "https://discourse.jalview.org/", "type": [ "Discussion forum" ], "note": null }, { "url": "https://issues.jalview.org/", "type": [ "Issue tracker" ], "note": null }, { "url": "https://www.jalview.org/development/jalview_develop/", "type": [ "Other" ], "note": "Latest development version" }, { "url": "https://gitlab.jalview.org/jalview/jalview.git", "type": [ "Repository" ], "note": null }, { "url": "https://twitter.com/Jalview", "type": [ "Social media" ], "note": "Twitter feed" }, { "url": "https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw", "type": [ "Social media" ], "note": "YouTube training videos" }, { "url": "https://www.linkedin.com/company/104771886/", "type": [ "Social media" ], "note": null } ], "download": [ { "url": "https://www.jalview.org/download", "type": "Downloads page", "note": null, "version": null }, { "url": "https://www.jalview.org/download/source/", "type": "Source code", "note": null, "version": null }, { "url": "https://www.jalview.org/download/?os=all", "type": "Binaries", "note": "Binaries for all platforms", "version": null }, { "url": "https://www.jalview.org/favicon.svg", "type": "Icon", "note": null, "version": null }, { "url": "https://www.jalview.org/download/other/jar/", "type": "Binaries", "note": "Executable JAR file", "version": null } ], "documentation": [ { "url": "https://www.jalview.org/about/citation", "type": [ "Citation instructions" ], "note": null }, { "url": "https://www.jalview.org/training/", "type": [ "Training material" ], "note": "Hands-on exercises, Training courses and Training videos" }, { "url": "https://www.jalview.org/help/faq", "type": [ "FAQ" ], "note": null }, { "url": "https://www.jalview.org/help/documentation/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp033", "pmid": "19151095", "pmcid": "PMC2672624", "type": [], "version": null, "note": null, "metadata": { "title": "Jalview Version 2-A multiple sequence alignment editor and analysis workbench", "abstract": "", "date": "2009-05-07T00:00:00Z", "citationCount": 7717, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Jim Procter", "email": null, "url": "http://www.lifesci.dundee.ac.uk/people/jim-procter", "orcidid": "https://orcid.org/0000-0002-7865-7382", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Geoff Barton", "email": null, "url": "https://www.lifesci.dundee.ac.uk/people/geoff-barton", "orcidid": "https://orcid.org/0000-0002-9014-5355", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "ben_s", "additionDate": "2019-02-13T17:01:40Z", "lastUpdate": "2025-12-11T14:16:30.074724Z", "editPermission": { "type": "group", "authors": [ "ben_s", "jimprocter" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "emapper2gbk", "description": "creation of genbank files from Eggnog-mapper annotation outputs", "homepage": "https://github.com/AuReMe/emapper2gbk", "biotoolsID": "emapper2gbk", "biotoolsCURIE": "biotools:emapper2gbk", "version": [ "0.3.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0925", "term": "Sequence assembly" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1233", "term": "Sequence set (protein)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [ { "uri": "http://edamontology.org/format_2305", "term": "GFF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_2205", "term": "GenBank-like format (text)" } ] } ], "note": "Genomic -single mode", "cmd": "genomes -fn genome.fna -fp proteome.faa -gff genome.gff -n \"Escherichia coli\"" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_4011", "term": "Data rescue" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "LGPL-3.0", "collectionID": [ "AuReMe" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/AuReMe/emapper2gbk", "type": [ "Repository" ], "note": null }, { "url": "https://pypi.org/project/emapper2gbk/", "type": [ "Software catalogue" ], "note": "Access to Python library" } ], "download": [ { "url": "https://github.com/AuReMe/emapper2gbk.git", "type": "Source code", "note": null, "version": "0.3.2" }, { "url": "https://pypi.org/project/emapper2gbk/#files", "type": "Software package", "note": null, "version": "0.3.2" } ], "documentation": [ { "url": "https://github.com/AuReMe/emapper2gbk", "type": [ "Installation instructions", "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Arnaud", "email": null, "url": "https://github.com/ArnaudBelcour", "orcidid": "https://orcid.org/0000-0003-1170-0785", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "Noe_Robert", "additionDate": "2025-12-10T13:18:28.703003Z", "lastUpdate": "2025-12-10T16:49:05.332576Z", "editPermission": { "type": "group", "authors": [ "jgot" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Mainzelliste", "description": "Mainzelliste is a web-based first-level pseudonymization service. It allows for the creation of personal identifiers (PID) from identifying attributes (IDAT), and thanks to the record linkage functionality, this is even possible with poor quality identifying data. The functions are available through a RESTful web interface. Mainzelliste also includes built-in consent management and supports FHIR APIs.", "homepage": "https://bitbucket.org/medicalinformatics/mainzelliste/", "biotoolsID": "mainzelliste", "biotoolsCURIE": "biotools:mainzelliste", "version": [ "v1.13.7" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_4044", "term": "Data protection" }, { "uri": "http://edamontology.org/topic_3345", "term": "Data identity and mapping" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [], "license": "AGPL-3.0", "collectionID": [ "eucaim", "EUCAIM", "Samply" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://helmholtz.software/software/mainzelliste", "type": [ "Software catalogue" ], "note": null }, { "url": "https://bitbucket.org/medicalinformatics/mainzelliste", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/medicalinformatics/mainzelliste-gui/", "type": [ "Repository" ], "note": null }, { "url": "https://docs.google.com/spreadsheets/d/1ipAPipeZa-3cBDFwQGn7kr07OsrhKSf_", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "https://bitbucket.org/medicalinformatics/mainzelliste/src/master/doc/getting-started.md", "type": [ "Quick start guide" ], "note": null }, { "url": "https://bitbucket.org/medicalinformatics/mainzelliste/src/master/doc/configuration-handbook.md", "type": [ "Installation instructions" ], "note": null }, { "url": "https://bitbucket.org/medicalinformatics/mainzelliste/src/master/docker.md", "type": [ "Installation instructions" ], "note": null }, { "url": "https://medicalinformatics.github.io/mainzelliste.de/api-doc/", "type": [ "API documentation" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/oxK6GtGg46tfRcc", "type": [ "Installation instructions" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/NCckRbAjYCj3ReR", "type": [ "Installation instructions" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/8bW9YY4Lz9KaFb7", "type": [ "Quick start guide" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/HWfZxafrzwZRMbg", "type": [ "Installation instructions" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/K84ykkt58Ze4eme", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1186/s12911-014-0123-5", "pmid": "25656224", "pmcid": "PMC4350982", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "A RESTful interface to pseudonymization services in modern web applications", "abstract": "", "date": "2015-02-07T00:00:00Z", "citationCount": 76, "authors": [], "journal": "BMC Medical Informatics and Decision Making" } } ], "credit": [], "owner": "enola", "additionDate": "2025-05-22T17:46:59.585364Z", "lastUpdate": "2025-12-10T14:03:09.546308Z", "editPermission": { "type": "group", "authors": [ "tkussel", "benamor" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "mpwt", "description": "Pathway Tools multiprocessing wrapper (for PathoLogic).", "homepage": "https://github.com/AuReMe/mpwt", "biotoolsID": "mpwt", "biotoolsCURIE": "biotools:mpwt", "version": [ "v0.8.8" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3660", "term": "Metabolic network modelling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_2305", "term": "GFF" }, { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_2013", "term": "Biological pathway or network format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [], "language": [], "license": "LGPL-3.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://anaconda.org/channels/fermentsdufutur/packages/mpwt/overview", "type": "Software package", "note": null, "version": null } ], "documentation": [], "publication": [], "credit": [], "owner": "agnesbarnabe", "additionDate": "2025-12-10T12:34:59.616360Z", "lastUpdate": "2025-12-10T12:34:59.619365Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Image Duplicates Checker", "description": "Detects duplicate or visually similar DICOM series using a tiered approach that combines metadata analysis, hash-based comparison, and pixel-level similarity metrics.\nIdeal for:\n1. High-level series comparison and classification, and\n2. Detecting duplicates even after post-processing (e.g., denoising, filtering).\n\nFor scenarios requiring strict, image-level deduplication based on pixel content, fully agnostic to metadata changes, consider using [insert link to Champalimaud/s implementation]", "homepage": "https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologies", "biotoolsID": "dicom_image_similarity-duplicate_checker", "biotoolsCURIE": "biotools:dicom_image_similarity-duplicate_checker", "version": [ "2.0" ], "otherID": [], "relation": [ { "biotoolsID": "data_integration_quality_check_tool_diqct", "type": "includedIn" } ], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "eucaim" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/10GsrgRCeyrZrdus04iI-967llth0o9yE/edit?usp=drive_link&ouid=108776251279939449410&rtpof=true&sd=true", "type": [ "General" ], "note": null } ], "publication": [], "credit": [], "owner": "difoto", "additionDate": "2025-05-28T23:55:08.439649Z", "lastUpdate": "2025-12-09T23:38:40.427406Z", "editPermission": { "type": "group", "authors": [ "authEucaim" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "InstaNovo", "description": "InstaNovo is a transformer neural network with the ability to translate fragment ion peaks into the sequence of amino acids that make up the studied peptide(s).", "homepage": "https://github.com/instadeepai/instanovo", "biotoolsID": "instanovo", "biotoolsCURIE": "biotools:instanovo", "version": [ "1.2.2" ], "otherID": [], "relation": [ { "biotoolsID": "matchms", "type": "uses" }, { "biotoolsID": "pyteomics", "type": "uses" }, { "biotoolsID": "spectrum_utils", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3644", "term": "de Novo sequencing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_3654", "term": "mzXML" }, { "uri": "http://edamontology.org/format_3651", "term": "MGF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": "instanovo predict --data-path /path/to/your/spectra.mgf --output-path predictions.csv" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "proteomics", "ms-utils" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/instadeepai/instanovo", "type": [ "Repository" ], "note": null }, { "url": "https://instanovo.ai/", "type": [ "Other" ], "note": null }, { "url": "https://github.com/instadeepai/InstaNovo/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/instadeepai/InstaNovo/discussions", "type": [ "Discussion forum" ], "note": null } ], "download": [ { "url": "https://github.com/instadeepai/InstaNovo/releases/tag/1.2.2", "type": "Source code", "note": null, "version": "1.1.2" } ], "documentation": [ { "url": "https://instadeepai.github.io/InstaNovo/", "type": [ "General" ], "note": null }, { "url": "https://instadeepai.github.io/InstaNovo/tutorials/getting_started/#installation", "type": [ "Installation instructions" ], "note": null }, { "url": "https://instadeepai.github.io/InstaNovo/tutorials/getting_started/", "type": [ "Quick start guide" ], "note": null }, { "url": "https://instadeepai.github.io/InstaNovo/reference/cli/", "type": [ "Command-line options" ], "note": null }, { "url": "https://instadeepai.github.io/InstaNovo/API/summary/", "type": [ "API documentation" ], "note": null }, { "url": "https://instadeepai.github.io/InstaNovo/citation/", "type": [ "Citation instructions" ], "note": null } ], "publication": [ { "doi": "10.1038/s42256-025-01019-5", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "1.1.4", "note": null, "metadata": { "title": "InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments", "abstract": "", "date": "2025-04-01T00:00:00Z", "citationCount": 7, "authors": [], "journal": "Nature Machine Intelligence" } } ], "credit": [ { "name": "Kevin Eloff", "email": "k.eloff@instadeep.com", "url": null, "orcidid": "https://orcid.org/0000-0003-1355-8743", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "Konstantinos Kalogeropoulos", "email": "konka@dtu.dk", "url": null, "orcidid": "https://orcid.org/0000-0003-3907-9281", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "Rachel Catzel", "email": "r.catzel@instadeep.com", "url": null, "orcidid": "https://orcid.org/0000-0002-2983-9833", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Maintainer" ], "note": null }, { "name": "Jeroen Van Goey", "email": "j.vangoey@instadeep.com", "url": null, "orcidid": "https://orcid.org/0000-0003-4480-5567", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Maintainer" ], "note": null }, { "name": "Timothy P. Jenkins", "email": "tpaje@dtu.dk", "url": null, "orcidid": "https://orcid.org/0000-0003-2979-5663", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null } ], "owner": "BioGeek", "additionDate": "2025-12-09T09:22:22.735091Z", "lastUpdate": "2025-12-09T21:41:17.117080Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "D-Genies", "description": "D-GENIES – for Dot plot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation.", "homepage": "https://dgenies.toulouse.inrae.fr/", "biotoolsID": "dgenies", "biotoolsCURIE": "biotools:dgenies", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3182", "term": "Genome alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2161", "term": "Sequence similarity plot" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0490", "term": "Dot plot plotting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2161", "term": "Sequence similarity plot" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/genotoul-bioinfo/dgenies", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.7717/peerj.4958", "pmid": "29888139", "pmcid": "PMC5991294", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "D-GENIES: Dot plot large genomes in an interactive, efficient and simple way", "abstract": "", "date": "2018-01-01T00:00:00Z", "citationCount": 487, "authors": [], "journal": "PeerJ" } } ], "credit": [ { "name": "Floréal Cabanettes", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Christophe Klopp", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-7126-5477", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Philippe Bordron", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-1975-0920", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Vincent Dominguez", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "GenoToul bioinformatics facility", "email": null, "url": "http://bioinfo.genotoul.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null } ], "owner": "pbordron", "additionDate": "2025-12-09T09:09:20.909736Z", "lastUpdate": "2025-12-09T11:03:03.972315Z", "editPermission": { "type": "group", "authors": [ "choede" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Mapping-based Genome Size Estimation", "description": "Mapping-based Genome Size Estimation (MGSE) predicts the size of a genome based on a (short) read mapping to an existing genome assembly. Low complexity sequences are often collapsed in a genome assembly thus the assembly size is smaller than the genome size. The actual copy number of sequences in the assembly is identified based on the coverage (sequencing depth) which allows the calculation of a genome size.", "homepage": "https://github.com/bpucker/MGSE", "biotoolsID": "mgse", "biotoolsCURIE": "biotools:mgse", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0157", "term": "Sequence composition, complexity and repeats" }, { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://doi.org/10.1186/s12864-025-11640-8", "type": [ "Repository" ], "note": "Publication in BMC Genomics" } ], "download": [ { "url": "https://github.com/bpucker/MGSE", "type": "Downloads page", "note": "MGSE is available on GitHub", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1186/s12864-025-11640-8", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Mapping-based genome size estimation", "abstract": "", "date": "2025-12-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "BMC Genomics" } } ], "credit": [ { "name": "Boas Pucker", "email": null, "url": "https://www.pbb.uni-bonn.de", "orcidid": "https://orcid.org/0000-0002-3321-7471", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer" ], "note": null } ], "owner": "bpucker", "additionDate": "2021-01-02T12:42:50Z", "lastUpdate": "2025-12-06T16:20:42.941757Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FAIR EVA for EUCAIM", "description": "FAIR EVA: Evaluator, Validator & Advisor has been developed to check the FAIRness level of digital objects from different repositories or data portals. It requires the object identifier (preferably persistent and unique identifier) and the repository to check. It also provides a generic and agnostic way to check digital objects.\nThis software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647.", "homepage": "https://github.com/IFCA-Advanced-Computing/FAIR_eva", "biotoolsID": "fair_eva_4_eucaim", "biotoolsCURIE": "biotools:fair_eva_4_eucaim", "version": [ "EUCAIM_plugin_0.3", "EUCAIM_plugin_0.3.1", "EUCAIM_plugin_0.4.0", "EUCAIM_0.4.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" }, { "uri": "http://edamontology.org/operation_2428", "term": "Validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1052", "term": "URL" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": null, "cmd": "python scripts/batch_runner.py --plugin eucaim_catalogue --out faireva_out" } ], "toolType": [ "Plug-in", "Command-line tool", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/IFCA-Advanced-Computing/FAIR_eva", "type": [ "Repository" ], "note": "Repository for FAIR EVA, without the EUCAIM specific plugin" } ], "download": [], "documentation": [ { "url": "https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.md", "type": [ "General" ], "note": "Documentation for the main package, EUCAIM plugin specific documentation not included." }, { "url": "https://gitlabpages.ifca.es/fair-eva-guide-608baa/", "type": [ "User manual" ], "note": "Wiki page with FAIR EVA for EUCAIM specific instructions." } ], "publication": [ { "doi": "10.1038/s41597-023-02652-8", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": null, "abstract": null, "date": null, "citationCount": 0, "authors": [], "journal": null } } ], "credit": [ { "name": "Fernando Aguilar", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-9462-4831", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer", "Documentor" ], "note": "Creator and devloper of the main package FAIR EVA.\nThis software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647." }, { "name": "David Rodríguez", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9160-5106", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": "Developer of the EUCAIM plugin." }, { "name": "Inés Victoria", "email": null, "url": null, "orcidid": "https://orcid.org/0009-0003-7950-3937", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Developer of the EUCAIM plugin." } ], "owner": "davrodgon", "additionDate": "2025-06-30T08:52:48.500476Z", "lastUpdate": "2025-12-04T10:57:20.901575Z", "editPermission": { "type": "group", "authors": [ "ines.ifca", "davrodgon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ML model for MR series categorisation (EUCAIM-SW-011_T-01-01-011)", "description": "A tool based on artificial intelligence that is able to perform a categorisation of MRI series by using standardized DICOM tags. The categorisation includes the type of sequence (e.g. spin echo, gradient echo), the weighting (e.g. T1W, T2W, DCE, ...), the presence of fat suppression and the detection of non-relevant / junk series (e.g. localizers, calibrations, screenshots...).", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab", "biotoolsID": "ml_model_for_mr_series_categorisation", "biotoolsCURIE": "biotools:ml_model_for_mr_series_categorisation", "version": [ "1.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2990", "term": "Classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": null, "cmd": "docker run -it --rm --name my-container \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n harbor.eucaim.cancerimage.eu/processing-tools/ml_model_for_mr_series_categorisation:<version> \\\n --config-string \"{'output_name': 'classification_results.json'}\"" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" }, { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://drive.google.com/file/d/1lIUixmLItQXOyBPIXL_AzPg_jlqDKwNE/view?usp=drive_link", "type": [ "User manual" ], "note": null }, { "url": "https://drive.google.com/file/d/1jF44iszmmiHd2paD8-YhFhW2uQJ0QBAZ/view?usp=drive_link", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1186/s40537-025-01086-w", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Automatic magnetic resonance imaging series labelling for large repositories", "abstract": "", "date": "2025-12-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Journal of Big Data" } } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": "gibi230@iislafe.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Armando Gomis-Maya", "email": "armago@alumni.uv.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9527-8093", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "pedromiguel_martinez_HULAFE", "additionDate": "2025-11-25T09:58:37.569343Z", "lastUpdate": "2025-12-03T15:35:26.140884Z", "editPermission": { "type": "group", "authors": [ "casopon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "hictkpy", "description": "Python bindings for hictk: read and write .cool and .hic files directly from Python", "homepage": "https://github.com/paulsengroup/hictkpy", "biotoolsID": "hictkpy", "biotoolsCURIE": "biotools:hictkpy", "version": [ "0.0.1", "0.0.2", "0.0.3", "0.0.4", "0.0.5", "1.0.0", "1.1.0", "1.2.0", "1.3.0", "1.4.0" ], "otherID": [], "relation": [ { "biotoolsID": "hictk", "type": "uses" } ], "function": [], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/paulsengroup/hictkpy", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/paulsengroup/hictkpy/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/paulsengroup/hictkpy/discussions", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "https://github.com/paulsengroup/hictkpy/releases", "type": "Downloads page", "note": null, "version": null }, { "url": "https://pypi.org/project/hictkpy/", "type": "Binaries", "note": null, "version": null }, { "url": "https://anaconda.org/bioconda/hictkpy", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://hictkpy.readthedocs.io", "type": [ "General" ], "note": null }, { "url": "https://hictkpy.readthedocs.io/en/stable/installation.html", "type": [ "Installation instructions" ], "note": null }, { "url": "https://hictkpy.readthedocs.io/en/stable/quickstart.html", "type": [ "Quick start guide" ], "note": null }, { "url": "https://hictkpy.readthedocs.io/en/stable/api/index.html", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btae408", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "hictk: blazing fast toolkit to work with. hic and. cool files", "abstract": "", "date": "2024-07-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Bioinformatics" } } ], "credit": [], "owner": "robomics", "additionDate": "2024-04-18T08:31:46.459964Z", "lastUpdate": "2025-12-03T14:44:30.069607Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "IQA DCE tool", "description": "The purpose of the tool is to provide a complete framework for automatic detection of image quality for Breast DCE MR images. The assessment is performed on the first post-contrast dynamic phase in order to assess the most clinically relevant sequence among a number of identical acquisitions. Two categories are available for image classification, i.e. high and low quality, depending on the level of noise, degree of blurring and presence of artifacts.", "homepage": "https://hub.docker.com/repository/docker/billykforth/iqa_dce_tool/general", "biotoolsID": "iqa_dce_tool", "biotoolsCURIE": "biotools:iqa_dce_tool", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "EUPL-1.1", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://hub.docker.com/r/billykforth/iqa_dce_tool", "type": "Container file", "note": null, "version": "1.0" } ], "documentation": [ { "url": "https://docs.google.com/document/d/1hG_M21gvO4D8zkHmwtbavT8Dp6bliRU4/edit", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.3390/jimaging11110417", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "billyk", "additionDate": "2025-11-26T13:27:32.776575Z", "lastUpdate": "2025-12-03T06:46:13.717361Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Asparaginase database", "description": "Asparaginases are one of the most successful biopharmaceuticals that play a pivotal role in the treatment of acute lymphoblastic leukemia. In order to find new asparaginases with improved properties (stability, substrate affinity, immunogenicity) or to achieve these goals by enzyme engineering, it is essential to collect and accurately classify asparaginases from various sources. The database covers 101 experimentally studied proteins from the literature, a manually curated set of 127 sequences from SwissProt, and more than 100,000 automatically curated enzymes.", "homepage": "https://asparaginasedb.com/", "biotoolsID": "asparaginase_database", "biotoolsCURIE": "biotools:asparaginase_database", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal", "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "CC-BY-4.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://asparaginasedb.cz/help.html", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "owner": "spiwokv", "additionDate": "2025-11-29T18:03:55.516541Z", "lastUpdate": "2025-12-02T22:00:20.857626Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AggreProt", "description": "AggreProt is a web server to predict and engineer protein aggregation. The tool provides a per-residue numerical aggregation propensity value and an overall protein aggregation propensity profile. Along with the protein solvent accessibility area and its transmembrane propensity, AggreProt predictions aid the users on designing soluble proteins.", "homepage": "https://loschmidt.chemi.muni.cz/aggreprot/", "biotoolsID": "aggreprot", "biotoolsCURIE": "biotools:aggreprot", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java", "JavaScript" ], "license": "Proprietary", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "Proteomics" ], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkae420", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "AggreProt: A web server for predicting and engineering aggregation prone regions in proteins", "abstract": "", "date": "2024-07-05T00:00:00Z", "citationCount": 17, "authors": [], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Joan Planas-Iglesias", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "David Bednar", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Jiri Damborsky", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Simeon Borko", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "m.musil", "additionDate": "2025-12-02T12:03:53.282983Z", "lastUpdate": "2025-12-02T12:03:53.285771Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "APE", "description": "APE (the Automated Pipeline Explorer) as a command-line tool and API for automated composition of scientific workflows. APE is easily configured to a new application domain by providing it with a domain ontology and semantically annotated tools. It can then be used to synthesize purpose-specific workflows based on a specification of the available workflow inputs, desired outputs and possibly additional constraints.", "homepage": "https://github.com/sanctuuary/APE/", "biotoolsID": "ape", "biotoolsCURIE": "biotools:ape", "version": [ "2.1.7" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3429", "term": "Generation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0949", "term": "Workflow metadata" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0949", "term": "Workflow metadata" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3857", "term": "CWL" }, { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Web API", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "Java" ], "license": "Apache-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/sanctuuary/ape", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://mvnrepository.com/artifact/io.github.sanctuuary/APE/2.1.7", "type": "Software package", "note": "Download APE java library or the CLI", "version": "2.1.7" } ], "documentation": [ { "url": "https://ape-framework.readthedocs.io/", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": null, "pmid": null, "pmcid": "PMC7304703", "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1021/acs.jproteome.0c00983", "pmid": "33720735", "pmcid": "PMC8041394", "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "APE in the Wild: Automated Exploration of Proteomics Workflows in the bio.tools Registry", "abstract": "", "date": "2021-04-02T00:00:00Z", "citationCount": 7, "authors": [], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "Vedran Kasalica", "email": "vedran.kasalica@health-ri.nl", "url": null, "orcidid": "https://orcid.org/0000-0002-0097-1056", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Anna-Lena Lamprecht", "email": "anna-lena.lamprecht@uni-potsdam.de", "url": null, "orcidid": "https://orcid.org/0000-0003-1953-5606", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "VKasalica", "additionDate": "2021-01-18T10:10:48Z", "lastUpdate": "2025-12-01T13:47:56.062392Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "HBAT", "description": "HBAT (Hydrogen Bond Analysis Tool) is a package to automate the analysis of potential hydrogen bonds and similar type of weak interactions in macromolecular structures, available in Protein Data Bank (PDB) file format. HBAT uses a geometric approach to identify molecular interactions by analysing distance and angular criteria.\n\nHBAT 1.1 was released in 2007 as closed source Windows binary and continue to be available via SourceForge. \n\nHBAT 2.0 was introduced in 2025 and a completed rewrite of original implementation with cross-platform support. HBAT 2.0 is open sourced under MIT License.", "homepage": "https://hbat.abhishek-tiwari.com", "biotoolsID": "hbat", "biotoolsCURIE": "biotools:hbat", "version": [ "2.x", "1.1, 1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1549", "term": "Protein hydrogen bonds" }, "format": [] } ], "note": null, "cmd": "hbat input.pdb" } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Perl", "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/abhishektiwari/hbat", "type": [ "Repository", "Issue tracker" ], "note": null }, { "url": "http://www.mybiosoftware.com/hbat-1-1-hydrogen-bond-analysis-tool.html", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "https://pypi.org/project/hbat/", "type": "Software package", "note": "Cross-platform PyPI Python Package", "version": "2.x" }, { "url": "https://github.com/abhishektiwari/hbat/releases", "type": "Binaries", "note": "Mac and Linux Binaries including AppImage, .deb, standalone executables.", "version": "2.x" }, { "url": "https://sourceforge.net/projects/hbat/", "type": "Binaries", "note": "Windows Binaries download from SourceForge", "version": "1.0, 1.1" } ], "documentation": [ { "url": "https://hbat.abhishek-tiwari.com", "type": [ "General", "API documentation", "Citation instructions", "Command-line options", "Installation instructions", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.3233/ISI-2007-00337", "pmid": "18467777", "pmcid": null, "type": [ "Primary" ], "version": null, "note": "Peer-reviewed paper for HBAT 1.0", "metadata": null }, { "doi": "10.5281/zenodo.17645321", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": "Preprint for HBAT 2.x software", "metadata": null } ], "credit": [ { "name": "Abhishek Tiwari", "email": null, "url": "https://www.abhishek-tiwari.com", "orcidid": "https://orcid.org/0000-0003-2222-2395", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "abhishektiwari", "additionDate": "2017-08-03T18:45:53Z", "lastUpdate": "2025-11-29T17:30:01.186940Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "gc-meox-tms", "description": "This package performs in-silico MeOX + TMS derivatization (as described e.g. in https://doi.org/10.1021/acs.analchem.7b01010):\n\nMethoximation: ketone R(C=O)R' and aldehyde (-HC=O) carbonyl groups are substituted with -C=NOCH3\nTrimethylsilylation: the acidic hydrogen in -OH, -SH, -COOH, -NH2, -NHR, =NH, the hydrogen is substituted with -Si(CH3)3 The substitution doesn't always have to happen; its probability is currently hardcoded in the package. Typically, multiple substitution attempts are run on each input molecule, and all distinct results are gathered.\nKnown limitation is methoximation on cycles which should be broken. This is not implemented yet.", "homepage": "https://github.com/RECETOX/gc-meox-tms", "biotoolsID": "gc-meox-tms", "biotoolsCURIE": "biotools:gc-meox-tms", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0231", "term": "Sequence editing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2301", "term": "SMILES string" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2301", "term": "SMILES string" }, "format": [] } ], "note": "Produces MeOX/TMS derivatives of given compounds", "cmd": "add_derivatization_groups()" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3370", "term": "Analytical chemistry" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "Metabolomics" ], "link": [ { "url": "https://github.com/RECETOX/gc-meox-tms", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/RECETOX/gc-meox-tms/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/RECETOX/gc-meox-tms.git", "type": "Software package", "note": null, "version": "v1.0.1" } ], "documentation": [ { "url": "https://github.com/RECETOX/gc-meox-tms/blob/master/README.md", "type": [ "Installation instructions", "Command-line options" ], "note": null }, { "url": "https://github.com/RECETOX/gc-meox-tms/blob/master/example/derivatization.ipynb", "type": [ "Quick start guide", "Training material" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.analchem.7b01010", "pmid": "28520403", "pmcid": null, "type": [], "version": null, "note": "The package is based on this publication", "metadata": { "title": "Integrated Strategy for Unknown EI-MS Identification Using Quality Control Calibration Curve, Multivariate Analysis, EI-MS Spectral Database, and Retention Index Prediction", "abstract": "", "date": "2017-06-20T00:00:00Z", "citationCount": 44, "authors": [], "journal": "Analytical Chemistry" } } ], "credit": [ { "name": "RECETOX SpecDatRI", "email": null, "url": "https://www.recetox.muni.cz/en/services/data-services-2/spectrometric-data-processing-and-analysis", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Maintainer", "Provider", "Primary contact", "Developer" ], "note": null } ], "owner": "Ondrej_Bucek", "additionDate": "2025-11-28T17:29:53.564906Z", "lastUpdate": "2025-11-28T17:42:43.031944Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Brain Metastasis Segmenter", "description": "The Brain Metastasis Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of brain metastases in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of brain metastases in MRI scans to support clinical decision-making in both diagnosis and prognosis.", "homepage": "https://github.com/BIT-UPM/EUCAIM/brain_metastasis_segmenter", "biotoolsID": "brain_metastasis_segmenter", "biotoolsCURIE": "biotools:brain_metastasis_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Workflow", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble with Adaptive Post-Processing", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Proceedings - International Symposium on Biomedical Imaging" } }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Contributor", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Contributor", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-11-04T18:24:22.573039Z", "lastUpdate": "2025-11-28T13:57:34.393084Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Sub-Saharan Africa Brain Glioma Segmenter", "description": "The Sub-Saharan Africa Brain Glioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of intercranial meningiomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of gliomas in brain MRI scans to support clinical decision-making in both diagnosis and prognosis. This tool was trained on a cohort of patients from Sub-Saharan Africa.", "homepage": "https://github.com/BIT-UPM/EUCAIM/sub_saharan_africa_brain_glioma_segmenter", "biotoolsID": "sub-saharan_africa_brain_glioma_segmenter", "biotoolsCURIE": "biotools:sub-saharan_africa_brain_glioma_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Workflow", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble with Adaptive Post-Processing", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Proceedings - International Symposium on Biomedical Imaging" } }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Contributor", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Contributor", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-11-05T11:45:08.078589Z", "lastUpdate": "2025-11-28T13:57:16.132700Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Intercranial Meningioma Segmenter", "description": "The Intercranial Meningioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of intercranial meningiomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of intercranial meningiomas in brain MRI scans to support clinical decision-making in both diagnosis and prognosis.", "homepage": "https://github.com/BIT-UPM/EUCAIM/intercranial_meningioma_segmenter", "biotoolsID": "intercranial_meningioma_segmenter", "biotoolsCURIE": "biotools:intercranial_meningioma_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Workflow", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble with Adaptive Post-Processing", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Proceedings - International Symposium on Biomedical Imaging" } }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Contributor", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Contributor", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-11-05T10:35:32.782850Z", "lastUpdate": "2025-11-28T13:56:53.168138Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Brain Glioma Segmenter", "description": "The Brain Glioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of brain gliomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of brain gliomas in MRI scans to support clinical decision-making in both diagnosis and prognosis.", "homepage": "https://github.com/BIT-UPM/EUCAIM/brain_glioma_segmenter", "biotoolsID": "brain_glioma_segmenter", "biotoolsCURIE": "biotools:brain_glioma_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow", "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble with Adaptive Post-Processing", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Proceedings - International Symposium on Biomedical Imaging" } }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor", "Developer", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-11-05T10:49:02.917891Z", "lastUpdate": "2025-11-28T13:56:29.777759Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Pediatric Brain Tumor Segmenter", "description": "The Pediatric Brain Tumor Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of pediatric brain tumors in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of pediatric brain tumors in MRI scans to support clinical decision-making in both diagnosis and prognosis.", "homepage": "https://github.com/BIT-UPM/EUCAIM/pediatric_brain_tumor_segmenter", "biotoolsID": "pediatric_brain_tumor_segmenter", "biotoolsCURIE": "biotools:pediatric_brain_tumor_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Workflow", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-SA-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble with Adaptive Post-Processing", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Proceedings - International Symposium on Biomedical Imaging" } }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Contributor", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Contributor", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-10-28T18:31:05.926498Z", "lastUpdate": "2025-11-28T13:55:19.273705Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MITK", "description": "The Medical Imaging Interaction Toolkit (MITK) is a free open-source software for the development of interactive medical image processing software. Based on MITK, there is the MITK Workbench, a powerful and free application to view, process, and segment medical images.", "homepage": "https://www.mitk.org/", "biotoolsID": "mitk", "biotoolsCURIE": "biotools:mitk", "version": [ "v2023.04" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3551", "term": "nrrd" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3551", "term": "nrrd" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Workbench", "Desktop application", "Library" ], "topic": [], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "C++" ], "license": "BSD-3-Clause", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/MITK/MITK/", "type": [ "Repository" ], "note": null }, { "url": "https://lists.sourceforge.net/lists/listinfo/mitk-users", "type": [ "Mailing list" ], "note": "If you have any questions related to the use of or the development with MITK, please use the official mailing list.\n\nNote that you have to subscribe to the mailing list in order to send mails" } ], "download": [ { "url": "https://www.mitk.org/wiki/Downloads", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://docs.mitk.org/2023.04/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.media.2005.04.005", "pmid": "15896995", "pmcid": null, "type": [], "version": null, "note": "Nolden, Marco, et al. \"The Medical Imaging Interaction Toolkit: challenges and advances: 10 years of open-source development.\"\nInternational journal of computer assisted radiology and surgery 8 (2013): 607-620", "metadata": { "title": "The medical imaging interaction toolkit", "abstract": "Thoroughly designed, open-source toolkits emerge to boost progress in medical imaging. The Insight Toolkit (ITK) provides this for the algorithmic scope of medical imaging, especially for segmentation and registration. But medical imaging algorithms have to be clinically applied to be useful, which additionally requires visualization and interaction. The Visualization Toolkit (VTK) has powerful visualization capabilities, but only low-level support for interaction. In this paper, we present the Medical Imaging Interaction Toolkit (MITK). The goal of MITK is to significantly reduce the effort required to construct specifically tailored, interactive applications for medical image analysis. MITK allows an easy combination of algorithms developed by ITK with visualizations created by VTK and extends these two toolkits with those features, which are outside the scope of both. MITK adds support for complex interactions with multiple states as well as undo-capabilities, a very important prerequisite for convenient user interfaces. Furthermore, MITK facilitates the realization of multiple, different views of the same data (as a multiplanar reconstruction and a 3D rendering) and supports the visualization of 3D+t data, whereas VTK is only designed to create one kind of view of 2D or 3D data. MITK reuses virtually everything from ITK and VTK. Thus, it is not at all a competitor to ITK or VTK, but an extension, which eases the combination of both and adds the features required for interactive, convenient to use medical imaging software. MITK is an open-source project (www.mitk.org) © 2005 Elsevier B.V. All rights reserved.", "date": "2005-12-01T00:00:00Z", "citationCount": 378, "authors": [ { "name": "Wolf I." }, { "name": "Vetter M." }, { "name": "Wegner I." }, { "name": "Bottger T." }, { "name": "Nolden M." }, { "name": "Schobinger M." }, { "name": "Hastenteufel M." }, { "name": "Kunert T." }, { "name": "Meinzer H.-P." } ], "journal": "Medical Image Analysis" } }, { "doi": "10.1007/s11548-013-0840-8", "pmid": "23588509", "pmcid": null, "type": [], "version": null, "note": "Nolden, Marco, et al. \"The Medical Imaging Interaction Toolkit: challenges and advances: 10 years of open-source development.\"\nInternational journal of computer assisted radiology and surgery 8 (2013): 607-620", "metadata": { "title": "The medical imaging interaction toolkit: Challenges and advances: 10 years of open-source development", "abstract": "Purpose: The Medical Imaging Interaction Toolkit (MITK) has been available as open-source software for almost 10 years now. In this period the requirements of software systems in the medical image processing domain have become increasingly complex. The aim of this paper is to show how MITK evolved into a software system that is able to cover all steps of a clinical workflow including data retrieval, image analysis, diagnosis, treatment planning, intervention support, and treatment control. Methods: MITK provides modularization and extensibility on different levels. In addition to the original toolkit, a module system, micro services for small, system-wide features, a service-oriented architecture based on the Open Services Gateway initiative (OSGi) standard, and an extensible and configurable application framework allow MITK to be used, extended and deployed as needed. A refined software process was implemented to deliver high-quality software, ease the fulfillment of regulatory requirements, and enable teamwork in mixed-competence teams. Results: MITK has been applied by a worldwide community and integrated into a variety of solutions, either at the toolkit level or as an application framework with custom extensions. The MITK Workbench has been released as a highly extensible and customizable end-user application. Optional support for tool tracking, image-guided therapy, diffusion imaging as well as various external packages (e.g. CTK, DCMTK, OpenCV, SOFA, Python) is available. MITK has also been used in several FDA/CE-certified applications, which demonstrates the high-quality software and rigorous development process. Conclusions: MITK provides a versatile platform with a high degree of modularization and interoperability and is well suited to meet the challenging tasks of today's and tomorrow's clinically motivated research. © 2013 CARS.", "date": "2013-01-01T00:00:00Z", "citationCount": 354, "authors": [ { "name": "Nolden M." }, { "name": "Zelzer S." }, { "name": "Seitel A." }, { "name": "Wald D." }, { "name": "Muller M." }, { "name": "Franz A.M." }, { "name": "Maleike D." }, { "name": "Fangerau M." }, { "name": "Baumhauer M." }, { "name": "Maier-Hein L." }, { "name": "Maier-Hein K.H." }, { "name": "Meinzer H.-P." }, { "name": "Wolf I." } ], "journal": "International Journal of Computer Assisted Radiology and Surgery" } } ], "credit": [ { "name": "German Cancer Research Center (DKFZ)", "email": null, "url": "https://www.dkfz.de/de", "orcidid": null, "gridid": "grid.7497.d", "rorid": "04cdgtt98", "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "sschaum", "additionDate": "2023-06-26T12:38:15.108087Z", "lastUpdate": "2025-11-28T09:27:43.812008Z", "editPermission": { "type": "group", "authors": [ "ASHISR" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)", "description": "The tool performs a DICOM quality check in terms of correct number of files per sequence, corrupted files, precise directory hierarchy, separated dynamic series merging them, interest series filtering/selection by specific series description lists and diffusion sequence identification by b-values. It applies the desired changes to the dataset and generates a report containing information about the selected sequences, corrupted files, missing files and merged files.\n\nStatus: Deployed", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "biotoolsID": "dicom_file_integrity_checker_by_gibi230", "biotoolsCURIE": "biotools:dicom_file_integrity_checker_by_gibi230", "version": [ "2.0.0", "2.1.0", "2.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "For Data Holders (ingestion-tools)", "cmd": "docker run -it --rm --name my-container \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n -v \"<config_path>:/config\" \\\n harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_file_integrity_checker:latest" }, { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "For Data Users (processing-tools)", "cmd": "docker run -it --rm --name my-container \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n harbor.eucaim.cancerimage.eu/processing-tools/dicom_file_integrity_checker:latest \\\n /app/entrypoint.sh --config-string \"{'QA': {'sequence_selection': ['ALL'], 'modality_selection': ['ALL'], 'input_directory': 'dataset_id'}}\"" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" }, { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "type": [ "Software catalogue" ], "note": "Link to EUCAIM's Harbor for Data Holders" }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/dicom_file_integrity_checker/artifacts-tab", "type": [ "Software catalogue" ], "note": "Link to EUCAIM's Harbor for Data Users" } ], "download": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "type": "Container file", "note": "EUCAIM user needed", "version": "2.1.0" } ], "documentation": [ { "url": "https://drive.google.com/file/d/1s8-nVAvSuAGTHWwun4AQcgHtRWclsFg2/view?usp=sharing", "type": [ "User manual" ], "note": null }, { "url": "https://drive.google.com/file/d/1pO_td7uvlsFWy6AZi8AOq3__hm4L2xSv/view?usp=drive_link", "type": [ "Terms of use" ], "note": null } ], "publication": [], "credit": [ { "name": "GIBI230 - HULAFE", "email": "gibi230@iislafe.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Adrian Galiana-Bordera", "email": "adrian_galiana@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8324-8284", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "pedromiguel_martinez_HULAFE", "additionDate": "2025-04-15T17:42:40.968987Z", "lastUpdate": "2025-11-27T13:23:38.501118Z", "editPermission": { "type": "group", "authors": [ "casopon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FTAG-Finder", "description": "Families and TAG Finder: a Snakemake workflow to identify gene families and detect Tandemly Arrayed Genes.", "homepage": "https://gitlab.com/sortion/FTAG-Finder", "biotoolsID": "ftag-finder", "biotoolsCURIE": "biotools:ftag-finder", "version": [ "0.1.0" ], "otherID": [], "relation": [ { "biotoolsID": "blast", "type": "uses" }, { "biotoolsID": "mmseqs2", "type": "uses" }, { "biotoolsID": "diamond", "type": "uses" }, { "biotoolsID": "biopython", "type": "uses" }, { "biotoolsID": "mcl", "type": "uses" } ], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "AWK", "C", "Bash", "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gitlab.com/sortion/FTAG-Finder", "type": [ "Repository" ], "note": null }, { "url": "https://gitlab.com/sortion/FTAG-Finder/-/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://gitlab.com/sortion/FTAG-Finder/-/releases", "type": "Downloads page", "note": null, "version": null } ], "documentation": [], "publication": [], "credit": [ { "name": "Carène Rizzon", "email": null, "url": "http://www.math-evry.cnrs.fr/members/crizzon/welcome", "orcidid": "https://orcid.org/0000-0003-1194-4130", "gridid": null, "rorid": "03jca6281", "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "Samuel Ortion", "email": null, "url": null, "orcidid": "https://orcid.org/0009-0001-0971-497X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "sortion", "additionDate": "2025-11-27T10:42:10.165590Z", "lastUpdate": "2025-11-27T10:42:10.168319Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "South Green Genome Hubs", "description": "The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cacao, Coffee, Grass, Rice, Vanilla, Citrus and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers).", "homepage": "https://banana-genome-hub.southgreen.fr/", "biotoolsID": "South_Green_Genome_Hubs", "biotoolsCURIE": "biotools:South_Green_Genome_Hubs", "version": [], "otherID": [], "relation": [ { "biotoolsID": "tripal", "type": "uses" }, { "biotoolsID": "banana_genome_hub", "type": "includes" }, { "biotoolsID": "coffee_genome_hub", "type": "includes" }, { "biotoolsID": "cocoa_genome_hub", "type": "includes" }, { "biotoolsID": "rice_genome_hub", "type": "includes" }, { "biotoolsID": "sugarcane_genome_hub", "type": "includes" }, { "biotoolsID": "southgreen", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3208", "term": "Genome visualisation" }, { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" } ], "operatingSystem": [], "language": [ "JavaScript", "PHP" ], "license": "GPL-2.0", "collectionID": [ "Genome Hub" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Data", "Tools" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/SouthGreenPlatform/genomehubs", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "https://banana-genome-hub.southgreen.fr/content/term-service", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1093/database/bat035", "pmid": "23707967", "pmcid": "PMC3662865", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The banana genome hub", "abstract": "", "date": "2013-12-01T00:00:00Z", "citationCount": 150, "authors": [], "journal": "Database" } }, { "doi": "10.1093/nar/gku1108", "pmid": "25392413", "pmcid": "PMC4383925", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The coffee genome hub: A resource for coffee genomes", "abstract": "", "date": "2015-01-28T00:00:00Z", "citationCount": 52, "authors": [], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/hr/uhac221", "pmid": "36479579", "pmcid": "PMC9720444", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The banana genome hub: a community database for genomics in the Musaceae", "abstract": "", "date": "2022-01-01T00:00:00Z", "citationCount": 29, "authors": [], "journal": "Horticulture Research" } }, { "doi": "10.1016/j.xplc.2022.100330", "pmid": "35617961", "pmcid": "PMC9482989", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly", "abstract": "", "date": "2022-09-12T00:00:00Z", "citationCount": 26, "authors": [], "journal": "Plant Communications" } } ], "credit": [ { "name": "Gaetan Droc", "email": "droc@cirad.fr", "url": null, "orcidid": "https://orcid.org/0000-0003-1849-1269", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Provider", "Support" ], "note": null }, { "name": "Alexis Dereeper", "email": "alexis.dereeper@ird.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Mathieu Rouard", "email": "m.rouard@cgiar.org", "url": null, "orcidid": "https://orcid.org/0000-0003-1849-1269", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Maintainer", "Support" ], "note": null }, { "name": "Valentin Guignon", "email": "v.guignon@cgiar.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Chrisitine Tranchant", "email": "christine.tranchant@ird.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Stéphanie Bocs", "email": "stephanie.sidibe-bocs@cirad.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "mrouard", "additionDate": "2020-02-26T09:24:43Z", "lastUpdate": "2025-11-27T09:14:28.500250Z", "editPermission": { "type": "group", "authors": [ "gdroc", "Droc" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "trimAl", "description": "Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.", "homepage": "https://trimal.readthedocs.io", "biotoolsID": "trimal", "biotoolsCURIE": "biotools:trimal", "version": [ "1.5.1", "2.0-RC" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1916", "term": "Alignment" }, "format": [ { "uri": "http://edamontology.org/format_1998", "term": "phylipnon" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "C++" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/inab/trimal", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/inab/trimal", "type": "Source code", "note": null, "version": "1.5.1" }, { "url": "https://github.com/inab/trimal/tree/2.0_RC", "type": "Source code", "note": null, "version": "2.0-RC" } ], "documentation": [ { "url": "http://trimal.cgenomics.org/", "type": [ "General" ], "note": "Old versions" }, { "url": "https://trimal.readthedocs.io", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp348", "pmid": "19505945", "pmcid": "PMC2712344", "type": [], "version": null, "note": null, "metadata": { "title": "trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses", "abstract": "", "date": "2009-08-01T00:00:00Z", "citationCount": 8679, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Salvador Capella-Gutierrez", "email": "salcagu@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": null, "email": "tgabaldon@crg.es", "url": "http://gabaldonlab.crg.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "scapella", "additionDate": "2017-04-15T08:42:53Z", "lastUpdate": "2025-11-26T09:30:50.611915Z", "editPermission": { "type": "group", "authors": [ "nico_bsc", "sergitobara" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }
