Resource List
List all resources, or create a new resource.
GET /api/t/?accessibility=%22Open+access%22
{ "count": 8910, "next": "?page=2", "previous": null, "list": [ { "name": "MetaboLink", "description": "A web application for Streamlined Processing and Analysis of Large-Scale Untargeted Metabolomics Data.", "homepage": "https://computproteomics.bmb.sdu.dk/MetaboLink/", "biotoolsID": "metabolink", "biotoolsCURIE": "biotools:metabolink", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3557", "term": "Imputation" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0153", "term": "Lipidomics" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/M3Metabolomics/MetaboLink/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/M3Metabolomics/MetaboLink/wiki", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/BIOINFORMATICS/BTAE459", "pmid": "39018180", "pmcid": "PMC11269424", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MetaboLink: a web application for streamlined processing and analysis of large-scale untargeted metabolomics data", "abstract": "", "date": "2024-07-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Ana Mendes", "email": "anamendesml@outlook.com", "url": null, "orcidid": "https://orcid.org/0009-0008-5170-0927", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Nils J Færgeman", "email": "nils.f@bmb.sdu.dk", "url": null, "orcidid": "https://orcid.org/0000-0002-9281-5287", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Pub2Tools", "additionDate": "2025-07-21T09:43:28.406602Z", "lastUpdate": "2025-09-16T08:41:00.482475Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "SLiM", "description": "Evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Includes a graphical modeling environment.", "homepage": "https://messerlab.org/slim/", "biotoolsID": "SLiM_software", "biotoolsCURIE": "biotools:SLiM_software", "version": [ "5.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0550", "term": "DNA substitution modelling" }, { "uri": "http://edamontology.org/operation_0230", "term": "Sequence generation" }, { "uri": "http://edamontology.org/operation_3946", "term": "Ecological modelling" } ], "input": [], "output": [], "note": "Run individual-based eco-evolutionary simulations with explicit genetics", "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0610", "term": "Ecology" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3299", "term": "Evolutionary biology" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://messerlab.org/slim/", "type": [ "Software catalogue" ], "note": "SLiM home page in the Messer Lab website" }, { "url": "https://github.com/MesserLab/SLiM", "type": [ "Repository" ], "note": "GitHub repository for SLiM" }, { "url": "https://groups.google.com/g/slim-discuss", "type": [ "Discussion forum" ], "note": "Discussion forum for SLiM questions" }, { "url": "https://groups.google.com/g/slim-announce", "type": [ "Mailing list" ], "note": "Announcements mailing list" } ], "download": [ { "url": "http://benhaller.com/slim/SLiM.zip", "type": "Source code", "note": "A source archive for the command-line `slim` tool only. Complete source code is on GitHub, but most platforms have an installer anyway; see the manual, chapter 2, for installation instructions.", "version": null }, { "url": "https://github.com/MesserLab/SLiM/releases/latest", "type": "Downloads page", "note": "The GitHub page for the current release version, to obtain full source code.", "version": null } ], "documentation": [ { "url": "http://benhaller.com/slim/SLiM_Manual.pdf", "type": [ "User manual" ], "note": "The manual for SLiM itself" }, { "url": "http://benhaller.com/slim/Eidos_Manual.pdf", "type": [ "User manual" ], "note": "The manual for Eidos, the scripting language used by SLiM" }, { "url": "http://benhaller.com/slim/SLiMEidosRefSheets.zip", "type": [ "Quick start guide" ], "note": "Quick reference sheets for SLiM and Eidos" } ], "publication": [ { "doi": "10.1093/molbev/msy228", "pmid": "30517680", "pmcid": "PMC6389312", "type": [ "Primary" ], "version": "3.0", "note": "B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond the Wright–Fisher Model. Molecular Biology and Evolution 36(3), 632–637.", "metadata": { "title": "SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model", "abstract": "", "date": "2019-03-01T00:00:00Z", "citationCount": 541, "authors": [], "journal": "Molecular Biology and Evolution" } }, { "doi": "10.1093/molbev/msy237", "pmid": "30590560", "pmcid": "PMC6501880", "type": [ "Method" ], "version": "3.0", "note": "B.C. Haller, P.W. Messer. (2019). Evolutionary modeling in SLiM 3 for beginners. Molecular Biology and Evolution 36(5), 1101–1109.", "metadata": { "title": "Evolutionary Modeling in SLiM 3 for Beginners", "abstract": "", "date": "2019-05-01T00:00:00Z", "citationCount": 13, "authors": [], "journal": "Molecular Biology and Evolution" } }, { "doi": "10.1111/1755-0998.12968", "pmid": "30565882", "pmcid": "PMC6393187", "type": [ "Primary" ], "version": "3.0", "note": "B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources 19(2), 552–566.", "metadata": { "title": "Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes", "abstract": "", "date": "2019-03-01T00:00:00Z", "citationCount": 123, "authors": [], "journal": "Molecular Ecology Resources" } }, { "doi": "10.1101/2025.08.07.669155", "pmid": "40832315", "pmcid": "PMC12363870", "type": [ "Primary" ], "version": "5.0", "note": "BC Haller, PL Ralph, PW Messer. (2025). SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes. bioRxiv, 2025.08. 07.669155", "metadata": null }, { "doi": "10.1086/723601", "pmid": "37130229", "pmcid": "PMC10793872", "type": [ "Primary" ], "version": "4.0", "note": "B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary modeling. The American Naturalist 201(5), E127–E139.", "metadata": { "title": "SLiM 4: Multispecies Eco-Evolutionary Modeling", "abstract": "", "date": "2023-05-01T00:00:00Z", "citationCount": 124, "authors": [], "journal": "American Naturalist" } } ], "credit": [ { "name": "Philipp Messer", "email": "messer@cornell.edu", "url": "https://messerlab.org", "orcidid": "https://orcid.org/0000-0001-8453-9377", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Benjamin C. Haller", "email": "bhaller@benhaller.com", "url": "http://benhaller.com", "orcidid": "https://orcid.org/0000-0003-1874-8327", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bchaller", "additionDate": "2019-05-27T16:59:15Z", "lastUpdate": "2025-09-13T19:34:39.164982Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CATS-rf", "description": "CATS-rf evaluates transcriptome assemblies using RNA-seq reads without requiring a reference genome", "homepage": "https://github.com/bodulic/CATS-rf", "biotoolsID": "cats-rf", "biotoolsCURIE": "biotools:cats-rf", "version": [ "1.0.3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_4019", "term": "Biosciences" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R", "Bash" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bodulic/CATS-rf", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/bodulic/CATS-rf", "type": "Source code", "note": null, "version": "1.0.2" }, { "url": "https://anaconda.org/bioconda/cats-rf", "type": "Software package", "note": null, "version": "1.0.2" }, { "url": "https://hub.docker.com/repository/docker/bodulic/cats-rf", "type": "Container file", "note": null, "version": "1.0.2" } ], "documentation": [ { "url": "https://github.com/bodulic/CATS-rf", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1101/2025.07.22.666112", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Kristian Bodulić", "email": "kristian.bodulic@gmail.com", "url": "https://orcid.org/0000-0002-1212-3302", "orcidid": "https://orcid.org/0000-0002-1212-3302", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer", "Documentor", "Primary contact" ], "note": null } ], "owner": "bodulic", "additionDate": "2025-09-03T07:50:00.879412Z", "lastUpdate": "2025-09-13T17:36:18.188276Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Atomic Charge Calculator II", "description": "Atomic Charge Calculator II (ACC II) is a web application for fast calculation of partial atomic charges.", "homepage": "https://acc2.ncbr.muni.cz", "biotoolsID": "atomic-charge-calculator-ii", "biotoolsCURIE": "biotools:atomic-charge-calculator-ii", "version": [ "2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3438", "term": "Calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" } ] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" } ] } ], "output": [], "note": "Calculation of partial atomic charges", "cmd": null } ], "toolType": [ "Web application", "Web API", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" } ], "operatingSystem": [], "language": [ "Python", "JavaScript", "C++" ], "license": "MIT", "collectionID": [ "ELIXIR-CZ" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "https://github.com/krab1k/AtomicChargeCalculator2", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/krab1k/ChargeFW2", "type": [ "Repository" ], "note": "Computational core" } ], "download": [], "documentation": [ { "url": "https://acc2.ncbr.muni.cz/static/manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkaa367", "pmid": "32402071", "pmcid": "PMC7319571", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Atomic charge calculator II: Web-based tool for the calculation of partial atomic charges", "abstract": "", "date": "2021-01-01T00:00:00Z", "citationCount": 46, "authors": [], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Radka Svobodová", "email": "radka.svobodova@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-3840-8760", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null }, { "name": "Tomáš Raček", "email": "tomas.racek@muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-0296-2452", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null } ], "owner": "ELIXIR-CZ", "additionDate": "2021-01-18T09:10:00Z", "lastUpdate": "2025-09-11T08:26:42.258113Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "fastplong", "description": "Ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.).", "homepage": "https://github.com/OpenGene/fastplong", "biotoolsID": "fastplong", "biotoolsCURIE": "biotools:fastplong", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3218", "term": "Sequencing quality control" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/OpenGene/fastplong", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/OpenGene/fastplong/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1002/imt2.107", "pmid": "38868435", "pmcid": "PMC10989850", "type": [ "Method" ], "version": null, "note": "Mentioned as Citation in the git repository. \nPublication describes only the (short read) tool fastp.", "metadata": { "title": "Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp", "abstract": "", "date": "2023-05-01T00:00:00Z", "citationCount": 716, "authors": [], "journal": "iMeta" } } ], "credit": [ { "name": "OpenGene", "email": null, "url": "https://github.com/OpenGene", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": "OpenGene - Open Source Genomics Toolbox\nOpen source tools for NGS data analysis" } ], "owner": "bart", "additionDate": "2025-09-10T13:36:20.945616Z", "lastUpdate": "2025-09-10T14:13:36.859562Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "REPET", "description": "The REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyze transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii)\n TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.", "homepage": "https://urgi.versailles.inrae.fr/Tools/REPET", "biotoolsID": "repet", "biotoolsCURIE": "biotools:repet", "version": [ "v3.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0379", "term": "Repeat sequence detection" }, { "uri": "http://edamontology.org/operation_0237", "term": "Repeat sequence analysis" } ], "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_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" } ] }, { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_1939", "term": "GFF3-seq" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0157", "term": "Sequence composition, complexity and repeats" }, { "uri": "http://edamontology.org/topic_0654", "term": "DNA" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "C++", "Python" ], "license": "CECILL-2.0", "collectionID": [ "REPET", "elixir-fr-sdp-2019", "URGI" ], "maturity": "Legacy", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://urgi.versailles.inrae.fr/download/repet/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://urgi.versailles.inrae.fr/download/repet/REPET_linux-x64-3.0.tar.gz", "type": "Source code", "note": null, "version": "v3.0" } ], "documentation": [ { "url": "https://urgi.versailles.inrae.fr/Tools/REPET", "type": [ "General" ], "note": "see also https://urgi.versailles.inrae.fr/Tools/REPET/README" }, { "url": "https://urgi.versailles.inrae.fr/Tools/REPET/INSTALL", "type": [ "Installation instructions" ], "note": null }, { "url": "https://urgi.versailles.inrae.fr/Tools/REPET/TEdenovo-tuto", "type": [ "User manual" ], "note": "See also https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto" }, { "url": "https://forgemia.inra.fr/urgi-anagen/wiki-repet/-/wikis/REPET-V3.0-tutorial", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0091929", "pmid": "24786468", "pmcid": "PMC4008368", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PASTEC: An automatic transposable element classification tool", "abstract": "", "date": "2014-05-02T00:00:00Z", "citationCount": 226, "authors": [], "journal": "PLoS ONE" } }, { "doi": "10.1371/journal.pone.0016526", "pmid": "21304975", "pmcid": "PMC3031573", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Considering transposable element diversification in de novo annotation approaches", "abstract": "", "date": "2011-02-09T00:00:00Z", "citationCount": 355, "authors": [], "journal": "PLoS ONE" } }, { "doi": "10.1371/journal.pcbi.0010022", "pmid": "16110336", "pmcid": "PMC1185648", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Combined evidence annotation of transposable elements in genome sequences", "abstract": "", "date": "2005-01-01T00:00:00Z", "citationCount": 279, "authors": [], "journal": "PLoS Computational Biology" } }, { "doi": "10.1007/s00239-003-0007-2", "pmid": "15008403", "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes", "abstract": "", "date": "2003-12-29T00:00:00Z", "citationCount": 65, "authors": [], "journal": "Journal of Molecular Evolution" } }, { "doi": "10.1109/JPROC.2016.2590833", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue", "abstract": "", "date": "2017-03-01T00:00:00Z", "citationCount": 18, "authors": [], "journal": "Proceedings of the IEEE" } } ], "credit": [ { "name": "URGI", "email": "urgi-repet@versailles.inrae.fr", "url": "http://urgi.versailles.inrae.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Developer", "Contributor", "Maintainer", "Provider", "Support", "Documentor" ], "note": "This tool has a \"Numero de depot APP\": FR 001 480007 000 R P 2008 000 31 235" } ], "owner": "Institut Francais de Bioinform", "additionDate": "2016-03-24T16:22:28Z", "lastUpdate": "2025-09-09T08:10:41.737859Z", "editPermission": { "type": "group", "authors": [ "vjamilloux", "johann_confais", "raphael.flores", "cmichotey" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PASTEClassifier", "description": "The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features. It browses the whole spectrum of possible classifications at order level using Wicker hierarchical system. It is also able to automatically classify other repeated elements like SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. The output is designed to facilitate manual curation by providing to the biologist all characteristics that have been found on each TE sequence.", "homepage": "https://urgi.versailles.inra.fr/Tools/PASTEClassifier", "biotoolsID": "PASTEClassifier", "biotoolsCURIE": "biotools:PASTEClassifier", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0157", "term": "Sequence composition, complexity and repeats" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python", "C++" ], "license": "CECILL-2.0", "collectionID": [ "URGI", "REPET" ], "maturity": "Legacy", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://urgi.versailles.inrae.fr/download/repet/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://urgi.versailles.inrae.fr/download/repet/PASTEC_linux-x64-2.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://urgi.versailles.inra.fr/Tools/PASTEClassifier/PASTEClassifier-tuto", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0091929", "pmid": "24786468", "pmcid": "PMC4008368", "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "PASTEC: An automatic transposable element classification tool", "abstract": "", "date": "2014-05-02T00:00:00Z", "citationCount": 226, "authors": [], "journal": "PLoS ONE" } } ], "credit": [ { "name": "URGI", "email": "urgi-repet@inrae.fr", "url": "https://urgi.versailles.inrae.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Developer", "Contributor", "Maintainer", "Provider", "Support", "Documentor" ], "note": null } ], "owner": "fruitshuang", "additionDate": "2019-12-23T00:50:02Z", "lastUpdate": "2025-09-09T08:10:04.310385Z", "editPermission": { "type": "group", "authors": [ "johann_confais", "cmichotey" ] }, "validated": 1, "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": [ "2.11.5.0" ], "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" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_0324", "term": "Phylogenetic tree analysis" }, { "uri": "http://edamontology.org/operation_3081", "term": "Sequence alignment editing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1939", "term": "GFF3-seq" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" }, { "uri": "http://edamontology.org/format_1938", "term": "GFF2-seq" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_3311", "term": "RNAML" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] }, { "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_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_3313", "term": "BLC" }, { "uri": "http://edamontology.org/format_3774", "term": "BioJSON (Jalview)" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" }, { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3466", "term": "EPS" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "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": [ "Linux", "Windows", "Mac" ], "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://source.jalview.org/crucible/browse/jalview", "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" } ], "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": 7499, "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": "2025-09-04T13:26:28.643607Z", "editPermission": { "type": "group", "authors": [ "ben_s", "jimprocter" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CATS-rb", "description": "CATS-rb evaluates transcriptome assemblies using the reference genome of the corresponding species", "homepage": "https://github.com/bodulic/CATS-rb", "biotoolsID": "cats-rb", "biotoolsCURIE": "biotools:cats-rb", "version": [ "1.0.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_4019", "term": "Biosciences" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R", "Bash" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bodulic/CATS-rb", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/bodulic/CATS-rb", "type": "Source code", "note": null, "version": "1.0.2" }, { "url": "https://anaconda.org/bioconda/cats-rb", "type": "Software package", "note": null, "version": "1.0.2" }, { "url": "https://hub.docker.com/repository/docker/bodulic/cats-rb", "type": "Container file", "note": null, "version": "1.0.2" } ], "documentation": [ { "url": "https://github.com/bodulic/CATS-rb", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1101/2025.07.22.666112", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Kristian Bodulić", "email": "kristian.bodulic@gmail.com", "url": "https://orcid.org/0000-0002-1212-3302", "orcidid": "https://orcid.org/0000-0002-1212-3302", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer", "Documentor", "Primary contact" ], "note": null } ], "owner": "bodulic", "additionDate": "2025-09-03T08:01:20.173602Z", "lastUpdate": "2025-09-03T08:01:20.176094Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "El-MAVEN", "description": "Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics.", "homepage": "https://github.com/ElucidataInc/ElMaven", "biotoolsID": "El-MAVEN", "biotoolsCURIE": "biotools:El-MAVEN", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ElucidataInc/ElMaven", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/ElucidataInc/ElMaven/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://elucidatainc.github.io/ElMaven/Downloads/", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/ElucidataInc/ElMaven/releases", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://elucidatainc.github.io/ElMaven/documentation/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1007/978-1-4939-9236-2_19", "pmid": "31119671", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "EL-MAVEN: A fast, robust, and user-friendly mass spectrometry data processing engine for metabolomics", "abstract": "", "date": "2019-01-01T00:00:00Z", "citationCount": 106, "authors": [], "journal": "Methods in Molecular Biology" } } ], "credit": [ { "name": null, "email": "info@elucidata.io", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": null, "email": "elmaven@elucidata.io", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hans", "additionDate": "2019-08-09T13:14:25Z", "lastUpdate": "2025-09-02T12:37:51.759364Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OmicFlow", "description": "A generalised data structure for fast and efficient loading and data munching of sparse omics data. The 'OmicFlow' requires an up-front validated metadata template from the user, which serves as a guide to connect all the pieces together by aligning them into a single object that is defined as an 'omics' class. Once this unified structure is established, users can perform manual subsetting, visualization, and statistical analysis, or leverage the automated 'autoFlow' method to generate a comprehensive report.", "homepage": "https://github.com/agusinac/OmicFlow", "biotoolsID": "omicflow", "biotoolsCURIE": "biotools:omicflow", "version": [ "1.3.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/agusinac/OmicFlow/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/agusinac/OmicFlow", "type": [ "Repository" ], "note": null }, { "url": "https://cran.r-project.org/package=OmicFlow", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://cran.r-project.org/web/packages/OmicFlow/OmicFlow.pdf", "type": [ "User manual" ], "note": null }, { "url": "https://github.com/agusinac/OmicFlow/blob/main/README.md", "type": [ "General" ], "note": "Metadata File Instructions" } ], "publication": [], "credit": [], "owner": "agusinac", "additionDate": "2025-08-20T09:24:38.732312Z", "lastUpdate": "2025-09-02T06:28:57.092837Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "European Health Research Data and Sample Catalogue", "description": "A collaborative effort to integrate the catalogues of diverse EU research projects and networks to accelerate reuse and improve citizens health.", "homepage": "https://molgeniscatalogue.org/", "biotoolsID": "molgenis_european_health_research_data_and_sample_catalogue", "biotoolsCURIE": "biotools:molgenis_european_health_research_data_and_sample_catalogue", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal" ], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1055/s-0042-1742522", "pmid": "36463884", "pmcid": "PMC9719789", "type": [], "version": null, "note": null, "metadata": { "title": "Towards an Interoperable Ecosystem of Research Cohort and Real-world Data Catalogues Enabling Multi-center Studies", "abstract": "", "date": "2022-12-04T00:00:00Z", "citationCount": 10, "authors": [], "journal": "Yearbook of Medical Informatics" } } ], "credit": [], "owner": "EleanorHyde", "additionDate": "2025-03-11T14:55:53.492167Z", "lastUpdate": "2025-09-01T08:50:33.437783Z", "editPermission": { "type": "group", "authors": [ "mswertz", "EleanorHyde" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bakta", "description": "Rapid & standardized annotation of bacterial genomes, MAGs & plasmids", "homepage": "https://github.com/oschwengers/bakta", "biotoolsID": "bakta", "biotoolsCURIE": "biotools:bakta", "version": [ "v1.11.4" ], "otherID": [], "relation": [ { "biotoolsID": "diamond", "type": "uses" }, { "biotoolsID": "hmmer3", "type": "uses" }, { "biotoolsID": "infernal", "type": "uses" }, { "biotoolsID": "trnascan-se", "type": "uses" }, { "biotoolsID": "blast", "type": "uses" }, { "biotoolsID": "aragorn", "type": "uses" }, { "biotoolsID": "pilercr", "type": "uses" }, { "biotoolsID": "deepsig", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "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_2914", "term": "Sequence features metadata" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [ { "uri": "http://edamontology.org/format_1975", "term": "GFF3" } ] }, { "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_1364", "term": "Hidden Markov model" }, "format": [ { "uri": "http://edamontology.org/format_3329", "term": "HMMER3" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" }, { "uri": "http://edamontology.org/format_1927", "term": "EMBL format" }, { "uri": "http://edamontology.org/format_1975", "term": "GFF3" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "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_2887", "term": "Nucleic acid sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": "bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fasta" } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/oschwengers/bakta", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://bioconda.github.io/recipes/bakta/README.html", "type": [ "Other" ], "note": null }, { "url": "https://bakta.computational.bio", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://zenodo.org/records/14916843", "type": "Other", "note": "Mandatory annotation database", "version": "v6.0" } ], "documentation": [ { "url": "https://github.com/oschwengers/bakta/blob/main/README.md", "type": [ "General" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.md", "type": [ "Contributions policy" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.md", "type": [ "Code of conduct" ], "note": null }, { "url": "https://bakta.readthedocs.io/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1099/mgen.0.000685", "pmid": "34739369", "pmcid": "PMC8743544", "type": [ "Primary" ], "version": "1.1", "note": null, "metadata": { "title": "Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free sequence identification", "abstract": "", "date": "2021-01-01T00:00:00Z", "citationCount": 582, "authors": [], "journal": "Microbial Genomics" } } ], "credit": [ { "name": "Oliver Schwengers", "email": "oliver.schwengers@cb.jlug.de", "url": "https://github.com/oschwengers", "orcidid": "https://orcid.org/0000-0003-4216-2721", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Justus Liebig University Giessen", "email": null, "url": "https://www.uni-giessen.de", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "oschwengers", "additionDate": "2021-05-08T17:25:21Z", "lastUpdate": "2025-09-01T07:59:35.735958Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "bebatut" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MetaSBT", "description": "MetaSBT is a scalable framework designed to automatically index microbial genomes and accurately characterize metagenome-assembled genomes using Sequence Bloom Trees.", "homepage": "https://github.com/cumbof/MetaSBT", "biotoolsID": "metasbt", "biotoolsCURIE": "biotools:metasbt", "version": [ "0.1.4.post1", "0.1.5" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/cumbof/MetaSBT", "type": [ "Repository" ], "note": "Framework Repository" }, { "url": "https://github.com/cumbof/MetaSBT-DBs", "type": [ "Repository" ], "note": "Repository with Public MetaSBT Databases" } ], "download": [ { "url": "https://pypi.io/packages/source/m/metasbt/metasbt-0.1.4.post1.tar.gz", "type": "Software package", "note": null, "version": "0.1.4" } ], "documentation": [ { "url": "https://github.com/cumbof/MetaSBT/wiki", "type": [ "General" ], "note": "Official MetaSBT Wiki" } ], "publication": [], "credit": [ { "name": "Fabio Cumbo", "email": "fabio.cumbo@gmail.com", "url": "https://cumbof.github.io", "orcidid": "https://orcid.org/0000-0003-2920-5838", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Maintainer", "Support" ], "note": null } ], "owner": "fabiocumbo", "additionDate": "2025-06-17T20:53:54.551980Z", "lastUpdate": "2025-08-29T00:30:28.809173Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ArrayAnalysis", "description": "ArrayAnalysis is a web-based application for transcriptomic data analysis. It supports the analysis of both microarray and RNA-seq data. The tool may also be installed locally as a desktop app, Docker image, or R package.", "homepage": "https://www.arrayanalysis.org", "biotoolsID": "arrayanalysis.org", "biotoolsCURIE": "biotools:arrayanalysis.org", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "CC-BY-4.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.arrayanalysis.org", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkt293", "pmid": "23620278", "pmcid": "PMC3692049", "type": [], "version": null, "note": null, "metadata": { "title": "User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org.", "abstract": "Quality control (QC) is crucial for any scientific method producing data. Applying adequate QC introduces new challenges in the genomics field where large amounts of data are produced with complex technologies. For DNA microarrays, specific algorithms for QC and pre-processing including normalization have been developed by the scientific community, especially for expression chips of the Affymetrix platform. Many of these have been implemented in the statistical scripting language R and are available from the Bioconductor repository. However, application is hampered by lack of integrative tools that can be used by users of any experience level. To fill this gap, we developed a freely available tool for QC and pre-processing of Affymetrix gene expression results, extending, integrating and harmonizing functionality of Bioconductor packages. The tool can be easily accessed through a wizard-like web portal at http://www.arrayanalysis.org or downloaded for local use in R. The portal provides extensive documentation, including user guides, interpretation help with real output illustrations and detailed technical documentation. It assists newcomers to the field in performing state-of-the-art QC and pre-processing while offering data analysts an integral open-source package. Providing the scientific community with this easily accessible tool will allow improving data quality and reuse and adoption of standards.", "date": "2013-01-01T00:00:00Z", "citationCount": 107, "authors": [ { "name": "Eijssen L.M." }, { "name": "Jaillard M." }, { "name": "Adriaens M.E." }, { "name": "Gaj S." }, { "name": "de Groot P.J." }, { "name": "Muller M." }, { "name": "Evelo C.T." } ], "journal": "Nucleic acids research" } }, { "doi": "10.1186/s12864-015-1689-8", "pmid": "26122086", "pmcid": "PMC4486126", "type": [], "version": null, "note": null, "metadata": { "title": "A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal", "abstract": "Background: Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. Results: To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. Conclusions: The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org. A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.", "date": "2015-06-30T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Eijssen L.M.T." }, { "name": "Goelela V.S." }, { "name": "Kelder T." }, { "name": "Adriaens M.E." }, { "name": "Evelo C.T." }, { "name": "Radonjic M." } ], "journal": "BMC Genomics" } } ], "credit": [ { "name": "Support Forum", "email": null, "url": "https://www.arrayanalysis.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "jarnokoetsier", "additionDate": "2017-05-16T12:28:07Z", "lastUpdate": "2025-08-28T07:09:05.106319Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "UCPH COVID19 DASHBOARD", "description": "The dashboard provides tools for visualizing the COVID-19 spread in individual countries over time, as well as comparing different countries on a similar time scale. We provide time series of Danish test data. Furthermore, we have implemented an estimator for the actual cumulative number of COVID19 cases for every country -- a.k.a. the dark numbers.", "homepage": "https://shiny.science.ku.dk/pbm/COVID19/", "biotoolsID": "ucph_covid19_dashboard", "biotoolsCURIE": "biotools:ucph_covid19_dashboard", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3324", "term": "Infectious disease" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0781", "term": "Virology" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "COVID-19" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/CSSEGISandData/COVID-19", "type": [ "Repository" ], "note": "COVID19 data" }, { "url": "https://www.ssi.dk/aktuelt/sygdomsudbrud/coronavirus/covid-19-i-danmark-epidemiologisk-overvaagningsrapport", "type": [ "Other" ], "note": "SSI data reports" }, { "url": "https://www.worldometers.info/world-population/population-by-country/", "type": [ "Other" ], "note": "Population data" } ], "download": [], "documentation": [ { "url": "https://github.com/CSSEGISandData/COVID-19", "type": [ "Terms of use" ], "note": null }, { "url": "https://github.com/nikolajthams/COVID-19/blob/master/wirvsvirus/draft/concept_online_version.pdf", "type": [ "Other" ], "note": "Analysis white paper" } ], "publication": [], "credit": [ { "name": "Nikolaj Theodor Thams", "email": "thams@math.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Martin Emil Jakobsen", "email": "m.jakobsen@math.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Phillip Bredahl Mogensen", "email": "pbm@math.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Copenhagen Causality Lab (CoCaLa)", "email": null, "url": "https://www.math.ku.dk/english/research/spt/cocala/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Johns Hopkins University", "email": null, "url": "https://www.jhu.edu/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Danish State Serum Institute (SSI)", "email": null, "url": "https://www.ssi.dk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Pbm", "additionDate": "2020-03-27T14:31:47Z", "lastUpdate": "2025-08-27T10:53:04.522927Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqseqpair", "description": "List names of sequence pairs from two FASTQ formatted files.", "homepage": "http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README", "biotoolsID": "fqseqpair", "biotoolsCURIE": "biotools:fqseqpair", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1933", "term": "FASTQ-solexa" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1933", "term": "FASTQ-solexa" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqtools/fqseqpair/1.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1477, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Kuster G.V." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:28:48Z", "lastUpdate": "2025-08-27T10:52:16.324100Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqseqname", "description": "List names of sequences from FASTQ formatted files.", "homepage": "http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README", "biotoolsID": "fqseqname", "biotoolsCURIE": "biotools:fqseqname", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Data formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1933", "term": "FASTQ-solexa" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" }, { "uri": "http://edamontology.org/topic_0077", "term": "Nucleic acids" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqtools/fqseqname/1.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1477, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Kuster G.V." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:29:17Z", "lastUpdate": "2025-08-27T10:51:46.964250Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqquality", "description": "Output reads with low quality bases trimmed (at the extremities) or masked and/or with quality descreased to the minimum. Output an extra singlet dataset if paired-end data provided.", "homepage": "http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README", "biotoolsID": "fqquality", "biotoolsCURIE": "biotools:fqquality", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqtools/fqquality/1.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1477, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Kuster G.V." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:29:40Z", "lastUpdate": "2025-08-27T10:51:05.950208Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqextract", "description": "Extract a subset of fastq reads.", "homepage": "http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README", "biotoolsID": "fqextract", "biotoolsCURIE": "biotools:fqextract", "version": [ "1.0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqtools/fqextract/1.0.1", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1477, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Kuster G.V." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:23:06Z", "lastUpdate": "2025-08-27T10:49:53.830123Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqduplicate", "description": "Detect duplicate reads. Outputs a list of read names corresponding to reads already seen in the dataset with a better quality sum score (duplicates).", "homepage": "http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README", "biotoolsID": "fqduplicate", "biotoolsCURIE": "biotools:fqduplicate", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3218", "term": "Sequencing quality control" }, { "uri": "http://edamontology.org/operation_3230", "term": "Read depth analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" }, { "uri": "http://edamontology.org/topic_0077", "term": "Nucleic acids" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqtools/fqduplicate/1.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1477, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Kuster G.V." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:22:09Z", "lastUpdate": "2025-08-27T10:49:28.510179Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqconvert", "description": "Convert quality scoring to Sanger in FASTQ files.", "homepage": "http://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README", "biotoolsID": "fqconvert", "biotoolsCURIE": "biotools:fqconvert", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0233", "term": "Sequence conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1933", "term": "FASTQ-solexa" }, { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/fqconvert2/fqconvert/1.0.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1477, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Kuster G.V." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:24:18Z", "lastUpdate": "2025-08-27T10:48:08.675794Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fqcleaner", "description": "Mini workflow for preprocessing fastq files, it includes quality trimming, duplicate and artefacts filters for FASTQ read files.", "homepage": "https://gensoft.pasteur.fr/docs/fqCleanER/21.10/", "biotoolsID": "fqcleaner", "biotoolsCURIE": "biotools:fqcleaner", "version": [ "0.4.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" }, { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur", "fqtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqcleaner/fqCleaner/0.4.1.1", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1477, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Kuster G.V." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:27:26Z", "lastUpdate": "2025-08-27T10:47:14.412802Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "datmat", "description": "‘datmat’ is a Python package aimed to easily gather data from a variety of sources and materialize it into a standardized format. It can download projects of imaging data from XNAT into the EUCAIM folder structure, and is designed to be extendible to support other inputs and outputs.", "homepage": "https://gitlab.com/radiology/infrastructure/data-materialisation/", "biotoolsID": "datmat", "biotoolsCURIE": "biotools:datmat", "version": [ "0.2.0" ], "otherID": [], "relation": [ { "biotoolsID": "xnatpy", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3802", "term": "Data sorting" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://pypi.org/project/datmat/", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "https://pypi.org/project/datmat/", "type": "Software package", "note": null, "version": null }, { "url": "https://gitlab.com/radiology/infrastructure/data-materialisation", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://datmat.readthedocs.io/latest/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Alexander Harms", "email": "alexander.harms@health-ri.nl", "url": null, "orcidid": "https://orcid.org/0009-0001-5727-6732", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Hakim Achterberg", "email": "h.achterberg@erasmusmc.nl", "url": null, "orcidid": "https://orcid.org/0000-0003-3772-4582", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Erasmus MC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "018906e22", "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null } ], "owner": "agjharms", "additionDate": "2025-08-25T14:36:13.568250Z", "lastUpdate": "2025-08-26T09:43:49.092198Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "img2catalog", "description": "This tool, 'img2catalog', is built to extract metadata from imaging data repositories, map it to a model class, and export it to a catalog. The tool is set up to be modular, but it currently supports extracting metadata from an XNAT server, converting it to the Health-RI Core v2 metadata model (https://github.com/Health-RI/health-ri-metadata/tree/v2.0.0), based on DCAT-AP v3 and Health-DCAT AP, as defined in Pydantic classes using SeMPyRO (https://github.com/Health-RI/SeMPyRO), and either writing it to an RDF file, or pushing it to a FAIR Data Point (FDP).", "homepage": "https://github.com/Health-RI/img2catalog", "biotoolsID": "img2catalog", "biotoolsCURIE": "biotools:img2catalog", "version": [ "1.0.1" ], "otherID": [], "relation": [ { "biotoolsID": "xnatpy", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_1812", "term": "Data parsing" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/Health-RI/img2catalog", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/Health-RI/img2catalog", "type": "Source code", "note": null, "version": null }, { "url": "https://pypi.org/project/img2catalog/", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/Health-RI/img2catalog/blob/main/README.md", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Alexander Harms", "email": "alexander.harms@health-ri.nl", "url": null, "orcidid": "https://orcid.org/0009-0001-5727-6732", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Health-RI", "email": null, "url": "https://www.health-ri.nl/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null } ], "owner": "agjharms", "additionDate": "2025-08-25T14:46:01.217831Z", "lastUpdate": "2025-08-25T14:46:01.219964Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EssSubgraph", "description": "EssSubgraph is a model algorithm that integrates omics data and network data to predict essential genes.", "homepage": "https://github.com/wenmm/EssSubgraph/tree/main", "biotoolsID": "esssubgraph", "biotoolsCURIE": "biotools:esssubgraph", "version": [], "otherID": [], "relation": [ { "biotoolsID": "MTGCN", "type": "includes" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0276", "term": "Protein interaction network analysis" } ], "input": [], "output": [], "note": null, "cmd": "python EssSubgraph.py --epochs 200 --device 0 --dataset ./data/esssubgraph_human_pc50_string.pkl" }, { "operation": [ { "uri": "http://edamontology.org/operation_2454", "term": "Gene prediction" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2949", "term": "Protein-protein interaction analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3360", "term": "Biomarkers" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/wenmm/EssSubgraph/tree/main", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/wenmm/EssSubgraph/tree/main", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/wenmm/EssSubgraph/tree/main", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1101/2025.07.21.665218", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": "https://www.biorxiv.org/content/10.1101/2025.07.21.665218v1.abstract", "metadata": null } ], "credit": [ { "name": "haimei wen", "email": "hudie.luoluo@gmail.com", "url": null, "orcidid": "https://orcid.org/0009-0006-1600-1210", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Susan Carpenter", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-5600-5404", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Karen McGinnis", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9564-8146", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Andrew Nelson", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-9896-1739", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Keriayn Smith", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-4351-2765", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Tian Hong", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-8212-7050", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null } ], "owner": "haimei", "additionDate": "2025-08-20T17:28:51.309591Z", "lastUpdate": "2025-08-20T18:13:15.065957Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MatHeat", "description": "MatHeat transforms your gene expression data into powerful insights, delivering interactive heatmaps, DEG analysis, volcano plots, advanced clustering, UMAP/K-Means, and Reactome pathway exploration.", "homepage": "https://matheat.streamlit.app/", "biotoolsID": "matheat", "biotoolsCURIE": "biotools:matheat", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3372", "term": "Software engineering" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://matheat.streamlit.app/", "type": [ "Service" ], "note": null }, { "url": "https://amin-mat.github.io/matheat-landing/", "type": [ "Other" ], "note": "Landing page of the MatHeat" }, { "url": "https://matheat.org/", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Seyyed Amin Seyyed Rezaei", "email": "seyyedamin1381@gmail.com", "url": "https://matheat.streamlit.app/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact", "Maintainer" ], "note": null } ], "owner": "Aminn", "additionDate": "2025-03-12T22:55:02.224894Z", "lastUpdate": "2025-08-13T11:45:03.617916Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "nf-CBRA-snvs", "description": "Workflow optimized for the analysis of rare diseases, designed to detect SNVs and INDELs in targeted sequencing data (CES/WES) and whole genome sequencing (WGS), built on Nextflow.", "homepage": "https://github.com/CIBERER/nf-CBRA-snvs", "biotoolsID": "nf-cbra-snvs", "biotoolsCURIE": "biotools:nf-cbra-snvs", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "MIT", "collectionID": [ "IMPaCT-Data" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/CIBERER/nf-CBRA-snvs", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/CIBERER/nf-CBRA-snvs", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "owner": "pminguez", "additionDate": "2025-08-12T09:03:01.228796Z", "lastUpdate": "2025-08-12T09:05:51.626707Z", "editPermission": { "type": "group", "authors": [ "yolandabq" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WHALE-FJD", "description": "Pipeline based on Nextflow and nf-core for long-read DNA sequencing analysis.", "homepage": "https://github.com/TBLabFJD/WHALE", "biotoolsID": "whale-fjd", "biotoolsCURIE": "biotools:whale-fjd", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "CC-BY-SA-4.0", "collectionID": [ "IMPaCT-Data" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/TBLabFJD/WHALE", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/TBLabFJD/WHALE", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "owner": "pminguez", "additionDate": "2025-08-12T08:52:25.808752Z", "lastUpdate": "2025-08-12T09:05:33.311501Z", "editPermission": { "type": "group", "authors": [ "yolandabq" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PARROT-FJD", "description": "Germline variant calling pipeline implemented in Nextflow which performs mapping, SNV/INDEL calling and annotation, and CNV calling and annotation for targeted sequencing (gene panels and WES) and whole genome sequencing.", "homepage": "https://github.com/TBLabFJD/PARROT-FJD", "biotoolsID": "parrot-fjd", "biotoolsCURIE": "biotools:parrot-fjd", "version": [], "otherID": [], "relation": [ { "biotoolsID": "fjd-pipeline", "type": "isNewVersionOf" }, { "biotoolsID": "priorr", "type": "usedBy" } ], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [], "language": [], "license": "CC-BY-NC-4.0", "collectionID": [ "IMPaCT-Data" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [], "elixirCommunity": [ "Rare Diseases" ], "link": [ { "url": "https://github.com/TBLabFJD/PARROT-FJD", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/TBLabFJD/PARROT-FJD", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "owner": "pminguez", "additionDate": "2024-06-19T09:33:56.106410Z", "lastUpdate": "2025-08-12T08:35:30.388356Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FJD-pipeline", "description": "Pipeline for Single Nucleotide Variants (SNVs) and Copy Number Variation (CNVs) variant calling. This tool is no longer maintained. See the new version: PARROT-FJD.", "homepage": "https://github.com/TBLabFJD/VariantCallingFJD", "biotoolsID": "fjd-pipeline", "biotoolsCURIE": "biotools:fjd-pipeline", "version": [], "otherID": [], "relation": [ { "biotoolsID": "priorr", "type": "usedBy" }, { "biotoolsID": "parrot-fjd", "type": "hasNewVersion" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" }, { "uri": "http://edamontology.org/operation_3961", "term": "Copy number variation detection" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1193", "term": "Tool name (FASTA)" }, "format": [ { "uri": "http://edamontology.org/format_2545", "term": "FASTQ-like format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python", "R", "Bash" ], "license": "CC-BY-NC-SA-4.0", "collectionID": [ "IMPaCT-Data" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/TBLabFJD/VariantCallingFJD", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://github.com/TBLabFJD/VariantCallingFJD", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/s41525-021-00278-6", "pmid": "35087072", "pmcid": "PMC8795168", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "An evaluation of pipelines for DNA variant detection can guide a reanalysis protocol to increase the diagnostic ratio of genetic diseases", "abstract": "Clinical exome (CE) sequencing has become a first-tier diagnostic test for hereditary diseases; however, its diagnostic rate is around 30–50%. In this study, we aimed to increase the diagnostic yield of CE using a custom reanalysis algorithm. Sequencing data were available for three cohorts using two commercial protocols applied as part of the diagnostic process. Using these cohorts, we compared the performance of general and clinically relevant variant calling and the efficacy of an in-house bioinformatic protocol (FJD-pipeline) in detecting causal variants as compared to commercial protocols. On the whole, the FJD-pipeline detected 99.74% of the causal variants identified by the commercial protocol in previously solved cases. In the unsolved cases, FJD-pipeline detects more INDELs and non-exonic variants, and is able to increase the diagnostic yield in 2.5% and 3.2% in the re-analysis of 78 cancer and 62 cardiovascular cases. These results were considered to design a reanalysis, filtering and prioritization algorithm that was tested by reassessing 68 inconclusive cases of monoallelic autosomal recessive retinal dystrophies increasing the diagnosis by 4.4%. In conclusion, a guided NGS reanalysis of unsolved cases increases the diagnostic yield in genetic disorders, making it a useful diagnostic tool in medical genetics.", "date": "2022-12-01T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Romero R." }, { "name": "de la Fuente L." }, { "name": "Del Pozo-Valero M." }, { "name": "Riveiro-Alvarez R." }, { "name": "Trujillo-Tiebas M.J." }, { "name": "Martin-Merida I." }, { "name": "Avila-Fernandez A." }, { "name": "Iancu I.-F." }, { "name": "Perea-Romero I." }, { "name": "Nunez-Moreno G." }, { "name": "Damian A." }, { "name": "Rodilla C." }, { "name": "Almoguera B." }, { "name": "Corton M." }, { "name": "Ayuso C." }, { "name": "Minguez P." } ], "journal": "npj Genomic Medicine" } } ], "credit": [ { "name": "Bioinformatics Unit IIS-FJD", "email": "pablo.minguez@quironsalud.es", "url": "https://www.translationalbioinformaticslab.es/", "orcidid": "https://orcid.org/0000-0003-4099-9421", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "iiancu", "additionDate": "2022-03-21T17:29:40.559556Z", "lastUpdate": "2025-08-12T08:31:29.574795Z", "editPermission": { "type": "group", "authors": [ "gonumo", "pminguez", "yolandabq" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MacSyLib", "description": "a Python package library that allow to model and detect macromolecular systems, genetic pathways… by similarity search in prokaryotes datasets.", "homepage": "https://github.com/gem-pasteur/macsylib", "biotoolsID": "macsylib", "biotoolsCURIE": "biotools:macsylib", "version": [ "1.0.1" ], "otherID": [], "relation": [ { "biotoolsID": "macsyfinder", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3949", "term": "Profile HMM" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1245", "term": "Sequence cluster (protein)" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "GEM Pasteur" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/gem-pasteur/macsylib", "type": [ "Repository" ], "note": null }, { "url": "https://pypi.org/project/MacSyLib/", "type": [ "Other" ], "note": null }, { "url": "https://macsylib.readthedocs.io/en/latest/", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://github.com/gem-pasteur/macsylib", "type": "Source code", "note": null, "version": "1.0.1" }, { "url": "https://pypi.org/project/MacSyLib/", "type": "Software package", "note": null, "version": "1.0.1" } ], "documentation": [ { "url": "https://macsylib.readthedocs.io/en/latest/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.24072/pcjournal.250", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes", "abstract": "Complex cellular functions are usually encoded by a set of genes in one or a few orga-nized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system. We hereby present a major release of MacSyFinder (version 2) coded in Python 3. The code was improved and rationalized to facilitate future maintainability. Several new features were added to allow more flexible modelling of the systems. We introduce a more intuitive and comprehensive search engine to identify all the best candidate systems and sub-optimal ones that respect the models’ constraints. We also introduce the novel macsydata companion tool that enables the easy installation and broad distribution of the models developed for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated and improved MacSyFinder popular mod-els: TXSScan to identify protein secretion systems, TFFscan to identify type IV filaments, CONJscan to identify conjugative systems, and CasFinder to identify CRISPR associated proteins. MacSyFinder and the updated models are available at: https://github.com/gem-pasteur/macsyfinder.", "date": "2023-01-01T00:00:00Z", "citationCount": 43, "authors": [ { "name": "Neron B." }, { "name": "Denise R." }, { "name": "Coluzzi C." }, { "name": "Touchon M." }, { "name": "Rocha E.P.C." }, { "name": "Abby S.S." } ], "journal": "Peer Community Journal" } } ], "credit": [ { "name": "Institut Pasteur", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "0495fxg12", "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "Microbial Evolutionary Genomics Unit", "email": null, "url": "https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Bioinformatics and Biostatistics HUB", "email": null, "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Eduardo P.C. Rocha", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-7704-822X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Sophie Abby", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-5231-3346", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Bertrand Néron", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-0220-0482", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bneron", "additionDate": "2025-08-07T10:25:22.118390Z", "lastUpdate": "2025-08-11T12:14:42.322020Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GENEX workflow", "description": "This is a computational workflow for detecting coordinates of microbial-like or human-like sequences in eukaryotic and prokaryotic reference genomes. The workflow accepts a reference genome in FASTA-format and outputs coordinates of microbial-like (human-like) regions in BED-format. The workflow builds a Bowtie2 index of the reference genome and aligns pre-computed microbial (GTDB v.214 or NCBI RefSeq release 213) or human (hg38) pseudo-reads to the reference, then custom scripts are used for detection of the positions of covered regions and quantification of most abundant microbial species, the latter is only when screening for microbial-like sequences in eukaryotic references.", "homepage": "https://github.com/NikolayOskolkov/MCWorkflow", "biotoolsID": "genex_workflow", "biotoolsCURIE": "biotools:genex_workflow", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" } ], "operatingSystem": [], "language": [], "license": "CC0-1.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/NikolayOskolkov/MCWorkflow", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/2025.03.19.644176", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "Nikolay_Oskolkov", "additionDate": "2025-08-10T14:15:14.443314Z", "lastUpdate": "2025-08-10T14:20:33.908626Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "FREEPII", "description": "FREEPII (Feature Representation Enhancement End-to-end Protein Interaction Inference) is a end-to-end learning method encompassing autonomous feature extraction and feature representation enhancement for PPIs and protein complexes inference.", "homepage": "https://github.com/qqpigass/FREEPII", "biotoolsID": "freepii", "biotoolsCURIE": "biotools:freepii", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [ "protein interaction infrerence" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "qqpigass", "additionDate": "2025-08-08T08:11:07.854401Z", "lastUpdate": "2025-08-08T08:11:07.857019Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Beyond Venetoclax Cryptic Pocket Pipeline", "description": "A machine-guided pipeline for cryptic pocket discovery in undruggable cancer targets. Combines long MD (100–200 ns), metastable state modeling (MSM), hydration thermodynamics, and PLIP-based interaction analysis to identify mutant-specific pockets absent in wild-type. Validated on TP53, KRAS G12D, MYC mutants, and fusion oncoproteins", "homepage": "https://sites.google.com/view/sn-biotech/home\"", "biotoolsID": "beyond_venetoclax_cryptic_pocket_pipeline", "biotoolsCURIE": "biotools:beyond_venetoclax_cryptic_pocket_pipeline", "version": [ "v1.0 (2025 release)" ], "otherID": [], "relation": [ { "biotoolsID": "gromacs", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3842", "term": "Molecular simulation data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2087", "term": "Molecular property" }, "format": [] } ], "note": "PLIP results, pocket volume, CryptoSite, Fpocket outputs,", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3842", "term": "Molecular simulation data" }, "format": [] } ], "note": "run md on structure", "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3678", "term": "Experimental design and studies" }, { "uri": "http://edamontology.org/topic_4019", "term": "Biosciences" } ], "operatingSystem": [], "language": [ "Bash", "Python", "PyMOL", "Other" ], "license": "Proprietary", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://chemrxiv.org/engage/chemrxiv/article-details/688744d6728bf9025e9ce1c2", "type": [ "Other" ], "note": "Describes the Beyond Venetoclax cryptic pocket pipeline for undruggable cancer targets." } ], "download": [ { "url": "https://chemrxiv.org/engage/chemrxiv/article-details/688744d6728bf9025e9ce1c2", "type": "Downloads page", "note": "Contains preprint with full pipeline description and figure references.", "version": "v1.0 (2025 release)" } ], "documentation": [ { "url": "https://chemrxiv.org/engage/chemrxiv/article-details/688744d6728bf9025e9ce1c2", "type": [ "Other" ], "note": "Contains preprint with full pipeline description and figure references." } ], "publication": [ { "doi": "10.26434/chemrxiv-2025-5vz5r", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": "v1.0 (2025 release)", "note": "Contains preprint with full pipeline description and figure references.", "metadata": null } ], "credit": [ { "name": "Hoosdally", "email": "shoosdally@moemu.org", "url": "https://sites.google.com/view/sn-biotech/home", "orcidid": "https://orcid.org/0009-0008-4144-718X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Shakeelh", "additionDate": "2025-08-01T05:53:13.245244Z", "lastUpdate": "2025-08-01T07:14:43.102445Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MaCPepDB - Mass Centric Peptide Database", "description": "A Database to Quickly Access All Tryptic Peptides of the UniProtKB", "homepage": "https://macpepdb.cubimed.rub.de/", "biotoolsID": "macpepdb_-_mass_centric_peptide_database", "biotoolsCURIE": "biotools:macpepdb_-_mass_centric_peptide_database", "version": [ "3.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [], "language": [ "Rust", "JavaScript", "Other" ], "license": null, "collectionID": [ "CUBiMed.RUB", "BioInfra.Prot" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/medbioinf/macpepdb", "type": [ "Repository" ], "note": "Backend implementation written in Rust / Axum" }, { "url": "https://github.com/medbioinf/macpepdb-frontend", "type": [ "Repository" ], "note": "Frontend implementation written in Rust / Dioxus" } ], "download": [], "documentation": [ { "url": "https://docs.rs/macpepdb/latest/macpepdb/web/index.html", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jproteome.0c00967", "pmid": "33724838", "pmcid": null, "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "MaCPepDB: A Database to Quickly Access All Tryptic Peptides of the UniProtKB", "abstract": "Protein sequence databases play a crucial role in the majority of the currently applied mass-spectrometry-based proteomics workflows. Here UniProtKB serves as one of the major sources, as it combines the information of several smaller databases and enriches the entries with additional biological information. For the identification of peptides in a sample by tandem mass spectra, as generated by data-dependent acquisition, protein sequence databases provide the basis for most spectrum identification search engines. In addition, for targeted proteomics approaches like selected reaction monitoring (SRM) and parallel reaction monitoring (PRM), knowledge of the peptide sequences, their masses, and whether they are unique for a protein is essential. Because most bottom-up proteomics approaches use trypsin to cleave the proteins in a sample, the tryptic peptides contained in a protein database are of great interest. We present a database, called MaCPepDB (mass-centric peptide database), that consists of the complete tryptic digest of the Swiss-Prot and TrEMBL parts of UniProtKB. This database is especially designed to not only allow queries of peptide sequences and return the respective information about connected proteins and thus whether a peptide is unique but also allow queries of specific masses of peptides or precursors of MS/MS spectra. Furthermore, posttranslational modifications can be considered in a query as well as different mass deviations for posttranslational modifications. Hence the database can be used by a sequence query not only to, for example, check in which proteins of the UniProt database a tryptic peptide can be found but also to find possibly interfering peptides in PRM/SRM experiments using the mass query. The complete database contains currently 5 939 244 990 peptides from 185 561 610 proteins (UniProt version 2020_03), for which a single query usually takes less than 1 s. For easy exploration of the data, a web interface was developed. A REST application programming interface (API) for programmatic and workflow access is also available at https://macpepdb.mpc.rub.de.", "date": "2021-04-02T00:00:00Z", "citationCount": 9, "authors": [ { "name": "Uszkoreit J." }, { "name": "Winkelhardt D." }, { "name": "Barkovits K." }, { "name": "Wulf M." }, { "name": "Roocke S." }, { "name": "Marcus K." }, { "name": "Eisenacher M." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "Julian Uszkoreit", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0001-7522-4007", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Dirk Winkelhardt", "email": "dirk.winkelhardt@rub.de", "url": null, "orcidid": "https://orcid.org/0000-0001-8770-2221", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "PD Dr. Martin Eisenacher", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-2687-7444", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "di_hardt", "additionDate": "2023-07-25T12:35:27.605861Z", "lastUpdate": "2025-07-31T09:03:29.192901Z", "editPermission": { "type": "group", "authors": [ "di_hardt", "julianu", "BioInfra.Prot" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WheatIS", "description": "This project aims at building an International Wheat Information System (WheatIS) to support the wheat research community. The main objective is to provide a single-access web based system to access to the available data resources and bioinformatics tools. The web portal indexes and makes findable any kind of data from wheat related species. \nThe WheatIS search is an implementation of DataDiscovery.", "homepage": "https://urgi.versailles.inrae.fr/wheatis/", "biotoolsID": "WheatIS", "biotoolsCURIE": "biotools:WheatIS", "version": [], "otherID": [], "relation": [ { "biotoolsID": "gnpis", "type": "uses" }, { "biotoolsID": "DataDiscovery", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3625", "term": "Relation extraction" }, { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" }, { "uri": "http://edamontology.org/operation_3908", "term": "Information retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2353", "term": "Ontology data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2093", "term": "Data reference" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application", "Web service", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0610", "term": "Ecology" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" } ], "operatingSystem": [], "language": [], "license": "BSD-3-Clause", "collectionID": [ "elixir-fr-sdp-2019", "URGI" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Data", "Interoperability" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "http://www.wheatis.org/", "type": [ "Other" ], "note": "WheatIS website" } ], "download": [], "documentation": [ { "url": "https://urgi.versailles.inra.fr/wheatis/about", "type": [ "General" ], "note": null }, { "url": "https://urgi.versailles.inra.fr/wheatis/join", "type": [ "Contributions policy" ], "note": null }, { "url": "https://urgi.versailles.inra.fr/wheatis/legal", "type": [ "Terms of use" ], "note": null }, { "url": "https://urgi.versailles.inra.fr/wheatis/help", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/s13059-018-1491-4", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": "Alaux M, Rogers J, Letellier T, Flores R, Alfama F, Pommier C, Mohellibi N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, International Wheat Genome Sequencing Consortium, Paux E, Eversole K, Adam-Blondon A-F, Quesneville H (2018) Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biology, 19:111", "metadata": { "title": "Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data", "abstract": "© 2018 The Author(s).The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.", "date": "2018-08-17T00:00:00Z", "citationCount": 88, "authors": [ { "name": "Alaux M." }, { "name": "Rogers J." }, { "name": "Letellier T." }, { "name": "Flores R." }, { "name": "Alfama F." }, { "name": "Pommier C." }, { "name": "Mohellibi N." }, { "name": "Durand S." }, { "name": "Kimmel E." }, { "name": "Michotey C." }, { "name": "Guerche C." }, { "name": "Loaec M." }, { "name": "Laine M." }, { "name": "Steinbach D." }, { "name": "Choulet F." }, { "name": "Rimbert H." }, { "name": "Leroy P." }, { "name": "Guilhot N." }, { "name": "Salse J." }, { "name": "Feuillet C." }, { "name": "Paux E." }, { "name": "Eversole K." }, { "name": "Adam-Blondon A.-F." }, { "name": "Quesneville H." } ], "journal": "Genome Biology" } } ], "credit": [ { "name": "Support service", "email": "urgi-support@inrae.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Support" ], "note": null } ], "owner": "jison", "additionDate": "2019-11-05T10:40:37Z", "lastUpdate": "2025-07-29T13:42:41.391722Z", "editPermission": { "type": "group", "authors": [ "nfrancillon", "raphael.flores", "cmichotey" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RARe", "description": "RARe is a research infrastructure registered on the french national roadmap that brings together five networks of BRCs conserving genetic, genomic, and biological resources assembled and characterized by research on domestic animals, model or cultivated plants, wild species related to domestic animals, forest trees, micro-organisms of agronomic or agri-food interest, micro-organisms and environmental organisms.\nThe purpose of this web portal is to facilitate the discoverability of these data. \nRARe search is an implementation of DataDiscovery.", "homepage": "https://urgi.versailles.inrae.fr/rare/", "biotoolsID": "RARe", "biotoolsCURIE": "biotools:RARe", "version": [], "otherID": [], "relation": [ { "biotoolsID": "DataDiscovery", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3625", "term": "Relation extraction" }, { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" }, { "uri": "http://edamontology.org/operation_3908", "term": "Information retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2353", "term": "Ontology data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2093", "term": "Data reference" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application", "Web service", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0610", "term": "Ecology" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" } ], "operatingSystem": [], "language": [], "license": "BSD-3-Clause", "collectionID": [ "elixir-fr-sdp-2019", "URGI" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Data", "Interoperability" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://www.agrobrc-rare.org/agrobrc-rare_eng/", "type": [ "Other" ], "note": "AgroBRC-RARe website" } ], "download": [], "documentation": [ { "url": "https://urgi.versailles.inrae.fr/rare/about", "type": [ "General" ], "note": null }, { "url": "https://urgi.versailles.inrae.fr/rare/join", "type": [ "Contributions policy" ], "note": null }, { "url": "https://urgi.versailles.inrae.fr/rare/legal", "type": [ "Terms of use" ], "note": null }, { "url": "https://urgi.versailles.inrae.fr/rare/help", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Support service", "email": "urgi-support@inrae.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Support" ], "note": null } ], "owner": "nfrancillon", "additionDate": "2020-02-13T15:34:59Z", "lastUpdate": "2025-07-29T13:42:40.608985Z", "editPermission": { "type": "group", "authors": [ "cpommier", "urgi-contact", "cmichotey", "raphael.flores" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DataDiscovery", "description": "DataDiscovery aims at providing researchers a simple and fast access to relevant biological data using specific keywords and easy to use filters.\n\nThis tool is expected to be easily customizable for specific filters, environments, or data schemas. Its current implementations supported by URGI are: WheatIS, Plant, RARe.", "homepage": "https://urgi.versailles.inrae.fr/data-discovery/", "biotoolsID": "DataDiscovery", "biotoolsCURIE": "biotools:DataDiscovery", "version": [], "otherID": [], "relation": [ { "biotoolsID": "wheatis", "type": "usedBy" }, { "biotoolsID": "RARe", "type": "usedBy" }, { "biotoolsID": "Plant_DataDiscovery", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3625", "term": "Relation extraction" }, { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" }, { "uri": "http://edamontology.org/operation_3908", "term": "Information retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2353", "term": "Ontology data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2093", "term": "Data reference" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application", "Web service", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0610", "term": "Ecology" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" } ], "operatingSystem": [ "Linux" ], "language": [ "JavaScript", "Java", "Bash" ], "license": "BSD-3-Clause", "collectionID": [ "elixir-fr-sdp-2019", "URGI" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data", "Tools", "Interoperability" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://forgemia.inra.fr/urgi-is/data-discovery", "type": [ "Repository" ], "note": "GitLab code repository for DataDiscovery" }, { "url": "https://github.com/gnpis/DataDiscovery/", "type": [ "Mirror" ], "note": "Code repository mirror link for DataDiscovery" } ], "download": [], "documentation": [ { "url": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/LEGAL-MENTIONS.md", "type": [ "Terms of use" ], "note": "General terms of use" }, { "url": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#contribute", "type": [ "Contributions policy" ], "note": "How to contribute" }, { "url": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/HELP.md", "type": [ "User manual" ], "note": "How to use" }, { "url": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#setup", "type": [ "Installation instructions" ], "note": "How to install" } ], "publication": [ { "doi": "10.3835/plantgenome2015.06.0038", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": "1-\tSpannagl, M., Alaux, M., Lange, M., Bolser, D. M., Bader, K. C., Letellier, T., Kimmel, E., Flores, R.-G., Pommier, C., Kerhornou, A., Walts, B., Nussbaumer, T., Grabmuller, C., Chen, J., Colmsee, C., Beier, S., Mascher, M., Schmutzer, T., Arend, D., Thanki, A., Ramirez-Gonzalez, R., Ayling, M., Ayling, S., Caccamo, M., Mayer, K. F. X., Scholz, U., Steinbach, D., Quesneville, H., Kersey, P. (2016). TransPLANT resources for triticeae genomic data. Plant Genome, 9 (1), 13 p.", "metadata": { "title": "TransPLANT resources for triticeae genomic data", "abstract": "The genome sequences of many important Triticeae species, including bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT (http://www.transplantdb.eu) is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access.", "date": "2016-03-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Spannagl M." }, { "name": "Alaux M." }, { "name": "Lange M." }, { "name": "Bolser D.M." }, { "name": "Bader K.C." }, { "name": "Letellier T." }, { "name": "Kimmel E." }, { "name": "Flores R." }, { "name": "Pommier C." }, { "name": "Kerhornou A." }, { "name": "Walts B." }, { "name": "Nussbaumer T." }, { "name": "Grabmuller C." }, { "name": "Chen J." }, { "name": "Colmsee C." }, { "name": "Beier S." }, { "name": "Mascher M." }, { "name": "Schmutzer T." }, { "name": "Arend D." }, { "name": "Thanki A." }, { "name": "Ramirez-Gonzalez R." }, { "name": "Ayling M." }, { "name": "Ayling S." }, { "name": "Caccamo M." }, { "name": "Mayer K.F.X." }, { "name": "Scholz U." }, { "name": "Steinbach D." }, { "name": "Quesneville H." }, { "name": "Kersey P.J." } ], "journal": "Plant Genome" } }, { "doi": "10.1038/hortres.2016.56", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "2-\tAdam-Blondon, A.-F., Alaux, M., Pommier, C., Cantu, D., Cheng, Z.-M., Cramer, G. R., Davies, C., Delrot, S., Deluc, L., di Gaspero, G., Grimplet, J., Fennell, A., Londo, J. P., Kersey, P., Mattivi, F., Naithani, S., Neveu, P., Nikolski, M., Pezzotti, M., Reisch, B. I., Topfer, R., Vivier, M., Ware, D., Quesneville, H. (2016). Towards an open grapevine information system. Horticulture Research, 3, 8 p. , DOI : 10.1038/hortres.2016.56", "metadata": { "title": "Towards an open grapevine information system", "abstract": "Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.", "date": "2016-11-23T00:00:00Z", "citationCount": 37, "authors": [ { "name": "Adam-Blondon A.-F." }, { "name": "Alaux M." }, { "name": "Pommier C." }, { "name": "Cantu D." }, { "name": "Cheng Z.-M." }, { "name": "Cramer G." }, { "name": "Davies C." }, { "name": "Delrot S." }, { "name": "Deluc L." }, { "name": "Di Gaspero G." }, { "name": "Grimplet J." }, { "name": "Fennell A." }, { "name": "Londo J." }, { "name": "Kersey P." }, { "name": "Mattivi F." }, { "name": "Naithani S." }, { "name": "Neveu P." }, { "name": "Nikolski M." }, { "name": "Pezzotti M." }, { "name": "Reisch B." }, { "name": "Topfer R." }, { "name": "Vivier M." }, { "name": "Ware D." }, { "name": "Quesneville H." } ], "journal": "Horticulture Research" } }, { "doi": "10.1186/s13059-018-1491-4", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "3-\tAlaux M, Rogers J, Letellier T, Flores R, Alfama F, Pommier C, Mohellibi N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, International Wheat Genome Sequencing Consortium, Paux E, Eversole K, Adam-Blondon A-F, Quesneville H (2018) Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biology, 19:111.", "metadata": { "title": "Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data", "abstract": "The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.", "date": "2018-08-17T00:00:00Z", "citationCount": 181, "authors": [ { "name": "Alaux M." }, { "name": "Rogers J." }, { "name": "Letellier T." }, { "name": "Flores R." }, { "name": "Alfama F." }, { "name": "Pommier C." }, { "name": "Mohellibi N." }, { "name": "Durand S." }, { "name": "Kimmel E." }, { "name": "Michotey C." }, { "name": "Guerche C." }, { "name": "Loaec M." }, { "name": "Laine M." }, { "name": "Steinbach D." }, { "name": "Choulet F." }, { "name": "Rimbert H." }, { "name": "Leroy P." }, { "name": "Guilhot N." }, { "name": "Salse J." }, { "name": "Feuillet C." }, { "name": "Paux E." }, { "name": "Eversole K." }, { "name": "Adam-Blondon A.-F." }, { "name": "Quesneville H." } ], "journal": "Genome Biology" } } ], "credit": [ { "name": "urgi-support", "email": "urgi-support@inrae.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Support" ], "note": null } ], "owner": "nfrancillon", "additionDate": "2020-01-21T16:40:38Z", "lastUpdate": "2025-07-29T13:42:39.375595Z", "editPermission": { "type": "group", "authors": [ "urgi-contact", "cpommier", "cmichotey", "erlefloch", "raphael.flores" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "XNATpy", "description": "Python package to interact with the XNAT REST API in a python data-science way", "homepage": "https://gitlab.com/radiology/infrastructure/xnatpy", "biotoolsID": "xnatpy", "biotoolsCURIE": "biotools:xnatpy", "version": [], "otherID": [], "relation": [ { "biotoolsID": "xnat-pic", "type": "usedBy" }, { "biotoolsID": "xnat", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Data deposition" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" }, { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" }, { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gitlab.com/radiology/infrastructure/xnatpy/", "type": [ "Repository" ], "note": null }, { "url": "https://gitlab.com/radiology/infrastructure/xnatpy/-/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://pypi.org/project/xnat/", "type": [ "Software catalogue" ], "note": null }, { "url": "https://anaconda.org/conda-forge/xnat", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "https://pypi.org/project/xnat/", "type": "Software package", "note": null, "version": null }, { "url": "https://anaconda.org/conda-forge/xnat", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://xnat.readthedocs.io/en/latest/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Hakim Achterberg", "email": "h.achterberg@erasmusmc.nl", "url": "https://bigr.nl/member/hakim/", "orcidid": "https://orcid.org/0000-0003-3772-4582", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Erasmus MC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "hachterberg", "additionDate": "2025-07-23T10:24:09.622930Z", "lastUpdate": "2025-07-24T08:55:06.000976Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "XNAT", "description": "XNAT is an open source imaging informatics platform developed by the Neuroinformatics Research Group at Washington University. XNAT was originally developed at Washington University in the Buckner Lab, which is now located at Harvard University. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data. Thanks to its extensibility, XNAT can be used to support a wide range of imaging-based projects.", "homepage": "https://xnat.org", "biotoolsID": "xnat", "biotoolsCURIE": "biotools:xnat", "version": [], "otherID": [], "relation": [ { "biotoolsID": "xnatpy", "type": "usedBy" }, { "biotoolsID": "rxnat", "type": "usedBy" }, { "biotoolsID": "xnat-pic", "type": "usedBy" }, { "biotoolsID": "bigr_xnat", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Data deposition" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3802", "term": "Data sorting" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3283", "term": "Anonymisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" }, { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3383", "term": "Bioimaging" }, { "uri": "http://edamontology.org/topic_3452", "term": "Tomography" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "BSD-2-Clause", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://groups.google.com/g/xnat_discussion/", "type": [ "Discussion forum" ], "note": null }, { "url": "https://bitbucket.org/xnatdev/workspace/repositories/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://xnat.org/download/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://wiki.xnat.org/documentation/", "type": [ "User manual" ], "note": null }, { "url": "https://wiki.xnat.org/xnat-api/xnat-rest-api-directory", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1385/ni:5:1:11", "pmid": "17426351", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The extensible neuroimaging archive toolkit: An informatics platform for managing, exploring, and sharing neuroimaging data", "abstract": "The Extensible Neuroimaging Archive Toolkit (XNAT) is a software platform designed to facilitate common management and productivity tasks for neuroimaging and associated data. In particular, XNAT enables qualitycontrol procedures and provides secure access to and storage of data. XNAT follows a threetiered architecture that includes a data archive, user interface, and middleware engine. Data can be entered into the archive as XML or through data entry forms. Newly added data are stored in a virtual quarantine until an authorized user has validated it. XNAT subsequently maintains a history profile to track all changes made to the managed data. User access to the archive is provided by a secure web application. The web application provides a number of quality control and productivity features, including data entry forms, data-type-specific searches, searches that combine across data types, detailed reports, and listings of experimental data, upload/download tools, access to standard laboratory workflows, and administration and security tools. XNAT also includes an online image viewer that supports a number of common neuroimaging formats, including DICOM and Analyze. The viewer can be extended to support additional formats and to generate custom displays. By managing data with XNAT, laboratories are prepared to better maintain the long-term integrity of their data, to explore emergent relations across data types, and to share their data with the broader neuroimaging community. © Copyright 2007 by Humana Press Inc. All rights of any nature whatsoever are reserved.", "date": "2007-03-01T00:00:00Z", "citationCount": 378, "authors": [ { "name": "Marcus D.S." }, { "name": "Olsen T.R." }, { "name": "Ramaratnam M." }, { "name": "Buckner R.L." } ], "journal": "Neuroinformatics" } }, { "doi": "10.1162/jocn.2009.21407", "pmid": "19929323", "pmcid": "PMC2895005", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Open access series of imaging studies: Longitudinal MRI data in nondemented and demented older adults", "abstract": "The Open Access Series of Imaging Studies is a series of neuroimaging data sets that are publicly available for study and analysis. The present MRI data set consists of a longitudinal collection of 150 subjects aged 60 to 96 years all acquired on the same scanner using identical sequences. Each subject was scanned on two or more visits, separated by at least 1 year for a total of 373 imaging sessions. Subjects were characterized using the Clinical Dementia Rating (CDR) as either nondemented or with very mild tomild Alzheimer's disease. Seventy-two of the subjects were characterized as nondemented throughout the study. Sixty-four of the included subjects were characterized as demented at the time of their initial visits and remained so for subsequent scans, including 51 individuals with CDR 0.5 similar level of impairment to individuals elsewhere considered to have \"mild cognitive impairment.\" Another 14 subjects were characterized as nondemented at the time of their initial visit (CDR 0) and were subsequently characterized as demented at a later visit (CDR > 0). The subjects were all right-handed and include bothmen (n=62) and women (n = 88). For each scanning session, three or four individual T1-weighted MRI scans were obtained. Multiple withinsession acquisitions provide extremely high contrast to noise, making the data amenable to a wide range of analytic approaches including automated computational analysis. Automated calculation of whole-brain volume is presented to demonstrate use of the data for measuring differences associated with normal aging and Alzheimer's disease. © 2010 Massachusetts Institute of Technology.", "date": "2010-12-01T00:00:00Z", "citationCount": 461, "authors": [ { "name": "Marcus D.S." }, { "name": "Fotenos A.F." }, { "name": "Csernansky J.G." }, { "name": "Morris J.C." }, { "name": "Buckner R.L." } ], "journal": "Journal of Cognitive Neuroscience" } } ], "credit": [ { "name": "Daniel Marcus", "email": "dmarcus@wustl.edu", "url": "https://profiles.wustl.edu/en/persons/daniel-marcus", "orcidid": "https://orcid.org/0000-0001-5662-5358", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hachterberg", "additionDate": "2025-07-24T08:48:17.637773Z", "lastUpdate": "2025-07-24T08:53:51.609723Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ETENLNC", "description": "ETENLNC (End-To-End-Novel-NonCoding) is a lncRNA identification and analysis framework", "homepage": "https://github.com/EvolOMICS-TU/ETENLNC", "biotoolsID": "etenlnc", "biotoolsCURIE": "biotools:etenlnc", "version": [ "1.0" ], "otherID": [], "relation": [ { "biotoolsID": "hisat2", "type": "uses" }, { "biotoolsID": "salmon", "type": "uses" }, { "biotoolsID": "fastqc", "type": "uses" }, { "biotoolsID": "fastp", "type": "uses" }, { "biotoolsID": "stringtie", "type": "uses" }, { "biotoolsID": "gffcompare", "type": "uses" }, { "biotoolsID": "cpc2", "type": "uses" }, { "biotoolsID": "ncbi_blast_plus", "type": "uses" }, { "biotoolsID": "tximport", "type": "uses" }, { "biotoolsID": "deseq2", "type": "uses" }, { "biotoolsID": "lnctar", "type": "uses" }, { "biotoolsID": "capsule-lpi", "type": "uses" }, { "biotoolsID": "seekr", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3219", "term": "Read pre-processing" }, { "uri": "http://edamontology.org/operation_3218", "term": "Sequencing quality control" }, { "uri": "http://edamontology.org/operation_3258", "term": "Transcriptome assembly" }, { "uri": "http://edamontology.org/operation_0415", "term": "Nucleic acid feature detection" }, { "uri": "http://edamontology.org/operation_3800", "term": "RNA-Seq quantification" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" }, { "uri": "http://edamontology.org/operation_0531", "term": "Heat map generation" }, { "uri": "http://edamontology.org/operation_0278", "term": "RNA secondary structure prediction" }, { "uri": "http://edamontology.org/operation_3472", "term": "k-mer counting" }, { "uri": "http://edamontology.org/operation_0389", "term": "Protein-nucleic acid interaction analysis" }, { "uri": "http://edamontology.org/operation_3901", "term": "RNA-binding protein prediction" }, { "uri": "http://edamontology.org/operation_2437", "term": "Gene regulatory network prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1288", "term": "Genome map" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_2306", "term": "GTF" }, { "uri": "http://edamontology.org/format_2305", "term": "GFF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2887", "term": "Nucleic acid sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1636", "term": "Heat map" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_0906", "term": "Protein interaction data" }, "format": [] } ], "note": "Run ETENLNC on paired-end raw RNA-Seq (.fastq) data", "cmd": "bash ETENLNC_docker.sh" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/EvolOMICS-TU/ETENLNC", "type": [ "Repository" ], "note": "GitHub Repo" } ], "download": [ { "url": "https://zenodo.org/records/14325721?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImVmYTllNWJkLWE4ODUtNGM3OC05YTAxLWM4ZDk5YTljZDZjMCIsImRhdGEiOnt9LCJyYW5kb20iOiI4M2I1YjBlZDQ4MmUyZTIxNDg2YmI0YTFkMWE5MTI1OCJ9.HeB3WrsPduNzMyXjH4x5HfCgmIp4NzYv0P_11XU9lcXC_ZxEaVndP-kD0LDkxwufHVNlroeAhdK33PR51F6jnw", "type": "Biological data", "note": "Sample/demo data for ETENLNC. A detailed guide on running ETENLNC using the demo data can be found in the ETENLNC manual (supplementary to our publication).", "version": "1.0" } ], "documentation": [ { "url": "https://github.com/EvolOMICS-TU/ETENLNC", "type": [ "Command-line options" ], "note": "A detailed guide on running ETENLNC using the demo data can be found in the ETENLNC manual (supplementary to our publication)" } ], "publication": [ { "doi": "10.1016/j.compbiolchem.2024.108140", "pmid": "38996755", "pmcid": null, "type": [ "Primary" ], "version": ".0", "note": null, "metadata": { "title": "ETENLNC: An end to end lncRNA identification and analysis framework to facilitate construction of known and novel lncRNA regulatory networks", "abstract": "Long non-coding RNAs (lncRNAs) play crucial roles in the regulation of gene expression and maintenance of genomic integrity through various interactions with DNA, RNA, and proteins. The availability of large-scale sequence data from various high-throughput platforms has opened possibilities to identify, predict, and functionally annotate lncRNAs. As a result, there is a growing demand for an integrative computational framework capable of identifying known lncRNAs, predicting novel lncRNAs, and inferring the downstream regulatory interactions of lncRNAs at the genome-scale. We present ETENLNC (End-To-End-Novel-Long-NonCoding), a user-friendly, integrative, open-source, scalable, and modular computational framework for identifying and analyzing lncRNAs from raw RNA-Seq data. ETENLNC employs six stringent filtration steps to identify novel lncRNAs, performs differential expression analysis of mRNA and lncRNA transcripts, and predicts regulatory interactions between lncRNAs, mRNAs, miRNAs, and proteins. We benchmarked ETENLNC against six existing tools and optimized it for desktop workstations and high-performance computing environments using data from three different species. ETENLNC is freely available on GitHub: https://github.com/EvolOMICS-TU/ETENLNC.", "date": "2024-10-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Nath P." }, { "name": "Bhuyan K." }, { "name": "Bhattacharyya D.K." }, { "name": "Barah P." } ], "journal": "Computational Biology and Chemistry" } } ], "credit": [ { "name": "Pankaj Barah", "email": "barah@tezu.ernet.in", "url": "https://www.tezu.ernet.in/dmbbt/profile/34", "orcidid": "https://orcid.org/0000-0001-7039-7996", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Maintainer" ], "note": "Assistant Professor at Department of Molecular Biology and Biotechnology, Tezpur University." }, { "name": "Prangan Nath", "email": "prangannathofficial@gmai.com", "url": null, "orcidid": "https://orcid.org/0000-0002-9451-7822", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "prangannath", "additionDate": "2025-07-23T10:27:57.572501Z", "lastUpdate": "2025-07-23T10:27:57.574879Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PhysiBoSS", "description": "A sustainable integration of stochastic Boolean and agent-based modelling frameworks.", "homepage": "https://github.com/PhysiBoSS/PhysiBoSS", "biotoolsID": "physiboss", "biotoolsCURIE": "biotools:physiboss", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" }, { "uri": "http://edamontology.org/operation_3927", "term": "Network analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "C++", "Python", "MATLAB" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/PhysiBoSS/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/PhysiBoSS/PhysiBoSS/blob/master/CODE_OF_CONDUCT.md", "type": [ "Code of conduct" ], "note": null } ], "publication": [ { "doi": "10.1101/2022.01.06.468363", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Alfonso Valencia", "email": "alfonso.valencia@bsc.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8937-6789", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Laurence Calzone", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-7835-1148", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Emmanuel Barillot", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-2724-2002", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Miguel Ponce-de-Leon", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-7496-844X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Arnau Montagud", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-7696-1241", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-09-17T13:13:51.109638Z", "lastUpdate": "2025-07-21T09:32:03.727618Z", "editPermission": { "type": "group", "authors": [ "vincent-noel", "ArnauMontagud" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "TinkerHap", "description": "TinkerHap is an accurate read-based phasing tool that integrates multiple methodologies to enhance phasing accuracy. It is designed to efficiently phase genomic data by linking sequencing reads across heterozygous sites, extending haplotype blocks, and incorporating pre-phased data when available.\n\nThe full paper detailing the methodology and validation of TinkerHap is available at bioRxiv\nDOI: https://doi.org/10.1101/2025.02.16.638517.", "homepage": "https://github.com/DZeevi-Lab/TinkerHap", "biotoolsID": "tinkerhap", "biotoolsCURIE": "biotools:tinkerhap", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/DZeevi-Lab/TinkerHap", "type": [ "Repository" ], "note": null }, { "url": "https://doi.org/10.1101/2025.02.16.638517", "type": [ "Other" ], "note": "Full paper detailing the methodology and validation" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/2025.02.16.638517", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Uri Hartmann", "email": null, "url": null, "orcidid": "https://orcid.org/0009-0002-0668-0249", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "uri2x", "additionDate": "2025-07-18T19:35:58.827790Z", "lastUpdate": "2025-07-18T19:36:52.558166Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SubtiWiki", "description": "SubtiWiki is a database for the model organism Bacillus subtilis.", "homepage": "https://subtiwiki.uni-goettingen.de/", "biotoolsID": "subtiwiki", "biotoolsCURIE": "biotools:subtiwiki", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3208", "term": "Genome visualisation" }, { "uri": "http://edamontology.org/operation_0435", "term": "Operon prediction" }, { "uri": "http://edamontology.org/operation_1781", "term": "Gene regulatory network analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkae957", "pmid": "39441067", "pmcid": "PMC11701700", "type": [ "Primary" ], "version": "5.0", "note": null, "metadata": { "title": "A new framework for SubtiWiki, the database for the model organism Bacillus subtilis", "abstract": "Bacillus subtilis is a Gram-positive model bacterium and one of the most-studied and best understood organisms. The complex information resulting from its investigation is compiled in the database SubtiWiki (https://subtiwiki.uni-goettingen.de/v5) in an integrated and intuitive manner. To enhance the utility of SubtiWiki, we have added novel features such as a viewer to interrogate conserved genomic organization, a widget that shows mutant fitness data for all non-essential genes, and a widget showing protein structures, structure predictions and complex structures. Moreover, we have integrated metabolites as new entities. The new framework also includes a documented API, enabling programmatic access to data for computational tasks. Here we present the recent developments of SubtiWiki and the current state of the data for this organism.", "date": "2025-01-06T00:00:00Z", "citationCount": 4, "authors": [ { "name": "Elfmann C." }, { "name": "Dumann V." }, { "name": "van den Berg T." }, { "name": "Stulke J." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Jörg Stülke", "email": "jstuelk@gwdg.de", "url": null, "orcidid": "https://orcid.org/0000-0001-5881-5390", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Christoph Elfmann", "email": "christoph.elfmann@uni-goettingen.de", "url": null, "orcidid": "https://orcid.org/0000-0002-7872-8232", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "PhD student in charge of SubtiWiki." } ], "owner": "ChristophElfmann", "additionDate": "2022-03-13T11:27:48.265908Z", "lastUpdate": "2025-07-16T13:05:53.746014Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "TiSim", "description": "TiSim-CellSys is a modular software tool for efficient off-lattice simulation of growth and organization processes in multicellular systems in two and three dimensions. It implements an agent-based model that approximates cells as isotropic, elastic and adhesive objects. Cell migration is modeled by an equation of motion for each cell. The software includes many modules specifically tailored to support the simulation and analysis of virtual tissues including real-time 3D visualization and VRML 2.0 support. All cell and environment parameters can be independently varied which facilitates species specific simulations and allows for detailed analyses of growth dynamics and links between cellular and multicellular phenotypes.", "homepage": "https://www.hoehme.com/software/tisim", "biotoolsID": "cellsys", "biotoolsCURIE": "biotools:cellsys", "version": [ "5.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0244", "term": "Simulation analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3869", "term": "Simulation" }, "format": [] } ], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "PerMedCoE" ], "maturity": null, "cost": null, "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://www.hoehme.com/software/tisim", "type": "Binaries", "note": null, "version": "5.0" } ], "documentation": [ { "url": "https://www.hoehme.com/images/Software/cellsys_user_guide.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btq437", "pmid": "20709692", "pmcid": "PMC2951083", "type": [], "version": null, "note": null, "metadata": { "title": "A cell-based simulation software for multi-cellular systems", "abstract": "CellSys is a modular software tool for efficient off-lattice simulation of growth and organization processes in multi-cellular systems in 2D and 3D. It implements an agent-based model that approximates cells as isotropic, elastic and adhesive objects. Cell migration is modeled by an equation of motion for each cell. The software includes many modules specifically tailored to support the simulation and analysis of virtual tissues including real-time 3D visualization and VRML 2.0 support. All cell and environment parameters can be independently varied which facilitates species specific simulations and allows for detailed analyses of growth dynamics and links between cellular and multi-cellular phenotypes. © The Author(s) 2010. Published by Oxford University Press.", "date": "2010-08-13T00:00:00Z", "citationCount": 139, "authors": [ { "name": "Hoehme S." }, { "name": "Drasdo D." } ], "journal": "Bioinformatics" } } ], "credit": [], "owner": "tntiniak", "additionDate": "2022-04-22T14:17:27.559879Z", "lastUpdate": "2025-07-16T09:46:10.555167Z", "editPermission": { "type": "public", "authors": [ "ArnauMontagud" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DUNE", "description": "A versatile neuroimaging encoder for extracting deep features from multisequence brain MRIs", "homepage": "https://github.com/gevaertlab/DUNE", "biotoolsID": "GevaertLab_DUNE", "biotoolsCURIE": "biotools:GevaertLab_DUNE", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3937", "term": "Feature extraction" } ], "input": [], "output": [], "note": "Extracts features from", "cmd": "python -m src.main process /path/to/dicom/folder /path/to/output" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/gevaertlab/DUNE", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/gevaertlab/DUNE", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/gevaertlab/DUNE/blob/main/README.md", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1101/2025.02.24.25322787", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Thomas Barba", "email": "thomas.barba@inserm.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "tbarba", "additionDate": "2025-07-15T16:04:03.513732Z", "lastUpdate": "2025-07-15T16:04:03.516083Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FAIR_EVA", "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.", "homepage": "https://github.com/IFCA-Advanced-Computing/FAIR_eva", "biotoolsID": "fair_eva_4_eucaim", "biotoolsCURIE": "biotools:fair_eva_4_eucaim", "version": [ "EUCAIM_plugin_1" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web service", "Script" ], "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": [], "download": [], "documentation": [ { "url": "https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.md", "type": [ "Quick start guide" ], "note": "Documentation for the main package, EUCAIM plugin specific documentation not included." } ], "publication": [ { "doi": "10.1038/s41597-023-02652-8", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "FAIR EVA: Bringing institutional multidisciplinary repositories into the FAIR picture", "abstract": "The FAIR Principles are a set of good practices to improve the reproducibility and quality of data in an Open Science context. Different sets of indicators have been proposed to evaluate the FAIRness of digital objects, including datasets that are usually stored in repositories or data portals. However, indicators like those proposed by the Research Data Alliance are provided from a high-level perspective that can be interpreted and they are not always realistic to particular environments like multidisciplinary repositories. This paper describes FAIR EVA, a new tool developed within the European Open Science Cloud context that is oriented to particular data management systems like open repositories, which can be customized to a specific case in a scalable and automatic environment. It aims to be adaptive enough to work for different environments, repository software and disciplines, taking into account the flexibility of the FAIR Principles. As an example, we present DIGITAL.CSIC repository as the first target of the tool, gathering the particular needs of a multidisciplinary institution as well as its institutional repository.", "date": "2023-12-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Aguilar Gomez F." }, { "name": "Bernal I." } ], "journal": "Scientific Data" } } ], "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": [], "note": "This 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." } ], "owner": "davrodgon", "additionDate": "2025-06-30T08:52:48.500476Z", "lastUpdate": "2025-07-15T09:45:40.672775Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "UniversalMer", "description": "UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists.", "homepage": "https://ugrammer.github.io", "biotoolsID": "UniversalMer", "biotoolsCURIE": "biotools:UniversalMer", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3472", "term": "k-mer counting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] }, { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1266", "term": "Base word frequencies table" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1265", "term": "Base frequencies table" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3671", "term": "Text" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3473", "term": "Data mining" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Windows", "Mac" ], "language": [ "C++", "C" ], "license": "Freeware", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "UK" ], "elixirCommunity": [], "link": [ { "url": "https://sourceforge.net/projects/universal-mer/", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://sourceforge.net/projects/universal-mer/", "type": "Command-line specification", "note": null, "version": "2.0" } ], "documentation": [], "publication": [], "credit": [], "owner": "Ugrammer", "additionDate": "2025-07-14T08:21:28.942611Z", "lastUpdate": "2025-07-14T08:21:28.944946Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ColoPola dataset for colorectal cancer detection", "description": "The dataset consists of 572 slices (specimens) with 20,592 images. There are 284 cancer samples and 288 normal samples. The lists of samples for training (train+val) set and testing set are provided in the Zenodo repository. Source code in Github is to train and validate five deep learning models using ColoPola dataset.", "homepage": "https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset", "biotoolsID": "colopola_dataset_for_colorectal_cancer_detection", "biotoolsCURIE": "biotools:colopola_dataset_for_colorectal_cancer_detection", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" } ], "operatingSystem": [ "Windows" ], "language": [ "Python" ], "license": "CC0-1.0", "collectionID": [ "Dataset" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset", "type": [ "Repository" ], "note": "Source code" }, { "url": "https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset", "type": "Source code", "note": "Python language", "version": "1.0" }, { "url": "https://zenodo.org/records/10554304", "type": "Test data", "note": "Dataset for running source code", "version": "1.2" } ], "documentation": [], "publication": [], "credit": [], "owner": "haile", "additionDate": "2025-07-10T03:21:50.923918Z", "lastUpdate": "2025-07-10T03:33:52.616431Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }
