Resource List
List all resources, or create a new resource.
GET /api/t?format=api
{ "count": 32987, "next": "?page=2", "previous": null, "list": [ { "name": "afktotogacor", "description": "AFKTOTO dikenal sebagai situs gacor berlisensi yang menawarkan pengalaman bermain digital dengan sistem yang stabil dan akses yang mudah. Platform ini dirancang untuk memberikan kenyamanan bagi pengguna dalam menjelajahi berbagai fitur yang tersedia. buruan daftar dan ambil hadiah mu sekarang juga!!", "homepage": "https://kecebanget.info/", "biotoolsID": "afktotogacor", "biotoolsCURIE": "biotools:afktotogacor", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "afktoto", "additionDate": "2026-04-06T11:38:43.105893Z", "lastUpdate": "2026-04-06T11:51:35.183127Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bemo88Disini", "description": "BEMO88 adalah platform permainan slot dan taruhan online dengan berbagai pilihan game seru, peluang jackpot besar, dan akses mudah kapan saja.", "homepage": "https://lit.link/en/platformbemo88", "biotoolsID": "Platform.Bemo88", "biotoolsCURIE": "biotools:Platform.Bemo88", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "PlatformBemo88", "additionDate": "2026-04-03T22:41:05.770861Z", "lastUpdate": "2026-04-03T22:41:05.773818Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bemo88Disini", "description": "BEMO88 adalah platform permainan slot dan taruhan online dengan berbagai pilihan game seru, peluang jackpot besar, dan akses mudah kapan saja.", "homepage": "https://hoo.be/bemo88register", "biotoolsID": "PlatformBemo88", "biotoolsCURIE": "biotools:PlatformBemo88", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "admin", "additionDate": "2026-04-03T22:17:08.433069Z", "lastUpdate": "2026-04-03T22:40:23.640934Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bemo88Disini", "description": "Bemo88BEMO88 adalah platform permainan slot dan taruhan online dengan berbagai pilihan game seru untuk para semua pemain, peluang jackpot besar dan akses mudah kapan saja terpecaya no 1", "homepage": "https://bio.tools/register", "biotoolsID": "bemo88disini", "biotoolsCURIE": "biotools:bemo88disini", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "admin", "additionDate": "2026-04-03T22:06:40.989927Z", "lastUpdate": "2026-04-03T22:09:58.105495Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RHINO88", "description": "🚨 RHINO88 🚨\nGacor tiap hari, banjir kemenangan! 🔥\nBonus melimpah & WD super cepat ⚡\nBuruan join sebelum ketinggalan!", "homepage": "https://hoo.be/rhino88", "biotoolsID": "rhino88", "biotoolsCURIE": "biotools:rhino88", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "Rhino88official", "additionDate": "2026-04-03T22:08:55.204237Z", "lastUpdate": "2026-04-03T22:09:04.464295Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "INIGAMATOGEL", "description": "Selamat Datang dan Bergabung Bersama Link Situs Official GAMATOGEL - Akses Mudah Layanan Terpercaya Bermain Game Toto Online Terlengkap Indonesia. gamatogel telah di setujui sebagai bandar togel online resmi 4d terpercaya dan situs toto togel slot gacor di indonesia bet 100 perak.", "homepage": "https://heylink.me/VVIPGAMAMURPHY91?utm_source=ig&utm_medium=social&utm_content=link_in_bio&fbclid=PAZXh0bgNhZW0CMTEAc3J0YwZhcHBfaWQMMjU2MjgxMDQwNTU4AAGni1YUAyefESmk2JRwN2gnat3OLLnG6s7jhSMY2zmryvS6nquiQCOfL4SzCuk_aem_cwxASPkXXnCcSIVAqdGW1A", "biotoolsID": "inigamatogel", "biotoolsCURIE": "biotools:inigamatogel", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "admin", "additionDate": "2026-04-03T21:55:06.076211Z", "lastUpdate": "2026-04-03T21:56:46.470681Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bemo88-Premium", "description": "BEMO88 hadir sebagai salah satu platform slot online yang menawarkan pengalaman bermain yang seru, cepat, dan penuh kejutan. Dengan tampilan modern serta pilihan game yang beragam, BEMO88 menjadi pilihan tepat bagi kamu yang ingin merasakan sensasi bermain slot dengan peluang kemenangan yang menarik.", "homepage": "https://hoo.be/bemo88-premium", "biotoolsID": "bemo88-premium", "biotoolsCURIE": "biotools:bemo88-premium", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "BEMO88PREMIUM", "additionDate": "2026-04-03T21:54:16.052743Z", "lastUpdate": "2026-04-03T21:55:08.260341Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WIRA99HADIR", "description": "WIRA99 merupakan platform hiburan digital yang menawarkan sensasi bermain yang menarik, praktis, dan penuh keuntungan. Dengan teknologi canggih dan pelayanan profesional, setiap momen bermain terasa lebih maksimal.", "homepage": "https://hoo.be/wra99", "biotoolsID": "wira99hadir", "biotoolsCURIE": "biotools:wira99hadir", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "wira99official", "additionDate": "2026-04-03T21:51:17.447727Z", "lastUpdate": "2026-04-03T21:51:17.453508Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BADAKRHINO88", "description": "🦏 RHINO88 Official\nPlatform terbaik untuk cuan tanpa batas 💎\nMinimal depo ringan, WD cepat tanpa drama ⚡\nSaatnya naik level jadi sultan!", "homepage": "https://creator.hoo.be/me", "biotoolsID": "badakrhino88", "biotoolsCURIE": "biotools:badakrhino88", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "Rhino88", "additionDate": "2026-04-03T21:49:45.645389Z", "lastUpdate": "2026-04-03T21:49:52.773293Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BERSAMARUMAHDUIT", "description": "“Rumahduit Gaming hadir sebagai pusat hiburan online dengan pengalaman bermain yang seru, cepat, dan penuh peluang. Didukung sistem modern dan layanan terbaik, setiap permainan menjadi lebih menyenangkan dan menguntungkan.”", "homepage": "https://sites.google.com/view/rumaharenagameonline/home", "biotoolsID": "bersamarumahduit", "biotoolsCURIE": "biotools:bersamarumahduit", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "gamerumahduit", "additionDate": "2026-04-03T21:41:03.662184Z", "lastUpdate": "2026-04-03T21:41:13.443424Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "groupgamatogel", "description": "“Gamatogel adalah platform hiburan online terpercaya yang menghadirkan berbagai permainan seru dengan sistem modern, akses cepat, dan pelayanan terbaik. Mengutamakan kenyamanan, keamanan, serta pengalaman bermain yang maksimal bagi setiap member.”", "homepage": "https://magic.ly/officialgamatogel", "biotoolsID": "groupgamatogel", "biotoolsCURIE": "biotools:groupgamatogel", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "admin", "additionDate": "2026-04-03T21:04:45.928572Z", "lastUpdate": "2026-04-03T21:09:44.957252Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bionoculars", "description": "Life science search engine providing access to 80M+ articles, from PubMed and OpenAlex, through complementary search pathways. \nCombines classical keyword search with AI-assisted exploration, including semantic keyword grouping, knowledge graph visualization, and AI-driven summarization. All AI-generated insights are traceable to source articles. Designed to support transparent, user-steered literature exploration for biology and biomedical research. Currently in early access.", "homepage": "https://www.bionoculars.com/", "biotoolsID": "bionoculars", "biotoolsCURIE": "biotools:bionoculars", "version": [], "otherID": [ { "value": "RRID:SCR_028217", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0305", "term": "Literature search" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_3344", "term": "Biomedical science" }, { "uri": "http://edamontology.org/topic_3303", "term": "Medicine" }, { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" }, { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_3068", "term": "Literature and language" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "Proprietary", "collectionID": [], "maturity": "Emerging", "cost": "Commercial", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.bionoculars.com/tutorial", "type": [ "Quick start guide" ], "note": null }, { "url": "https://www.bionoculars.com/blog/early-access", "type": [ "Release notes" ], "note": null } ], "publication": [], "credit": [], "owner": "SyllogistTeam", "additionDate": "2026-03-28T10:21:22.720256Z", "lastUpdate": "2026-04-03T12:40:30.115237Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Lethe DICOM Anonymizer", "description": "A DICOM Anonymization pipeline in a Docker container. This pipeline is designed to anonymize DICOM files according to the EUCAIM standard and includes the following steps:\n\nStep 1 (Optional): Perform OCR on DICOM pixel data to remove sensitive information (burned-in information).\nStep 2: Deidentify DICOM metadata using the RSNA CTP Anonymizer and the EUCAIM anonymization script. \nStep 3 (Optional): Deidentify clinical data provided in CSV files so that the referenced patient id is anonymized the same way CTP does in Step 2.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/lethe-dicom-anonymizer/info-tab", "biotoolsID": "lethe_dicom_anonymizer", "biotoolsCURIE": "biotools:lethe_dicom_anonymizer", "version": [ "0.9.12", "0.10.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3283", "term": "Anonymisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Desktop application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" }, { "uri": "http://edamontology.org/topic_4044", "term": "Data protection" }, { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "EUPL-1.2", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/cbml-forth/lethe_anon_pipeline", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/cbml-forth/lethe_anon_pipeline/blob/main/README.md", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.5281/zenodo.19097245", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Computational BioMedicine Laboratory, Foundation for Research and Technology Hellas (FORTH)", "email": null, "url": "https://www.ics.forth.gr/cbml/?lang=en", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "vkalokyri", "additionDate": "2025-10-29T08:08:30.731334Z", "lastUpdate": "2026-04-02T14:39:36.234580Z", "editPermission": { "type": "group", "authors": [ "ssfak" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "pathotypr", "description": "A fast, offline, pathogen-agnostic toolkit for lineage classification and marker-driven genotyping from whole-genome sequencing data. Bring your own SNP marker panel for any microbial pathogen — pathotypr handles the rest. Ships with curated panels for Mycobacterium tuberculosis complex (MTBC): 3,707 lineage-defining SNPs and over 102,000 resistance-associated mutations. Works with assembled genomes (FASTA) and raw reads (FASTQ). Available as command-line interface and cross-platform desktop GUI (Tauri).", "homepage": "https://github.com/PathoGenOmics-Lab/pathotypr", "biotoolsID": "pathotypr", "biotoolsCURIE": "biotools:pathotypr", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0920", "term": "Genotype/phenotype report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "train — Build a Random Forest classifier from labeled genomes.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0920", "term": "Genotype/phenotype report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "predict — Assign lineages to genomes using a pre-trained Random Forest model.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0920", "term": "Genotype/phenotype report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "classify — Call known SNP markers in assembled genomes against a user-defined marker panel.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0920", "term": "Genotype/phenotype report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "split-fastq — Alignment-free genotyping directly from raw reads using k-mer matching.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0920", "term": "Genotype/phenotype report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "match — Find the closest reference genome from a set of references for raw reads.", "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_3305", "term": "Public health and epidemiology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [], "language": [ "Rust" ], "license": "AGPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/PathoGenOmics-Lab/pathotypr/releases", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/PathoGenOmics-Lab/pathotypr", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/PathoGenOmics-Lab/pathotypr/tree/main/docs", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.64898/2026.03.24.714002", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Paula Ruiz-Rodriguez", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0727-5974", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Mireia Coscolla", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0752-0538", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "I2SysBio (CSIC - Universitat de València)", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "PathoGenOmics Lab", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null } ], "owner": "paururo", "additionDate": "2026-04-02T11:29:54.022786Z", "lastUpdate": "2026-04-02T11:29:54.029869Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "COVID19-dataset", "description": "COVID-19 sequencing data obtained from hundreds of exomes.", "homepage": "https://portfolio-covid19-dataset.imib.es/", "biotoolsID": "covid19-dataset", "biotoolsCURIE": "biotools:covid19-dataset", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "IMPaCT-Data", "IMPaCT-ISCIII" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Ángel Esteban", "email": "angel.esteban@ffis.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "angel.esteban", "additionDate": "2026-04-01T10:07:48.810565Z", "lastUpdate": "2026-04-01T10:07:48.812607Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "COLPORTAL", "description": "Platform for the combined analysis of clinical data and various omics data applied to a cohort of colorectal cancer patients.", "homepage": "https://colportal.imib.es/", "biotoolsID": "colportal", "biotoolsCURIE": "biotools:colportal", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [], "license": null, "collectionID": [ "IMPaCT-Data", "IMPaCT-ISCIII" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Ángel Esteban", "email": "angel.esteban@ffis.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "angel.esteban", "additionDate": "2026-04-01T09:54:16.773562Z", "lastUpdate": "2026-04-01T09:55:05.660444Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "eddymotion", "description": "Eddymotion is an open-source framework for volume-to-volume artifact estimation in neuroimaging, inspired by FSL’s eddy. It offers an alternative to FSL's eddy without commercial limitations and generalizes beyond eddy current distortions of diffusion MRI.", "homepage": "https://github.com/nipreps/eddymotion", "biotoolsID": "eddymotion", "biotoolsCURIE": "biotools:eddymotion", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" }, { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Legacy", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.31234/OSF.IO/GFNY9", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "pub2tools2024", "additionDate": "2026-01-15T11:57:34.490366Z", "lastUpdate": "2026-04-01T09:54:26.864866Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DIGEVAR", "description": "Platform for analyzing genomic study results.", "homepage": "https://portfolio-digevar.imib.es/", "biotoolsID": "digevar", "biotoolsCURIE": "biotools:digevar", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Ángel Esteban", "email": "angel.esteban@ffis.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "angel.esteban", "additionDate": "2026-04-01T09:47:21.081699Z", "lastUpdate": "2026-04-01T09:47:21.084818Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DataRaiders", "description": "Semantic enrichment of biomedical resources.", "homepage": "https://portfolio-dataraiders.imib.es/", "biotoolsID": "dataraiders", "biotoolsCURIE": "biotools:dataraiders", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "IMPaCT-ISCIII", "IMPaCT-Data" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Ángel Esteban", "email": "angel.esteban@ffis.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "angel.esteban", "additionDate": "2026-04-01T09:43:18.056267Z", "lastUpdate": "2026-04-01T09:43:18.058742Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ELORA", "description": "Software for managing the lifecycle of biological samples—from collection to analysis.", "homepage": "https://portfolio-elora.imib.es/", "biotoolsID": "elora", "biotoolsCURIE": "biotools:elora", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3337", "term": "Biobank" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [], "license": null, "collectionID": [ "IMPaCT-Data", "IMPaCT-ISCIII" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Ángel Esteban", "email": "angel.esteban@ffis.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "angel.esteban", "additionDate": "2026-04-01T09:38:26.497572Z", "lastUpdate": "2026-04-01T09:38:26.500307Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SemanticCRF", "description": "Web-based data collection forms.", "homepage": "https://portfolio-semanticcrf.imib.es/", "biotoolsID": "semanticcrf", "biotoolsCURIE": "biotools:semanticcrf", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_3571", "term": "Data governance" }, { "uri": "http://edamontology.org/topic_3345", "term": "Data identity and mapping" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [ "IMPaCT-ISCIII", "IMPaCT-Data" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Angel Esteban", "email": "angel.esteban@ffis.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "angel.esteban", "additionDate": "2026-04-01T09:33:02.922356Z", "lastUpdate": "2026-04-01T09:33:02.924971Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EUCAIM ETL toolset", "description": "Modular toolchain for an extensible and customizable ETL pipeline that extracts, transforms, and loads clinical data and medical imaging metadata, applying dataset-specific mappings to generate outputs compatible with the EUCAIM Common Data Model (CDM). Its design aims to minimize manual data preparation efforts and facilitate customization and integration with other components, such as data quality assurance tools.\nContainerized, currently supports input datasets in CSV, JSON, XLSX.", "homepage": "https://github.com/EUCAIM/etl-toolset/", "biotoolsID": "eetl_toolset", "biotoolsCURIE": "biotools:eetl_toolset", "version": [ "0.1.1", "0.1.2", "0.2.1" ], "otherID": [], "relation": [ { "biotoolsID": "tabular_data_curator", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Data formatting" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Data deposition" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3345", "term": "Data identity and mapping" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Linux", "Windows" ], "language": [ "Java", "Python" ], "license": "Apache-2.0", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access (with restrictions)", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Spain" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/EUCAIM/etl-toolset/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/1QNiqAvVVVsg_3-YuUp1YGNWwakL8yap-", "type": [ "General" ], "note": "Tool documentation from EUCAIM WP5 Task Force 2 effort" } ], "publication": [], "credit": [], "owner": "victorsp", "additionDate": "2025-04-24T13:00:12.867477Z", "lastUpdate": "2026-03-31T09:51:42.443383Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Lipid Molecular Dynamics Simulation", "description": "Lipid molecular dynamics simulation is a powerful tool for investigating the structure and dynamics of biological membranes and their molecular interactions. Leveraging advanced computational biology and extensive experience, CD ComputaBio offers comprehensive lipid simulation services, spanning atomic to mesoscopic scales, to support drug development, materials science, and basic biology research. The simulation bridges the gap between theory and experiment, providing unparalleled insights into lipid membranes and their interactions.", "homepage": "https://www.computabio.com/lipid-molecular-dynamics-simulation.html", "biotoolsID": "lipid-molecular-dynamics-simulation", "biotoolsCURIE": "biotools:lipid-molecular-dynamics-simulation", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:30:07.983895Z", "lastUpdate": "2026-03-31T09:30:07.985832Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Protein Molecular Dynamics Simulation", "description": "Protein molecular dynamics simulation employs physical principles to computationally track the dynamic behavior of proteins at atomic resolution, revealing crucial insights into their conformational changes, interaction mechanisms, and functional regulation. CD ComputaBio integrates state-of-the-art algorithms, powerful computing resources, and artificial intelligence to provide clients with high-precision simulation services, driving advancements in drug design, enzyme engineering, and basic biological research.", "homepage": "https://www.computabio.com/protein-molecular-dynamics-simulation.html", "biotoolsID": "protein-molecular-dynamics-simulation", "biotoolsCURIE": "biotools:protein-molecular-dynamics-simulation", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:27:37.603974Z", "lastUpdate": "2026-03-31T09:27:37.606182Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Molecular Dynamics Simulation Service", "description": "Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. CD ComputaBio can simulate thousands or even millions of atoms and molecules, which are often used to simulate particles in liquids, ensembles of solids, and vapors, and can also use different force fields and boundary conditions to simulate all atoms, polymers, biological, metallic, granular and coarsening systems.", "homepage": "https://www.computabio.com/molecular-dynamics-simulation-service.html", "biotoolsID": "molecular-dynamics-simulation-service", "biotoolsCURIE": "biotools:molecular-dynamics-simulation-service", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:23:51.094267Z", "lastUpdate": "2026-03-31T09:23:51.096714Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Carbohydrate Molecule Modeling Service", "description": "Carbohydrates, often referred to as glycans, are one of the four fundamental biomolecules essential for life, alongside proteins, lipids, and nucleic acids. Despite their critical roles in biological systems, carbohydrates remain understudied compared to their molecular counterparts. Carbohydrate modeling is crucial for understanding structure and function. It employs various methods, including molecular dynamics simulations, quantum chemical calculations, geometry optimization, and experimental data-driven structure prediction. CD ComputaBio provides its clients with high-quality computational modeling services, encompassing a wide range of scientific areas, including carbohydrate modeling.", "homepage": "https://www.computabio.com/carbohydrate-molecule-modeling-service.html", "biotoolsID": "carbohydrate-molecule-modeling-service", "biotoolsCURIE": "biotools:carbohydrate-molecule-modeling-service", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:22:56.535087Z", "lastUpdate": "2026-03-31T09:22:56.537193Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Inhibitor Modeling Service", "description": "Inhibitors are central to modern drug discovery, providing therapeutic opportunities through the selective blockade of disease-related proteins, enzymes, and signaling pathways. The global demand for targeted therapies has grown substantially, particularly in oncology, neurodegenerative disorders, and infectious diseases. As a premier CRO specializing in computational biotechnologies, CD ComputaBio offers comprehensive inhibitor modeling solutions designed to accelerate drug discovery initiatives.", "homepage": "https://www.computabio.com/inhibitor-modeling-service.html", "biotoolsID": "inhibitor-modeling-service", "biotoolsCURIE": "biotools:inhibitor-modeling-service", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:21:45.471695Z", "lastUpdate": "2026-03-31T09:21:45.475729Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Metal Complex Modeling Service", "description": "Metal complexes are ubiquitous and essential components of biological systems, exhibiting a remarkable diversity in their structure and function. Metal complex modeling, a core competency at CD ComputaBio, provides a powerful lens through which to investigate these intricate molecules, offering invaluable insights for understanding fundamental biological processes and for the discovery and design of novel therapeutic agents inspired by nature.", "homepage": "https://www.computabio.com/metal-complex-modeling-service.html", "biotoolsID": "metal-complex-modeling-service", "biotoolsCURIE": "biotools:metal-complex-modeling-service", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:20:39.418356Z", "lastUpdate": "2026-03-31T09:20:39.420422Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Natural Product Modeling Service", "description": "Natural products, with their intricate structural diversity and remarkable biological activities, have long been a cornerstone of drug discovery. However, the journey from identifying a promising natural product to developing a life-saving therapeutic is often complex and resource-intensive. CD ComputaBio offers natural product modeling services, leveraging the power of computational chemistry and advanced modeling methods to accelerate your research and unlock the full potential of nature's pharmacy.", "homepage": "https://www.computabio.com/natural-product-modeling-service.html", "biotoolsID": "natural-product-modeling-service", "biotoolsCURIE": "biotools:natural-product-modeling-service", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:12:43.035791Z", "lastUpdate": "2026-03-31T09:12:43.038462Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Small Molecule Modeling Services", "description": "Small molecule modeling is a fundamental tool in computational biology and drug discovery, employing computer simulation to investigate interactions between potential drug candidates and biological macromolecules. By predicting binding modes, binding affinities, and molecular dynamics behavior, this method provides a scientific foundation for drug screening and optimization, facilitating a deeper understanding of molecular mechanisms and accelerating new drug development. CD ComputaBio provides small molecule modeling services to streamline drug discovery.", "homepage": "https://www.computabio.com/small-molecule-modeling-services.html", "biotoolsID": "small-molecule-modeling-services", "biotoolsCURIE": "biotools:small-molecule-modeling-services", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:11:48.690318Z", "lastUpdate": "2026-03-31T09:11:48.692453Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Cyclic Peptide Modeling Services", "description": "Cyclic peptides, with their unique structures, offer higher target affinity, metabolic stability, and membrane penetration than linear peptides, making them a focus in drug development. However, their complex conformations and verification challenges hinder their design. CD ComputaBio uses a top computational biology platform, combining AI, MD simulations, and QM calculations to offer comprehensive cyclic peptide modeling services, from design to evaluation, overcoming traditional experimental limitations.", "homepage": "https://www.computabio.com/cyclic-peptide-structure-modeing-services.html", "biotoolsID": "cyclic-peptide-modeling-services", "biotoolsCURIE": "biotools:cyclic-peptide-modeling-services", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:10:52.874541Z", "lastUpdate": "2026-03-31T09:10:52.876846Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Signal Peptides Structure Modeling Services", "description": "Signal peptides are short sequences of amino acids, typically between 15 and 30 residues long, found at the N-terminal of proteins. They serve a critical function in directing the transport of proteins throughout the cell. CD ComputaBio offers a comprehensive suite of services dedicated to supporting your signal peptides discovery initiatives.", "homepage": "https://www.computabio.com/signal-peptides-structure-modeling-services.html", "biotoolsID": "signal_peptides_structure_modeling_services", "biotoolsCURIE": "biotools:signal_peptides_structure_modeling_services", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:09:57.244299Z", "lastUpdate": "2026-03-31T09:09:57.246423Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Peptide Modeling Services", "description": "Peptides are made up of amino acid molecules, which are the \"building blocks\" of proteins. Peptides are short proteins, approximately 2-100 amino acids in length. CD ComputaBio offers a range of peptide modeling services to assist researchers and pharmaceutical companies in peptide drug discovery and development.", "homepage": "https://www.computabio.com/peptide-modeling-services.html", "biotoolsID": "peptide_modeling_services", "biotoolsCURIE": "biotools:peptide_modeling_services", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:09:03.489615Z", "lastUpdate": "2026-03-31T09:09:03.492174Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Antibody Modeling Services", "description": "Antibodies are large, Y-shaped glycoproteins produced by B cells as the primary immune defense. CD ComputaBio is a professional service provider for the antibody modeling industry. With rich experience, our expert team has participated in some university scientific research projects and mastered a variety of advanced antibody modeling technologies.", "homepage": "https://www.computabio.com/antibody-modeling-services.html", "biotoolsID": "antibody_modeling_services", "biotoolsCURIE": "biotools:antibody_modeling_services", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:08:18.826777Z", "lastUpdate": "2026-03-31T09:08:18.829908Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Protein Modeling Service", "description": "At CD ComputaBio, we have a proven track record of meeting our client's needs in protein modeling. One of our core competencies is our expertise in protein modeling services. Protein modeling is especially valuable for understanding the function of proteins, designing drugs, and studying the mechanisms of diseases.", "homepage": "https://www.computabio.com/protein-modeling-service.html", "biotoolsID": "protein_modeling_service", "biotoolsCURIE": "biotools:protein_modeling_service", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:07:08.089200Z", "lastUpdate": "2026-03-31T09:07:08.091083Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Virtual Cell Modeling Service", "description": "Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantities such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines.", "homepage": "https://www.computabio.com/virtual-cell-modeling-service.html", "biotoolsID": "virtual_cell_modeling_service", "biotoolsCURIE": "biotools:virtual_cell_modeling_service", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T09:06:06.499130Z", "lastUpdate": "2026-03-31T09:06:06.500955Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Antibody-Antigen Docking Service", "description": "The Antibody-Antigen Docking Service is a crucial tool in modern biomedical research. It allows for in-depth exploration of how antibodies bind to their specific antigens, which is fundamental for understanding immune responses and developing new treatments. CD ComputaBio's docking service is designed to aid researchers in their quest to develop more efficient and effective therapeutics.", "homepage": "https://www.computabio.com/antibody-antigen-docking-service.html", "biotoolsID": "antibody-antigen_docking_service", "biotoolsCURIE": "biotools:antibody-antigen_docking_service", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T08:59:57.575542Z", "lastUpdate": "2026-03-31T08:59:57.577677Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Protein-RNA Docking Service", "description": "The interactions between proteins and RNA molecules play a vital role in a wide array of biological processes. These interactions are implicated in gene expression regulation, RNA splicing, translation initiation, and many other essential cellular functions. At CD ComputaBio, we offer a sophisticated Protein-RNA Docking Service that aims to provide in-depth insights into these complex molecular associations.", "homepage": "https://www.computabio.com/protein-rna-docking-service.html", "biotoolsID": "protein-rna_docking_service", "biotoolsCURIE": "biotools:protein-rna_docking_service", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T08:58:54.665985Z", "lastUpdate": "2026-03-31T08:58:54.667970Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Protein-DNA Docking Service", "description": "With a professional background in computational biology, CD ComputaBio offers cutting-edge solutions for protein-DNA docking research. Our protein-DNA docking service enables researchers to explore the intricate interactions between proteins and DNA. Leveraging our expertise and sophisticated computational tools, we provide a comprehensive, customized approach to meet the unique needs of our clients.", "homepage": "https://www.computabio.com/protein-dna-docking-service.html", "biotoolsID": "protein-dna_docking_service", "biotoolsCURIE": "biotools:protein-dna_docking_service", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T08:58:00.489874Z", "lastUpdate": "2026-03-31T08:58:00.492003Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Protein-Peptide Docking Service", "description": "CD ComputaBio offers specialized protein-peptide docking services that are designed to facilitate your research and development projects. Our deep expertise in computational biology, combined with advanced docking techniques, enables us to deliver insights that can drive innovations in various fields, including drug discovery, vaccine development, and therapeutic interventions.", "homepage": "https://www.computabio.com/protein-peptide-docking-service.html", "biotoolsID": "protein-peptide_docking_service", "biotoolsCURIE": "biotools:protein-peptide_docking_service", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T08:57:14.234038Z", "lastUpdate": "2026-03-31T08:57:14.235856Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Protein-Protein Docking Service", "description": "Protein-protein interactions (PPIs) govern virtually every biological process, from signal transduction and immune recognition to enzymatic regulation and multi-protein complex assembly. Understanding how two proteins associate at the structural level is essential for mechanistic studies, antibody design, protein engineering, and therapeutic target validation. However, experimental determination of complex structures by X-ray crystallography, cryo-EM, or NMR remains time-consuming and resource-intensive.\n\nCD ComputaBio's Protein-Protein Docking Service provides a robust and scientifically rigorous computational solution to predict biologically relevant protein complex structures with high confidence. By integrating advanced conformational sampling, multi-criteria scoring, structural refinement, and interface hotspot analysis, we deliver ranked docking models that are not only structurally plausible but also experimentally actionable.", "homepage": "https://www.computabio.com/protein-protein-docking-service.html", "biotoolsID": "protein-protein_docking_service", "biotoolsCURIE": "biotools:protein-protein_docking_service", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T08:55:11.241433Z", "lastUpdate": "2026-03-31T08:55:11.244310Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Molecular Docking Services", "description": "CD ComputaBio provides a comprehensive molecular docking and structure-based drug design (SBDD) platform, offering high-accuracy simulations across small molecules, proteins, peptides, antibodies, RNA, and nucleic acids. Powered by proprietary AI engines—including BioAI-Dock, TurboAI-Screen, FlexAI-Fit, and FragAI-Grow—the service supports virtual screening, binding mode prediction, covalent docking, PPI modeling, peptide flexibility handling, and fragment-based drug design. Applications span small-molecule discovery, enzyme engineering, antibody design, RNA therapeutics, protein engineering, and macrocycle optimization. Through a streamlined workflow from consultation to data delivery, the platform enables researchers and biotech teams to accelerate hit identification, lead optimization, and complex biological interface analysis with speed, precision, and scientific rigor.", "homepage": "https://www.computabio.com/molecular-docking-service.html", "biotoolsID": "molecular_docking_services", "biotoolsCURIE": "biotools:molecular_docking_services", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "CDComputaBio", "additionDate": "2026-03-31T08:54:00.374906Z", "lastUpdate": "2026-03-31T08:54:00.377679Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PAL2NAL", "description": "PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated.", "homepage": "http://www.bork.embl.de/pal2nal/", "biotoolsID": "pal2nal", "biotoolsCURIE": "biotools:pal2nal", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0550", "term": "DNA substitution modelling" }, { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" }, { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_0654", "term": "DNA" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkl315", "pmid": "16845082", "pmcid": "PMC1538804", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Mikita Suyama", "email": "mikita@bioreg.kyushu-u.ac.jp", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-02-10T14:14:50Z", "lastUpdate": "2026-03-30T20:15:48.108734Z", "editPermission": { "type": "group", "authors": [ "Antonio_GS" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Search Ontologies", "description": "Search Ontologies is a tool for the automated extraction of ontology ID codes from web-based ontology repositories using metadata values. It supports the mapping of metadata fields from a structured Excel template to standardized ontology terms by using the BioPortal Search API.", "homepage": "https://github.com/cim-unito/SearchOntologies", "biotoolsID": "search_ontologies", "biotoolsCURIE": "biotools:search_ontologies", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "francesco.gammaraccio", "additionDate": "2026-03-30T14:45:56.214720Z", "lastUpdate": "2026-03-30T14:45:56.217379Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Autoencoder_RF_TabPFN for Cross-Cancer Metabolomics", "description": "Accurate and rapid disease diagnosis, particularly in prostate cancer (PC) and breast cancer (BC), is critical for early intervention and improved patient outcomes. Metabolomic signatures represent a robust molecular framework for elucidating cancer-associated biochemical reprogramming. The use of Artificial Intelligence (AI) in biology in recent years has become widespread and promising. This study introduces a novel predictive method that integrates an Autoencoder, random forest based feature selection and Tabular Prior-data Fitted Network (TabPFN) to achieve high diagnostic accuracy from metabolomics data of prostate and breast cancer patients.", "homepage": "https://github.com/SvenHauns/metabolomic_classifier.git", "biotoolsID": "autoencoder_rf_tabpfn_for_cross-cancer_metabolomics", "biotoolsCURIE": "biotools:autoencoder_rf_tabpfn_for_cross-cancer_metabolomics", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2990", "term": "Classification" } ], "input": [], "output": [], "note": null, "cmd": "python main.py --dataset {dataset_to_be_used} --setting {ae or rf} --size {size}\n\npython main.py --test_dataset {./data/toy_predict.csv} --dataset {./data/toy_train.csv} --predict True --setting {ae or rf} --size {size}\n\nsee Readme for detailed instructions" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2815", "term": "Human biology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/SvenHauns/metabolomic_classifier.git", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/SvenHauns/metabolomic_classifier.git", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/SvenHauns/metabolomic_classifier.git", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Sven Hauns", "email": "haunss@informatik.uni-freiburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "haunssv", "additionDate": "2026-03-30T13:34:06.425220Z", "lastUpdate": "2026-03-30T13:34:06.427392Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "bc-GenExMiner", "description": "Breast cancer gene-expression miner (bc-GenExMiner) 4.5 is a mining module computes breast cancer differential gene expression analyses. It is a statistical mining tool of published annotated breast cancer transcriptomic data (DNA microarrays and RNA-seq). It offers the possibility to explore gene-expression of genes of interest in breast cancer.", "homepage": "http://bcgenex.ico.unicancer.fr", "biotoolsID": "bc-genexminer", "biotoolsCURIE": "biotools:bc-genexminer", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3463", "term": "Expression correlation analysis" }, { "uri": "http://edamontology.org/operation_0531", "term": "Heat map generation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3518", "term": "Microarray experiment" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/DATABASE/BAAB007", "pmid": "33599248", "pmcid": "PMC7904047", "type": [], "version": null, "note": null, "metadata": { "title": "Bc-GenExMiner 4.5: New mining module computes breast cancer differential gene expression analyses", "abstract": "© 2021 The Author(s) 2021. Published by Oxford University Press.'Breast cancer gene-expression miner' (bc-GenExMiner) is a breast cancer-associated web portal (http://bcgenex.ico.unicancer.fr) Here, we describe the development of a new statistical mining module, which permits several differential gene expression analyses, i.e. 'Expression' module. Sixty-two breast cancer cohorts and one healthy breast cohort with their corresponding clinicopathological information are included in bc-GenExMiner v4.5 version. Analyses are based on microarray or RNAseq transcriptomic data. Thirty-nine differential gene expression analyses, grouped into 13 categories, according to clinicopathological and molecular characteristics ('Targeted' and 'Exhaustive') and gene expression ('Customized'), have been developed. Output results are visualized in four forms of plots. This new statistical mining module offers, among other things, the possibility to compare gene expression in healthy (cancer-free), tumour-adjacent and tumour tissues at once and in three triple-negative breast cancer subtypes (i.e. C1: molecular apocrine tumours; C2: basal-like tumours infiltrated by immune suppressive cells and C3: basal-like tumours triggering an ineffective immune response). Several validation tests showed that bioinformatics process did not alter the pathobiological information contained in the source data. In this work, we developed and demonstrated that bc-GenExMiner 'Expression' module can be used for exploratory and validation purposes. Database URL: http://bcgenex.ico.unicancer.fr", "date": "2021-01-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Jezequel P." }, { "name": "Gouraud W." }, { "name": "Ben Azzouz F." }, { "name": "Guerin-Charbonnel C." }, { "name": "Juin P.P." }, { "name": "Lasla H." }, { "name": "Campone M." } ], "journal": "Database" } } ], "credit": [ { "name": "Pascal Jézéquel", "email": "pascal.jezequel@ico.unicancer.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "w.gouraud", "additionDate": "2021-03-19T08:57:45Z", "lastUpdate": "2026-03-30T09:22:12.633153Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PROVEAN", "description": "A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.", "homepage": "http://provean.jcvi.org/index.php", "biotoolsID": "provean", "biotoolsCURIE": "biotools:provean", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0361", "term": "Sequence annotation" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3120", "term": "Protein variants" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Shell" ], "license": "GPL-3.0", "collectionID": [ "Animal and Crop Genomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://provean.jcvi.org/index.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0046688", "pmid": "23056405", "pmcid": "PMC3466303", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Predicting the Functional Effect of Amino Acid Substitutions and Indels", "abstract": "As next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of sequence variations and narrow down the search of casual variants for disease phenotypes. Different classes of sequence variations at the nucleotide level are involved in human diseases, including substitutions, insertions, deletions, frameshifts, and non-sense mutations. Frameshifts and non-sense mutations are likely to cause a negative effect on protein function. Existing prediction tools primarily focus on studying the deleterious effects of single amino acid substitutions through examining amino acid conservation at the position of interest among related sequences, an approach that is not directly applicable to insertions or deletions. Here, we introduce a versatile alignment-based score as a new metric to predict the damaging effects of variations not limited to single amino acid substitutions but also in-frame insertions, deletions, and multiple amino acid substitutions. This alignment-based score measures the change in sequence similarity of a query sequence to a protein sequence homolog before and after the introduction of an amino acid variation to the query sequence. Our results showed that the scoring scheme performs well in separating disease-associated variants (n = 21,662) from common polymorphisms (n = 37,022) for UniProt human protein variations, and also in separating deleterious variants (n = 15,179) from neutral variants (n = 17,891) for UniProt non-human protein variations. In our approach, the area under the receiver operating characteristic curve (AUC) for the human and non-human protein variation datasets is ~0.85. We also observed that the alignment-based score correlates with the deleteriousness of a sequence variation. In summary, we have developed a new algorithm, PROVEAN (Protein Variation Effect Analyzer), which provides a generalized approach to predict the functional effects of protein sequence variations including single or multiple amino acid substitutions, and in-frame insertions and deletions. The PROVEAN tool is available online at http://provean.jcvi.org. © 2012 Choi et al.", "date": "2012-10-08T00:00:00Z", "citationCount": 2199, "authors": [ { "name": "Choi Y." }, { "name": "Sims G.E." }, { "name": "Murphy S." }, { "name": "Miller J.R." }, { "name": "Chan A.P." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": null, "email": null, "url": "http://provean.jcvi.org/contact.php", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ahmad_raza", "additionDate": "2017-08-20T17:18:10Z", "lastUpdate": "2026-03-30T09:22:11.430833Z", "editPermission": { "type": "group", "authors": [ "animalandcropgenomics", "ahmad_raza" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Gromacs", "description": "Versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since it is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.", "homepage": "http://www.gromacs.org/", "biotoolsID": "gromacs", "biotoolsCURIE": "biotools:gromacs", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2476", "term": "Molecular dynamics" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_0176", "term": "Molecular dynamics" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "LGPL-2.1", "collectionID": [ "BioExcel" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://www.gromacs.org/Downloads", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "http://www.gromacs.org/Documentation", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.softx.2015.06.001", "pmid": null, "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers", "abstract": "GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU-GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported.", "date": "2015-01-01T00:00:00Z", "citationCount": 15418, "authors": [ { "name": "Abraham M.J." }, { "name": "Murtola T." }, { "name": "Schulz R." }, { "name": "Pall S." }, { "name": "Smith J.C." }, { "name": "Hess B." }, { "name": "Lindah E." } ], "journal": "SoftwareX" } }, { "doi": "10.1002/jcc.20291", "pmid": "16211538", "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "GROMACS: Fast, flexible, and free", "abstract": "This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org. © 2005 Wiley Periodicals, Inc.", "date": "2005-12-01T00:00:00Z", "citationCount": 14137, "authors": [ { "name": "Van Der Spoel D." }, { "name": "Lindahl E." }, { "name": "Hess B." }, { "name": "Groenhof G." }, { "name": "Mark A.E." }, { "name": "Berendsen H.J.C." } ], "journal": "Journal of Computational Chemistry" } }, { "doi": "10.1063/5.0018516", "pmid": "33032406", "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS", "abstract": "The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these benefits, it has been necessary to reformulate some of the most fundamental algorithms, including the Verlet list, pair searching, and cutoffs. Here, we present the heterogeneous parallelization and acceleration design of molecular dynamics implemented in the GROMACS codebase over the last decade. The setup involves a general cluster-based approach to pair lists and non-bonded pair interactions that utilizes both GPU and central processing unit (CPU) single instruction, multiple data acceleration efficiently, including the ability to load-balance tasks between CPUs and GPUs. The algorithm work efficiency is tuned for each type of hardware, and to use accelerators more efficiently, we introduce dual pair lists with rolling pruning updates. Combined with new direct GPU-GPU communication and GPU integration, this enables excellent performance from single GPU simulations through strong scaling across multiple GPUs and efficient multi-node parallelization.", "date": "2020-10-07T00:00:00Z", "citationCount": 349, "authors": [ { "name": "Pall S." }, { "name": "Zhmurov A." }, { "name": "Bauer P." }, { "name": "Abraham M." }, { "name": "Lundborg M." }, { "name": "Gray A." }, { "name": "Hess B." }, { "name": "Lindahl E." } ], "journal": "Journal of Chemical Physics" } }, { "doi": "10.1007/978-3-319-15976-8_1", "pmid": null, "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Tackling exascale software challenges in molecular dynamics simulations with GROMACS", "abstract": "GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.", "date": "2015-01-01T00:00:00Z", "citationCount": 752, "authors": [ { "name": "Pall S." }, { "name": "Abraham M.J." }, { "name": "Kutzner C." }, { "name": "Hess B." }, { "name": "Lindahl E." } ], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1093/bioinformatics/btt055", "pmid": "23407358", "pmcid": "PMC3605599", "type": [], "version": null, "note": null, "metadata": { "title": "GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit", "abstract": "Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources.Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. © 2013 The Author. Published by Oxford University Press. All rights reserved.", "date": "2013-04-01T00:00:00Z", "citationCount": 5927, "authors": [ { "name": "Pronk S." }, { "name": "Pall S." }, { "name": "Schulz R." }, { "name": "Larsson P." }, { "name": "Bjelkmar P." }, { "name": "Apostolov R." }, { "name": "Shirts M.R." }, { "name": "Smith J.C." }, { "name": "Kasson P.M." }, { "name": "Van Der Spoel D." }, { "name": "Hess B." }, { "name": "Lindahl E." } ], "journal": "Bioinformatics" } }, { "doi": "10.1021/ct700301q", "pmid": "26620784", "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "GRGMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation", "abstract": "Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes. © 2008 American Chemical Society.", "date": "2008-03-01T00:00:00Z", "citationCount": 13627, "authors": [ { "name": "Hess B." }, { "name": "Kutzner C." }, { "name": "Van Der Spoel D." }, { "name": "Lindahl E." } ], "journal": "Journal of Chemical Theory and Computation" } }, { "doi": "10.1007/s008940100045", "pmid": null, "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "GROMACS 3.0: A package for molecular simulation and trajectory analysis", "abstract": "GROMACS 3.0 is the latest release of a versatile and very well optimized package for molecular simulation. Much effort has been devoted to achieving extremely high performance on both workstations and parallel computers. The design includes an extraction of virial and periodic boundary conditions from the loops over pairwise interactions, and special software routines to enable rapid calculation of x-1/2. Inner loops are generated automatically in C or Fortran at compile time, with optimizations adapted to each architecture. Assembly loops using SSE and 3DNow! Multimedia instructions are provided for x86 processors, resulting in exceptional performance on inexpensive PC workstations. The interface is simple and easy to use (no scripting language), based on standard command line arguments with self-explanatory functionality and integrated documentation. All binary files are independent of hardware endian and can be read by versions of GROMACS compiled using different floating-point precision. A large collection of flexible tools for trajectory analysis is included, with output in the form of finished Xmgr/Grace graphs. A basic trajectory viewer is included, and several external visualization tools can read the GROMACS trajectory format.", "date": "2001-12-01T00:00:00Z", "citationCount": 6227, "authors": [ { "name": "Lindahl E." }, { "name": "Hess B." }, { "name": "van der Spoel D." } ], "journal": "Journal of Molecular Modeling" } }, { "doi": "10.1016/0010-4655(95)00042-E", "pmid": null, "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "GROMACS: A message-passing parallel molecular dynamics implementation", "abstract": "A parallel message-passing implementation of a molecular dynamics (MD) program that is useful for bio(macro)molecules in aqueous environment is described. The software has been developed for a custom-designed 32-processor ring GROMACS (GROningen MAchine for Chemical Simulation) with communication to and from left and right neighbours, but can run on any parallel system onto which a a ring of processors can be mapped and which supports PVM-like block send and receive calls. The GROMACS software consists of a preprocessor, a parallel MD and energy minimization program that can use an arbitrary number of processors (including one), an optional monitor, and several analysis tools. The programs are written in ANSI C and available by ftp (information: gromacs@chem.rug.nl) The functionality is based on the GROMOS (GROningen MOlecular Simulation) package (van Gunsteren and Berendsen, 1987; BIOMOS B.V., Nijenborgh 4, 9747 AG Groningen). Conversion programs between GROMOS and GROMACS formats are included. The MD program can handle rectangular periodic boundary conditions with temperature and pressure scaling. The interactions that can be handled without modification are variable non-bonded pair interactions with Coulomb and Lennard-Jones or Buckingham potentials, using a twin-range cut-off based on charge groups, and fixed bonded interactions of either harmonic or constraint type for bonds and bond angles and either periodic or cosine power series interactions for dihedral angles. Special forces can be added to groups of particles (for non-equilibrium dynamics or for position restraining) or between particles (for distance restraints). The parallelism is based on particle decomposition. Interprocessor communication is largely limited to position and force distribution over the ring once per time step. © 1995.", "date": "1995-09-02T00:00:00Z", "citationCount": 8425, "authors": [ { "name": "Berendsen H.J.C." }, { "name": "van der Spoel D." }, { "name": "van Drunen R." } ], "journal": "Computer Physics Communications" } }, { "doi": "10.1002/jcc.24030", "pmid": "26238484", "pmcid": "PMC5042102", "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Best bang for your buck: GPU nodes for GROMACS biomolecular simulations", "abstract": "The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well-exploited with a combination of single instruction multiple data, multithreading, and message passing interface (MPI)-based single program multiple data/multiple program multiple data parallelism while graphics processing units (GPUs) can be used as accelerators to compute interactions off-loaded from the CPU. Here, we evaluate which hardware produces trajectories with GROMACS 4.6 or 5.0 in the most economical way. We have assembled and benchmarked compute nodes with various CPU/GPU combinations to identify optimal compositions in terms of raw trajectory production rate, performance-to-price ratio, energy efficiency, and several other criteria. Although hardware prices are naturally subject to trends and fluctuations, general tendencies are clearly visible. Adding any type of GPU significantly boosts a node's simulation performance. For inexpensive consumer-class GPUs this improvement equally reflects in the performance-to-price ratio. Although memory issues in consumer-class GPUs could pass unnoticed as these cards do not support error checking and correction memory, unreliable GPUs can be sorted out with memory checking tools. Apart from the obvious determinants for cost-efficiency like hardware expenses and raw performance, the energy consumption of a node is a major cost factor. Over the typical hardware lifetime until replacement of a few years, the costs for electrical power and cooling can become larger than the costs of the hardware itself. Taking that into account, nodes with a well-balanced ratio of CPU and consumer-class GPU resources produce the maximum amount of GROMACS trajectory over their lifetime.", "date": "2015-10-01T00:00:00Z", "citationCount": 198, "authors": [ { "name": "Kutzner C." }, { "name": "Pall S." }, { "name": "Fechner M." }, { "name": "Esztermann A." }, { "name": "De Groot B.L." }, { "name": "Grubmuller H." } ], "journal": "Journal of Computational Chemistry" } }, { "doi": "10.1002/jcc.26011", "pmid": "31260119", "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "More bang for your buck: Improved use of GPU nodes for GROMACS 2018", "abstract": "We identify hardware that is optimal to produce molecular dynamics (MD) trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate it to the costs of the nodes, which may include their lifetime costs for energy and cooling. In agreement with our earlier investigation using GROMACS 4.6 on hardware of 2014, the performance to price ratio of consumer GPU nodes is considerably higher than that of CPU nodes. However, with GROMACS 2018, the optimal CPU to GPU processing power balance has shifted even more toward the GPU. Hence, nodes optimized for GROMACS 2018 and later versions enable a significantly higher performance to price ratio than nodes optimized for older GROMACS versions. Moreover, the shift toward GPU processing allows to cheaply upgrade old nodes with recent GPUs, yielding essentially the same performance as comparable brand-new hardware. © 2019 Wiley Periodicals, Inc.", "date": "2019-10-15T00:00:00Z", "citationCount": 288, "authors": [ { "name": "Kutzner C." }, { "name": "Pall S." }, { "name": "Fechner M." }, { "name": "Esztermann A." }, { "name": "de Groot B.L." }, { "name": "Grubmuller H." } ], "journal": "Journal of Computational Chemistry" } } ], "credit": [ { "name": "GROMACS support", "email": null, "url": "http://www.gromacs.org/support/mailing_lists", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "jdianes", "additionDate": "2016-10-03T14:08:36Z", "lastUpdate": "2026-03-30T09:22:03.645037Z", "editPermission": { "type": "group", "authors": [ "adam.hospital@irbbarcelona.org", "gelpi@ub.edu", "sergitobara", "n.m.palmblad@lumc.nl" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "quac", "description": "QuaC is a snakemake-based pipeline that runs several QC tools for WGS/WES samples and then summarizes their results using pre-defined, configurable QC thresholds.", "homepage": "https://github.com/uab-cgds-worthey/quac", "biotoolsID": "quac", "biotoolsCURIE": "biotools:quac", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "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_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "Sequencing" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/uab-cgds-worthey/quac", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/uab-cgds-worthey/quac/releases/tag/2.0", "type": "Source code", "note": null, "version": "2.0" } ], "documentation": [ { "url": "https://quac.readthedocs.io/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.21105/joss.05313", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Manavalan Gajapathy", "email": null, "url": "https://github.com/ManavalanG", "orcidid": "https://orcid.org/0000-0002-8606-0113", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "sdhutchins", "additionDate": "2026-03-26T02:15:51.819440Z", "lastUpdate": "2026-03-28T20:53:47.092010Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Genxflo", "description": "GenXflo is a no-code visual Nextflow pipeline builder for bioinformatics. Users design workflows on a drag-and-drop canvas and export clean, production-ready Nextflow DSL2 code. Supports Docker and Singularity containerisation, local, HPC, and cloud deployment on AWS, Azure, and Google Cloud, and includes AI-assisted workflow validation.", "homepage": "https://www.genxflo.com", "biotoolsID": "genxflo", "biotoolsCURIE": "biotools:genxflo", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2428", "term": "Validation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2430", "term": "Design" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workbench" ], "topic": [ { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [], "language": [ "JavaScript", "Python", "TypeScript", "CWL" ], "license": null, "collectionID": [], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://genxflo.com/app/resources", "type": [ "Software catalogue" ], "note": "documentation on how to use the tool" }, { "url": "https://genxflo.com/product/overview", "type": [ "Other" ], "note": "Product Overview" } ], "download": [], "documentation": [ { "url": "https://genxflo.com/app/resources", "type": [ "Quick start guide" ], "note": null } ], "publication": [], "credit": [], "owner": "genxflo", "additionDate": "2026-03-28T18:52:56.484093Z", "lastUpdate": "2026-03-28T19:21:38.419258Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }