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{ "count": 33254, "next": "?page=2", "previous": null, "list": [ { "name": "Computase", "description": "Local Python sequence utilities for nucleotide composition, DNA and RNA reverse complements, NCBI genetic-code translation, six-frame candidate ORF enumeration, and IUPAC motif searches. 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/host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-liver-tumour" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Run nnUnet pretrained on Task004_Hippocampus MRI data targeting posterior and anterior parts of the hippocampus", "cmd": "docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-hippocampus-segmentation" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Run nnUnet pretrained on Task010_Colon targeting are colon cancer primaries.", "cmd": "docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-colon-cancer" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": 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Currently not public." }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/fair_eucaim/artifacts-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/fair_eucaim_web/artifacts-tab", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.md", "type": [ "General" ], "note": "Documentation for the main package, EUCAIM plugin specific documentation not included." }, { "url": "https://gitlabpages.ifca.es/fair-eva-guide-608baa/", "type": [ "User manual" ], "note": "Wiki page with FAIR EVA for EUCAIM specific instructions." } ], "publication": [ { "doi": "10.1038/s41597-023-02652-8", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Fernando Aguilar", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-9462-4831", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer", "Documentor" ], "note": "Creator and devloper of the main package FAIR EVA.\nThis software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647." }, { "name": "David Rodríguez", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9160-5106", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": "Developer of the EUCAIM plugin." }, { "name": "Inés Victoria", "email": null, "url": null, "orcidid": "https://orcid.org/0009-0003-7950-3937", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Developer of the EUCAIM plugin." } ], "owner": "davrodgon", "additionDate": "2025-06-30T08:52:48.500476Z", "lastUpdate": "2026-08-05T08:12:34.409744Z", "editPermission": { "type": "group", "authors": [ "ines.ifca", "davrodgon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PySMACKS", "description": "Python computational framework for analysis of single-molecule FRET data", "homepage": "https://github.com/molcretb/PySMACKS", "biotoolsID": "pysmacks", "biotoolsCURIE": "biotools:pysmacks", "version": [ "1.0.0" ], "otherID": [ { "value": "RRID:SCR_028788", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [], "output": [], "note": "Run the GUI of PySMACKS", "cmd": "PySMACKS_GUI" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3306", "term": "Biophysics" }, { "uri": "http://edamontology.org/topic_3383", "term": "Bioimaging" } ], "operatingSystem": [ 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"https://orcid.org/0000-0002-5995-5376", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer", "Contributor" ], "note": "full-stack developer of PySMACKS" }, { "name": "Sonja Schmid", "email": "sonja.schmid@unibas.ch", "url": "https://schmid.chemie.unibas.ch/en/", "orcidid": "https://orcid.org/0000-0002-3710-5602", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": "Team leader at the University of Basel, in which PySMACKS is developed" } ], "owner": "bastien", "additionDate": "2026-08-04T08:45:27.787408Z", "lastUpdate": "2026-08-04T08:45:27.789840Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "picklet", "description": "Browser-based tool to open almost any file that carries sequence — FASTA, FASTQ, GenBank, EMBL, Swiss-Prot, 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The format is detected from the file content, not from the extension, so unlabelled or misnamed files still open, and gzip-compressed files are unpacked in place. Turns any of them into FASTA without a command line and without an account. Runs entirely in the browser — files are never uploaded.", "homepage": "https://fishka.bio/picklet", "biotoolsID": "picklet", "biotoolsCURIE": "biotools:picklet", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0233", "term": "Sequence conversion" }, { "uri": "http://edamontology.org/operation_2121", "term": "Sequence file editing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_1963", "term": "UniProtKB format" }, { "uri": "http://edamontology.org/format_3001", "term": "ACE" }, { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" }, { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_1632", "term": "SCF" }, { "uri": "http://edamontology.org/format_3975", "term": "GFA 1" }, { "uri": "http://edamontology.org/format_3000", "term": "AB1" }, { "uri": "http://edamontology.org/format_1927", "term": "EMBL format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1975", "term": "GFF3" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_3976", "term": "GFA 2" }, { "uri": "http://edamontology.org/format_1991", "term": "mega" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "TypeScript" ], "license": "Freeware", "collectionID": [ "fishka.bio" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://fishka.bio", "type": [ "Software catalogue" ], "note": "fishka.bio — the tool collection picklet belongs to" } ], "download": [ { "url": "https://fishka.bio/download", "type": "Downloads page", "note": "Offline build — the same application as a self-contained archive, runs from local files with no server", "version": null } ], "documentation": [], "publication": [ { "doi": "10.5281/zenodo.21444547", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": "2026.07.19", "note": "Software deposit (concept DOI — resolves to the latest version) covering the fishka.bio tools, including picklet.", "metadata": null } ], "credit": [ { "name": "Fishka Bio", "email": "swim@fishka.bio", "url": "https://fishka.bio", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null } ], "owner": "fishka", "additionDate": "2026-07-11T21:51:46.808639Z", "lastUpdate": "2026-08-04T00:11:19.984212Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "gbatlas", "description": "Browser-based viewer for GenBank and GenPept records — .gb, .gbk, .gbff, .gp and plain GenBank text. Renders an interactive linear and circular feature map, including circular plasmid maps, alongside the annotated source text and the nucleotide/protein sequence. \n\nTranslates CDS features using the record's own genetic code and translation qualifiers, flags where the stored /translation disagrees with a plain translation, and adds optional computed layers: ORF prediction and restriction-site mapping. Filters features by type, handles multi-record files, and keeps open records as local sessions, so a closed tab can be picked up where it was left. 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