{"count":233,"next":"https://catalogue.france-bioinformatique.fr/api/tool/?format=json&limit=20&offset=160&ordering=tool_licence","previous":"https://catalogue.france-bioinformatique.fr/api/tool/?format=json&limit=20&offset=120&ordering=tool_licence","results":[{"id":131,"name":"jvenn","description":"Plug-in for the jQuery Javascript library. It is an integrative tool for comparing lists with Venn Diagrams.","homepage":"http://bioinfo.genotoul.fr/jvenn/","biotoolsID":"jvenn","biotoolsCURIE":"biotools:jvenn","tool_type":["Command-line tool"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0092","http://edamontology.org/topic_2269"],"primary_publication":[],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":null,"email":"support.genopole@toulouse.inra.fr","url":"http://bioinfo.genotoul.fr/jvenn/index.html","orcidid":null,"gridid":null,"typeEntity":"Person","note":null}],"tool_licence":null,"documentation":"http://jvenn.toulouse.inra.fr/app/index.html","maturity":null,"cost":null,"unique_visits":0,"citations":null,"annual_visits":0,"last_update":"2024-11-25T14:53:20.499445Z","teams":[],"source_repository":null},{"id":46,"name":"HBVdb","description":"","homepage":null,"biotoolsID":"","biotoolsCURIE":"","tool_type":["Database portal"],"collection":[],"scientific_topics":[],"primary_publication":[],"operating_system":[],"tool_credit":[],"tool_licence":null,"documentation":null,"maturity":null,"cost":null,"unique_visits":null,"citations":null,"annual_visits":null,"last_update":null,"teams":[],"source_repository":null},{"id":121,"name":"LoRDEC","description":"Program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads.","homepage":"http://www.atgc-montpellier.fr/lordec/","biotoolsID":"lordec","biotoolsCURIE":"biotools:lordec","tool_type":["Command-line tool"],"collection":["elixir-fr-sdp-2019"],"scientific_topics":["http://edamontology.org/topic_3168","http://edamontology.org/topic_0654","http://edamontology.org/topic_3071","http://edamontology.org/topic_0091"],"primary_publication":[],"operating_system":["Linux"],"tool_credit":[{"type_role":["Primary contact"],"name":"Leena Salmela","email":"leena.salmela@cs.Helsinki.FI","url":"https://www.cs.helsinki.fi/u/lmsalmel/","orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":"Eric Rivals","email":"rivals@lirmm.fr","url":"http://www.lirmm.fr/~rivals/","orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Provider"],"name":"LIRMM","email":null,"url":"http://www.lirmm.fr/","orcidid":null,"gridid":null,"typeEntity":"Institute","note":null}],"tool_licence":null,"documentation":"http://www.atgc-montpellier.fr/lordec/","maturity":"Mature","cost":null,"unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2024-11-25T14:01:03.046535Z","teams":["ATGC"],"source_repository":null},{"id":179,"name":"MACSIMS","description":"Multiple alignment-based information management system that combines the advantages of both knowledge-based and ab initio sequence analysis methods.","homepage":"http://www.lbgi.fr/~julie/MACSIMS/","biotoolsID":"macsims","biotoolsCURIE":"biotools:macsims","tool_type":["Web application"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0092"],"primary_publication":["10.1186/1471-2105-7-318"],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":"Julie Thompson","email":"julie@igbmc.u-strasbg.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Provider"],"name":"IFB ELIXIR-FR","email":null,"url":null,"orcidid":null,"gridid":null,"typeEntity":"Institute","note":null}],"tool_licence":null,"documentation":"http://www.lbgi.fr/~julie/MACSIMS/Documentation/","maturity":null,"cost":null,"unique_visits":0,"citations":null,"annual_visits":0,"last_update":"2024-11-25T15:53:38.069848Z","teams":["BiGEst"],"source_repository":null},{"id":81,"name":"MatrixDB","description":"It is a database focused on interactions established by extracellular proteins and polysaccharides. It takes into account the multimeric nature of several extracellular protein families for the curation of interactions, and reports interactions with individual polypeptide chains or with multimers, considered as permanent complexes.","homepage":"http://matrixdb.univ-lyon1.fr/","biotoolsID":"matrixdb","biotoolsCURIE":"biotools:matrixdb","tool_type":["Database portal"],"collection":["elixir-fr-sdp-2019"],"scientific_topics":["http://edamontology.org/topic_0078","http://edamontology.org/topic_0128","http://edamontology.org/topic_0602","http://edamontology.org/topic_0623"],"primary_publication":[],"operating_system":["Linux"],"tool_credit":[{"type_role":["Primary contact"],"name":"MatrixDB Support","email":"sylvie.ricard-blum@univ-lyon1.fr","url":null,"orcidid":"https://orcid.org/0000-0001-9263-1851","gridid":null,"typeEntity":"Person","note":"Professor at University Lyon 1, head of a team working on structure-interaction-function relationships of the extracellular matrix and extracellular matrix interaction networks."}],"tool_licence":null,"documentation":"http://matrixdb.univ-lyon1.fr/","maturity":null,"cost":null,"unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2024-11-24T20:29:32.794189Z","teams":[],"source_repository":null},{"id":130,"name":"MEMHDX","description":"This tool allows users to perform an automated workflow to analyze, validate and visualize large HDX-MS datasets. The input file is the output of DynamX software from Waters. Output files provide a plot of the data, the fitted model for each peptide, a plot of the calculated p -values, and a global visualization of the experiment. User could also obtain an overview of all peptides on the 3D structure.","homepage":"http://memhdx.c3bi.pasteur.fr/","biotoolsID":"memhdx","biotoolsCURIE":"biotools:memhdx","tool_type":["Web application"],"collection":["Proteomics"],"scientific_topics":["http://edamontology.org/topic_3520"],"primary_publication":["10.1093/bioinformatics/btw420"],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Provider"],"name":"Structural Mass Spectrometry and Proteomics","email":null,"url":"https://research.pasteur.fr/en/team/structural-mass-spectrometry-and-proteomics/","orcidid":null,"gridid":null,"typeEntity":"Division","note":null},{"type_role":["Developer","Primary contact"],"name":"Véronique Hourdel","email":"vhourdel@pasteur.fr","url":"https://research.pasteur.fr/en/member/veronique-hourdel/","orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Support","Primary contact"],"name":"Marie-Agnès Dillies","email":"marie-agnes.dillies@pasteur.fr","url":"https://research.pasteur.fr/en/member/marie-agnes-dillies/","orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Maintainer","Primary contact"],"name":"Stevenn Volant","email":"svolant@pasteur.fr","url":"https://research.pasteur.fr/en/member/stevenn-volant/","orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Support","Primary contact"],"name":"Sébastien Brier","email":"sbrier@pasteur.fr","url":"https://research.pasteur.fr/en/member/sebastien-brier/","orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Provider"],"name":"Institut Pasteur","email":null,"url":"https://research.pasteur.fr","orcidid":null,"gridid":null,"typeEntity":"Institute","note":null},{"type_role":[],"name":"C3BI","email":null,"url":"https://research.pasteur.fr/en/center/c3bi/","orcidid":null,"gridid":null,"typeEntity":"Division","note":null},{"type_role":["Provider"],"name":"Bioinformatics and Biostatistics Hub","email":null,"url":"https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/","orcidid":null,"gridid":null,"typeEntity":"Division","note":null}],"tool_licence":null,"documentation":"https://www.youtube.com/watch?v=WeCt1sVyHio&feature=youtu.be","maturity":"Mature","cost":"Free of charge","unique_visits":833,"citations":null,"annual_visits":1524,"last_update":"2024-11-25T14:14:10.281449Z","teams":["Pasteur HUB"],"source_repository":null},{"id":88,"name":"MetExplore","description":"Metabolic network curation, visualisation and omics data analysis. It is possible to curate and annotate metabolic networks in a collaborative environment. Several tools are available for metabolomics data mapping in networks and visualisation.","homepage":"http://www.metexplore.fr/","biotoolsID":"metexplore","biotoolsCURIE":"biotools:metexplore","tool_type":["Web service","Web application","Workbench"],"collection":["elixir-fr-sdp-2019","EBI Training Tools"],"scientific_topics":["http://edamontology.org/topic_0602"],"primary_publication":["10.1093/nar/gky301","10.1093/nar/gkq312"],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":null,"email":"ludovic.cottret@inra.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Support"],"name":null,"email":"metexplore@oulouse.inra.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":[],"name":"MetaboHub","email":null,"url":null,"orcidid":null,"gridid":null,"typeEntity":"Consortium","note":null},{"type_role":["Primary contact"],"name":"Fabien JOURDAN","email":"fabien.jourdan@inra.fr","url":"https://sites.google.com/site/fabienjourdan/","orcidid":"https://orcid.org/0000-0001-9401-2894","gridid":null,"typeEntity":"Person","note":null}],"tool_licence":null,"documentation":"https://metexplore.toulouse.inra.fr/metexploreViz/doc/documentation.php","maturity":"Mature","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2025-04-28T07:17:11.601858Z","teams":[],"source_repository":null},{"id":93,"name":"MicroScope platform","description":"MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts.","homepage":"https://mage.genoscope.cns.fr/microscope/","biotoolsID":"MicroScope_platform","biotoolsCURIE":"biotools:MicroScope_platform","tool_type":["Bioinformatics portal","Web application","Workbench"],"collection":["elixir-fr-sdp-2019","fr"],"scientific_topics":["http://edamontology.org/topic_0085","http://edamontology.org/topic_3301","http://edamontology.org/topic_0797","http://edamontology.org/topic_0621","http://edamontology.org/topic_0219","http://edamontology.org/topic_2259"],"primary_publication":["10.1093/nar/gks1194","10.1093/nar/gkw1101","10.1093/database/bap021","10.1093/nar/gkj406","10.1093/bib/bbx113","10.1093/nar/gkz926"],"operating_system":[],"tool_credit":[{"type_role":["Provider","Developer","Support","Primary contact"],"name":"LABGeM - CEA/Genosocope - UMR8030","email":"labgem@genoscope.cns.fr","url":"https://labgem.genoscope.cns.fr","orcidid":null,"gridid":null,"typeEntity":"Institute","note":null}],"tool_licence":null,"documentation":"https://microscope.readthedocs.io/en/stable/","maturity":"Mature","cost":"Free of charge (with restrictions)","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2020-06-16T10:55:28Z","teams":["MicroScope"],"source_repository":null},{"id":45,"name":"BLC2db","description":"","homepage":null,"biotoolsID":"","biotoolsCURIE":"","tool_type":["Database portal"],"collection":[],"scientific_topics":[],"primary_publication":[],"operating_system":[],"tool_credit":[],"tool_licence":null,"documentation":null,"maturity":null,"cost":null,"unique_visits":null,"citations":null,"annual_visits":null,"last_update":null,"teams":[],"source_repository":null},{"id":208,"name":"MindTheGap","description":"Performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome.","homepage":"https://gatb.inria.fr/software/mind-the-gap/","biotoolsID":"mindthegap","biotoolsCURIE":"biotools:mindthegap","tool_type":["Command-line tool"],"collection":["GATB"],"scientific_topics":["http://edamontology.org/topic_0199"],"primary_publication":["10.1093/bioinformatics/btu545"],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":"Claire Lemaitre","email":"claire.lemaitre@inria.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Provider"],"name":"GenOuest","email":null,"url":null,"orcidid":null,"gridid":null,"typeEntity":"Institute","note":null}],"tool_licence":null,"documentation":"https://gatb.inria.fr/software/mind-the-gap/","maturity":"Emerging","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2024-11-24T20:58:48.627968Z","teams":["GenOuest"],"source_repository":null},{"id":43,"name":"MeryB","description":"","homepage":null,"biotoolsID":"","biotoolsCURIE":"","tool_type":["Database portal"],"collection":[],"scientific_topics":[],"primary_publication":[],"operating_system":[],"tool_credit":[],"tool_licence":null,"documentation":null,"maturity":null,"cost":null,"unique_visits":null,"citations":null,"annual_visits":null,"last_update":null,"teams":[],"source_repository":null},{"id":40,"name":"BactPepDB","description":"","homepage":null,"biotoolsID":"","biotoolsCURIE":"","tool_type":["Database portal"],"collection":[],"scientific_topics":[],"primary_publication":[],"operating_system":[],"tool_credit":[],"tool_licence":null,"documentation":null,"maturity":null,"cost":null,"unique_visits":null,"citations":null,"annual_visits":null,"last_update":null,"teams":[],"source_repository":null},{"id":3,"name":"Rice Genome Hub","description":"An open source database(s) for genetics, genomics and functional research in rice species","homepage":"https://rice-genome-hub.southgreen.fr/","biotoolsID":"Rice_Genome_Hub","biotoolsCURIE":"biotools:Rice_Genome_Hub","tool_type":["Database portal"],"collection":["Genome Hub","elixir-fr-sdp-2019"],"scientific_topics":["http://edamontology.org/topic_3321","http://edamontology.org/topic_3366","http://edamontology.org/topic_0780"],"primary_publication":[],"operating_system":["Linux"],"tool_credit":[{"type_role":["Primary contact"],"name":null,"email":"gaetan.droc@cirad.fr","url":null,"orcidid":"https://orcid.org/0000-0003-1849-1269","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":null,"email":"manuel.ruiz@cirad.fr","url":null,"orcidid":"https://orcid.org/0000-0001-8153-276X","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":null,"email":"christine.tranchant@ird.fr","url":null,"orcidid":"https://orcid.org/0000-0001-6934-1215","gridid":null,"typeEntity":"Person","note":null},{"type_role":[],"name":"CRP Rice","email":null,"url":"http://ricecrp.org/","orcidid":null,"gridid":null,"typeEntity":"Funding agency","note":null}],"tool_licence":null,"documentation":null,"maturity":"Mature","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2020-06-16T10:55:27Z","teams":["South Green"],"source_repository":null},{"id":72,"name":"Insyght","description":"Browser that helps navigate among abundant homologies, syntenies and genes annotations.","homepage":"http://genome.jouy.inra.fr/Insyght","biotoolsID":"insyght","biotoolsCURIE":"biotools:insyght","tool_type":["Database portal","Command-line tool"],"collection":[],"scientific_topics":["http://edamontology.org/topic_3301","http://edamontology.org/topic_0080","http://edamontology.org/topic_3053","http://edamontology.org/topic_3071"],"primary_publication":[],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":null,"email":"insyght@inra.fr","url":"http://genome.jouy.inra.fr/Insyght","orcidid":null,"gridid":null,"typeEntity":"Person","note":null}],"tool_licence":null,"documentation":"http://genome.jouy.inra.fr/Insyght_doc_online/","maturity":null,"cost":null,"unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2024-11-25T14:51:03.945288Z","teams":[],"source_repository":null},{"id":37,"name":"GreenPhyl","description":"","homepage":null,"biotoolsID":"","biotoolsCURIE":"","tool_type":["Database portal"],"collection":[],"scientific_topics":[],"primary_publication":[],"operating_system":[],"tool_credit":[],"tool_licence":null,"documentation":null,"maturity":null,"cost":null,"unique_visits":null,"citations":null,"annual_visits":null,"last_update":null,"teams":["South Green"],"source_repository":null},{"id":42,"name":"ISfinder","description":"It is a dedicated insertion sequence (IS) database which assigns names to individual ISs to maintain a coherent nomenclature, an IS repositaory including >3000 individual ISs from both bacteria and archaea and provides a basis for IS classification. Each IS is indexed in ISfinder with various associated pieces of information and classified into a group or family to provide some insight into its phylogeny.","homepage":"http://www-is.biotoul.fr","biotoolsID":"isfinder","biotoolsCURIE":"biotools:isfinder","tool_type":["Database portal"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0798","http://edamontology.org/topic_3068","http://edamontology.org/topic_0084","http://edamontology.org/topic_0621","http://edamontology.org/topic_3168"],"primary_publication":[],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":"Patricia Siguier","email":"Patricia.Siguier@ibcg.biotoul.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null}],"tool_licence":null,"documentation":"https://www-is.biotoul.fr/general_information.php","maturity":null,"cost":null,"unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2025-01-24T09:59:36.949842Z","teams":[],"source_repository":null},{"id":167,"name":"MPscan","description":"MPscan (multi-pattern scan) is a program for mapping short reads (<30bp) exactly on a set of reference sequences (eg, a genome) without indexing the reference. MPscan performs only exact mapping (no substitution, nor indels), is fast (optimal complexity), and easy to use.","homepage":"http://www.atgc-montpellier.fr/mpscan/","biotoolsID":"mpscan","biotoolsCURIE":"biotools:mpscan","tool_type":["Command-line tool"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0622","http://edamontology.org/topic_3308"],"primary_publication":["10.1007/978-3-642-04241-6_21"],"operating_system":["Linux","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":"Vincent Lefort","email":"Vincent.Lefort@lirmm.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null}],"tool_licence":null,"documentation":"http://www.atgc-montpellier.fr/download/papers/mpscan_manual_2008.pdf","maturity":null,"cost":null,"unique_visits":100,"citations":null,"annual_visits":0,"last_update":"2021-04-22T06:40:43Z","teams":["ATGC"],"source_repository":null},{"id":75,"name":"NAPP","description":"Nucleic Acid Phylogenetic Profile Database: classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes.","homepage":"http://napp.u-psud.fr/","biotoolsID":"napp","biotoolsCURIE":"biotools:napp","tool_type":["Database portal"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0077","http://edamontology.org/topic_0097","http://edamontology.org/topic_0659","http://edamontology.org/topic_3511","http://edamontology.org/topic_0082"],"primary_publication":[],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":"NAPP Support","email":"napp.biologie@u-psud.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null}],"tool_licence":null,"documentation":"http://rna.igmors.u-psud.fr/NAPP/Help.php","maturity":null,"cost":null,"unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2024-11-25T15:05:27.630660Z","teams":[],"source_repository":null},{"id":187,"name":"Nebula","description":"Web service powered by Galaxy which allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data.","homepage":"https://nebula.curie.fr/","biotoolsID":"nebula","biotoolsCURIE":"biotools:nebula","tool_type":["Web application"],"collection":["Nebula"],"scientific_topics":["http://edamontology.org/topic_3365","http://edamontology.org/topic_3125","http://edamontology.org/topic_3169"],"primary_publication":[],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":null,"email":"galaxy.contact@curie.fr","url":"http://bioinfo-out.curie.fr/","orcidid":null,"gridid":null,"typeEntity":"Person","note":null}],"tool_licence":null,"documentation":"http://nebula.curie.fr/static/nebula_tutorial.pdf","maturity":null,"cost":null,"unique_visits":7384,"citations":null,"annual_visits":2815653,"last_update":"2024-11-25T14:22:06.393280Z","teams":["Institut Curie - Bioinformatique"],"source_repository":null},{"id":244,"name":"NGphylogeny.fr","description":"Free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences.","homepage":"https://ngphylogeny.fr/","biotoolsID":"NGphylogeny.fr","biotoolsCURIE":"biotools:NGphylogeny.fr","tool_type":["Bioinformatics portal","Web application","Workflow"],"collection":[],"scientific_topics":["http://edamontology.org/topic_3293","http://edamontology.org/topic_0091"],"primary_publication":["10.1093/nar/gkz303"],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Developer"],"name":"Damien Correia","email":null,"url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Developer","Maintainer","Primary contact"],"name":"Frédéric Lemoine","email":"frederic.lemoine@pasteur.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Contributor"],"name":"Fabien Mareuil","email":"fmareuil@pasteur.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact","Contributor"],"name":"Vincent Lefort","email":"vincent.lefort@lirmm.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null}],"tool_licence":null,"documentation":"https://ngphylogeny.fr/documentation","maturity":"Emerging","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2024-11-24T20:59:31.390401Z","teams":[],"source_repository":null}]}