{"count":233,"next":"https://catalogue.france-bioinformatique.fr/api/tool/?format=json&limit=20&offset=180&ordering=-cost","previous":"https://catalogue.france-bioinformatique.fr/api/tool/?format=json&limit=20&offset=140&ordering=-cost","results":[{"id":158,"name":"Fpocket","description":"Web server which detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).","homepage":"https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::fpocket","biotoolsID":"fpocket","biotoolsCURIE":"biotools:fpocket","tool_type":["Web application"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0166"],"primary_publication":["10.1186/1471-2105-10-168"],"operating_system":[],"tool_credit":[{"type_role":["Primary contact"],"name":"Pierre Tufféry","email":"pierre.tuffery@univ-paris-diderot.fr","url":null,"orcidid":"https://orcid.org/0000-0003-1033-9895","gridid":null,"typeEntity":"Person","note":null}],"tool_licence":"Freeware","documentation":"https://bioserv.rpbs.univ-paris-diderot.fr/services/fpocket/","maturity":"Mature","cost":"Free of charge","unique_visits":960,"citations":null,"annual_visits":2470,"last_update":"2024-11-24T20:59:53.208420Z","teams":["RPBS"],"source_repository":null},{"id":146,"name":"fqtools","description":"A package that provides tools for efficient FASTQ files manipulation.","homepage":"https://bioweb.pasteur.fr/packages/pack@fqtools@1.1","biotoolsID":"fqtools","biotoolsCURIE":"biotools:fqtools","tool_type":["Suite"],"collection":["fqtools"],"scientific_topics":["http://edamontology.org/topic_0080"],"primary_publication":[],"operating_system":[],"tool_credit":[{"type_role":["Primary contact","Maintainer"],"name":"Nicolas Joly","email":"njoly@pasteur.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null}],"tool_licence":"Unlicense","documentation":null,"maturity":"Mature","cost":"Free of charge","unique_visits":0,"citations":null,"annual_visits":0,"last_update":"2020-06-16T10:55:24Z","teams":["Pasteur HUB"],"source_repository":"ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README"},{"id":160,"name":"Frog","description":"Frog2 (Free Online Drug Conformation 2) is a service aimed at generating 3D conformations for small molecules starting from their 1D, 2D or 3D descriptions (smiles, sdf or mol2 input formats). Frog2 improves upon Frog1 by embedding new energy minimization and ring generation capacities.","homepage":"https://mobyle2.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Frog2","biotoolsID":"frog2","biotoolsCURIE":"biotools:frog2","tool_type":["Web application"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0154","http://edamontology.org/topic_2275"],"primary_publication":["10.1093/nar/gkq325"],"operating_system":[],"tool_credit":[{"type_role":["Primary contact"],"name":"Frederic Guyon","email":"frederic.guyon@univ-paris-diderot.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":"Maria A. Miteva","email":"maria.mitev@inserm.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":"Pierre Tufféry","email":"pierre.tuffery@univ-paris-diderot.fr","url":null,"orcidid":"https://orcid.org/0000-0003-1033-9895","gridid":null,"typeEntity":"Person","note":null}],"tool_licence":"Freeware","documentation":"https://bioserv.rpbs.univ-paris-diderot.fr/services/Frog2/","maturity":"Mature","cost":"Free of charge","unique_visits":960,"citations":null,"annual_visits":6400,"last_update":"2026-03-19T13:27:15.551602Z","teams":["RPBS"],"source_repository":null},{"id":101,"name":"Genomicus-plants","description":"Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.","homepage":"https://www.genomicus.biologie.ens.fr/genomicus-plants","biotoolsID":"Genomicus-Plants","biotoolsCURIE":"biotools:Genomicus-Plants","tool_type":["Database portal","Web application"],"collection":["elixir-fr-sdp-2019","GENOMICUS"],"scientific_topics":["http://edamontology.org/topic_3943","http://edamontology.org/topic_3299","http://edamontology.org/topic_0797","http://edamontology.org/topic_0621","http://edamontology.org/topic_0622","http://edamontology.org/topic_0780","http://edamontology.org/topic_0623"],"primary_publication":["10.1093/nar/gks1156","10.1093/pcp/pcu177"],"operating_system":[],"tool_credit":[{"type_role":["Support"],"name":null,"email":"genomicus-web@ens.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":null,"note":null},{"type_role":["Primary contact"],"name":"Hugues Roest Crollius","email":"hrc@ens.fr","url":"http://www.ibens.ens.fr/?rubrique43","orcidid":"http://orcid.org/0000-0002-8209-173X","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":"Alexandra Louis","email":"alouis@biologie.ens.fr","url":"http://www.ibens.ens.fr/spip.php?article182","orcidid":"http://orcid.org/0000-0001-7032-5650","gridid":null,"typeEntity":"Person","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":["PB-IBENS"],"source_repository":null},{"id":161,"name":"PEP-SiteFinder","description":"PEP-SiteFinder is a web server tool for the blind identification of peptide binding sites on protein surfaces.","homepage":"https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-SiteFinder","biotoolsID":"pep-sitefinder","biotoolsCURIE":"biotools:pep-sitefinder","tool_type":["Web application"],"collection":[],"scientific_topics":["http://edamontology.org/topic_3534","http://edamontology.org/topic_2275"],"primary_publication":["10.1093/nar/gku404"],"operating_system":[],"tool_credit":[{"type_role":["Primary contact"],"name":"Pierre Tufféry","email":"pierre.tuffery@univ-paris-diderot.fr","url":null,"orcidid":"https://orcid.org/0000-0003-1033-9895","gridid":null,"typeEntity":"Person","note":null}],"tool_licence":"Freeware","documentation":"https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-SiteFinder","maturity":"Mature","cost":"Free of charge","unique_visits":347,"citations":null,"annual_visits":1482,"last_update":"2024-11-24T20:59:55.640056Z","teams":["RPBS"],"source_repository":null},{"id":237,"name":"D-GENIES","description":"D-GENIES – for Dot plot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualization.","homepage":"https://dgenies.toulouse.inrae.fr/","biotoolsID":"d-genies","biotoolsCURIE":"biotools:d-genies","tool_type":["Web application","Command-line tool"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0622","http://edamontology.org/topic_0092","http://edamontology.org/topic_0080"],"primary_publication":["10.7717/peerj.4958"],"operating_system":["Linux","Mac"],"tool_credit":[{"type_role":["Developer"],"name":"Vincent Dominguez","email":null,"url":null,"orcidid":null,"gridid":null,"typeEntity":null,"note":null},{"type_role":["Developer"],"name":"Floréal Cabanettes","email":null,"url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":"Christophe Klopp","email":"christophe.klopp@inrae.fr","url":null,"orcidid":"https://orcid.org/0000-0001-7126-5477","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact","Developer"],"name":"Philippe Bordron","email":null,"url":null,"orcidid":"https://orcid.org/0000-0003-1975-0920","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":"Christophe Klopp","email":"christophe.klopp@toulouse.inra.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Provider"],"name":"GenoToul bioinformatics facility","email":null,"url":"http://bioinfo.genotoul.fr/","orcidid":null,"gridid":null,"typeEntity":"Division","note":null}],"tool_licence":null,"documentation":"https://dgenies.readthedocs.io/en/latest/index.html","maturity":"Mature","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2025-12-18T10:02:18.098079Z","teams":[],"source_repository":"https://github.com/genotoul-bioinfo/dgenies"},{"id":205,"name":"DiscoSNP","description":"This software is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).","homepage":"https://colibread.inria.fr/software/discosnp/","biotoolsID":"discosnp","biotoolsCURIE":"biotools:discosnp","tool_type":["Command-line tool"],"collection":["GATB"],"scientific_topics":["http://edamontology.org/topic_2885","http://edamontology.org/topic_0199","http://edamontology.org/topic_3053","http://edamontology.org/topic_3168"],"primary_publication":["10.1093/nar/gku1187"],"operating_system":["Linux"],"tool_credit":[{"type_role":["Primary contact"],"name":"Pierre Peterlongo","email":"pierre.peterlongo@inria.fr","url":"https://colibread.inria.fr/","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://colibread.inria.fr/software/discosnp/","maturity":"Emerging","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2024-11-25T14:25:58.458039Z","teams":["GenOuest"],"source_repository":null},{"id":102,"name":"Sugarcane Genome Hub","description":"The Sugarcane Genome Hub is an integrated web-based database providing centralized access to the sugarcane reference genome sequences and genomic resources.","homepage":"https://sugarcane-genome.cirad.fr/","biotoolsID":"Sugarcane_Genome_Hub","biotoolsCURIE":"biotools:Sugarcane_Genome_Hub","tool_type":["Database portal"],"collection":["Genome Hub","elixir-fr-sdp-2019"],"scientific_topics":["http://edamontology.org/topic_0621","http://edamontology.org/topic_0622","http://edamontology.org/topic_0091","http://edamontology.org/topic_3810"],"primary_publication":[],"operating_system":["Linux"],"tool_credit":[{"type_role":["Primary contact"],"name":"Olivier Garsmeur","email":"olivier.garsmeur@cirad.fr","url":null,"orcidid":"https://orcid.org/0000-0001-8869-3689","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Developer"],"name":"Gaetan Droc","email":"droc@cirad.fr","url":null,"orcidid":"https://orcid.org/0000-0003-1849-1269","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Maintainer"],"name":"CIRAD","email":null,"url":null,"orcidid":null,"gridid":null,"typeEntity":"Institute","note":null}],"tool_licence":"GPL-2.0","documentation":null,"maturity":"Emerging","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":241,"name":"iPPI-DB","description":"IPPI-DB is a database of modulators of protein-protein interactions. It contains exclusively small molecules and therefore no peptides. The data are retrieved from the literature either peer reviewed scientific articles or world patents. A large variety of data is stored within IPPI-DB: structural, pharmacological, binding and activity profile, pharmacokinetic and cytotoxicity when available, as well as some data about the PPI targets themselves.","homepage":"https://ippidb.pasteur.fr","biotoolsID":"ippi-db","biotoolsCURIE":"biotools:ippi-db","tool_type":["Database portal"],"collection":[],"scientific_topics":["http://edamontology.org/topic_3343"],"primary_publication":[],"operating_system":[],"tool_credit":[{"type_role":[],"name":"Olivier Sperandio","email":null,"url":null,"orcidid":"https://orcid.org/0000-0001-6610-2729","gridid":null,"typeEntity":null,"note":null}],"tool_licence":null,"documentation":null,"maturity":"Mature","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2021-01-14T17:37:37Z","teams":[],"source_repository":"https://gitlab.pasteur.fr/ippidb/ippidb-web/"},{"id":197,"name":"JASS","description":"software package that handles the computation of the joint statistics over sets of selected GWAS results, and the interactive exploration of the results through a web interface.","homepage":"http://statistical-genetics.pages.pasteur.fr/jass/","biotoolsID":"jass","biotoolsCURIE":"biotools:jass","tool_type":["Web service","Web application","Command-line tool"],"collection":["Institut Pasteur"],"scientific_topics":["http://edamontology.org/topic_3517","http://edamontology.org/topic_3053","http://edamontology.org/topic_2269"],"primary_publication":["10.1093/nargab/lqaa003","10.1101/714832v1"],"operating_system":["Linux"],"tool_credit":[{"type_role":["Developer"],"name":"Hanna Julienne","email":"hanna.julienne@pasteur.fr","url":"https://research.pasteur.fr/fr/member/hanna-julienne/","orcidid":"https://orcid.org/0000-0001-8214-9412","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Developer"],"name":"Vincent Guillemot","email":"vincent.guillemot@pasteur.fr","url":"https://research.pasteur.fr/fr/member/vincent-guillemot/","orcidid":"https://orcid.org/0000-0002-7421-0655","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Developer"],"name":"Pierre Lechat","email":"pierre.lechat@pasteur.fr","url":"https://research.pasteur.fr/fr/member/pierre-lechat/","orcidid":"https://orcid.org/0000-0003-1050-5582","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Developer"],"name":"Carla Lasry","email":null,"url":"https://research.pasteur.fr/fr/member/carla-lasry/","orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Contributor"],"name":"Chunzi Yao","email":"chunzi.yao@pasteur.fr","url":"https://research.pasteur.fr/fr/member/chunzi-yao/","orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Contributor"],"name":"Vincent Laville","email":"vincent.laville@pasteur.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Contributor"],"name":"Bjarni Vilhjalmsson","email":null,"url":"https://pure.au.dk/portal/en/persons/bjarni-johann-vilhjlmsson(35c047ab-0899-4434-91bb-121e4878ec76).html","orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Developer"],"name":"Hervé Ménager","email":"herve.menager@pasteur.fr","url":"https://research.pasteur.fr/fr/search/herve%20menager","orcidid":"https://orcid.org/0000-0002-7552-1009","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":"Hugues Aschard","email":"hugues.aschard@pasteur.fr","url":"https://research.pasteur.fr/fr/member/hugues-aschard/","orcidid":"http://orcid.org/0000-0002-7554-6783","gridid":null,"typeEntity":"Person","note":null}],"tool_licence":null,"documentation":"http://statistical-genetics.pages.pasteur.fr/jass/","maturity":"Mature","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2024-11-24T14:46:08.475046Z","teams":[],"source_repository":"https://gitlab.pasteur.fr/statistical-genetics/jass"},{"id":53,"name":"LepidoDB","description":"Genomics of two major lepidopteran pests.","homepage":"http://www.inra.fr/lepidodb","biotoolsID":"lepidodb","biotoolsCURIE":"biotools:lepidodb","tool_type":["Database portal"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0622"],"primary_publication":[],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":"BIPAA platform","email":"bipaa@rennes.inra.fr","url":"http://www.inra.fr/bipaa","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":"http://bipaa.genouest.org/is/lepidodb/","maturity":null,"cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2018-12-11T18:57:25Z","teams":["GenOuest"],"source_repository":null},{"id":106,"name":"Lifemap","description":"Explorer of the entire tree of life. Lifemap allows visualizing the entire NCBI taxonomy on a single page with a deep zoom interface and performing easy search, mrca detection, subtree download, etc.","homepage":"http://lifemap.univ-lyon1.fr","biotoolsID":"Lifemap","biotoolsCURIE":"biotools:Lifemap","tool_type":["Web service","Web application"],"collection":["elixir-fr-sdp-2019"],"scientific_topics":["http://edamontology.org/topic_3050","http://edamontology.org/topic_3299"],"primary_publication":[],"operating_system":["Linux","Windows","Mac"],"tool_credit":[],"tool_licence":"CC-BY-NC-4.0","documentation":"http://lifemap.univ-lyon1.fr/help/","maturity":"Legacy","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2020-06-16T10:55:27Z","teams":[],"source_repository":"https://github.com/damiendevienne/Lifemap"},{"id":100,"name":"Genomicus-fungi","description":"Genomicus-fungi is a genome browser that enables users to navigate in fungi genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.","homepage":"http://www.genomicus.biologie.ens.fr/genomicus-fungi/","biotoolsID":"Genomicus-fungi","biotoolsCURIE":"biotools:Genomicus-fungi","tool_type":["Database portal","Web application"],"collection":["elixir-fr-sdp-2019","GENOMICUS"],"scientific_topics":["http://edamontology.org/topic_3943","http://edamontology.org/topic_3299","http://edamontology.org/topic_0797","http://edamontology.org/topic_0621","http://edamontology.org/topic_0622","http://edamontology.org/topic_0194","http://edamontology.org/topic_0623"],"primary_publication":["10.1093/nar/gks1156"],"operating_system":[],"tool_credit":[{"type_role":["Support"],"name":null,"email":"genomicus-web@ens.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":null,"note":null},{"type_role":["Primary contact"],"name":"Hugues Roest Crollius","email":"hrc@ens.fr","url":"http://www.ibens.ens.fr/?rubrique43","orcidid":"http://orcid.org/0000-0002-8209-173X","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":"Alexandra Louis","email":"alouis@biologie.ens.fr","url":"http://www.ibens.ens.fr/spip.php?article182","orcidid":"http://orcid.org/0000-0001-7032-5650","gridid":null,"typeEntity":"Person","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":["PB-IBENS"],"source_repository":null},{"id":98,"name":"Genomicus-metazoa","description":"Genomicus-metazoa is a genome browser that enables users to navigate in metazoa genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.","homepage":"http://www.genomicus.biologie.ens.fr/genomicus-metazoa/","biotoolsID":"Genomicus-metazoa","biotoolsCURIE":"biotools:Genomicus-metazoa","tool_type":["Database portal","Web application"],"collection":["elixir-fr-sdp-2019","GENOMICUS"],"scientific_topics":["http://edamontology.org/topic_3943","http://edamontology.org/topic_3299","http://edamontology.org/topic_0797","http://edamontology.org/topic_0621","http://edamontology.org/topic_0622","http://edamontology.org/topic_0194","http://edamontology.org/topic_0623"],"primary_publication":["10.1093/nar/gks1156"],"operating_system":[],"tool_credit":[{"type_role":["Support"],"name":null,"email":"genomicus-web@ens.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":null,"note":null},{"type_role":["Primary contact"],"name":"Hugues Roest Crollius","email":"hrc@ens.fr","url":"http://www.ibens.ens.fr/?rubrique43","orcidid":"http://orcid.org/0000-0002-8209-173X","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":"Alexandra Louis","email":"alouis@biologie.ens.fr","url":"http://www.ibens.ens.fr/spip.php?article182","orcidid":"http://orcid.org/0000-0001-7032-5650","gridid":null,"typeEntity":"Person","note":null}],"tool_licence":null,"documentation":null,"maturity":"Mature","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2024-11-24T14:56:24.333237Z","teams":["PB-IBENS"],"source_repository":null},{"id":99,"name":"Genomicus-protists","description":"Genomicus-protists is a genome browser that enables users to navigate in protists genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.","homepage":"http://www.genomicus.biologie.ens.fr/genomicus-protists/","biotoolsID":"Genomicus-protists","biotoolsCURIE":"biotools:Genomicus-protists","tool_type":["Database portal","Web application"],"collection":["elixir-fr-sdp-2019","GENOMICUS"],"scientific_topics":["http://edamontology.org/topic_3943","http://edamontology.org/topic_3299","http://edamontology.org/topic_0797","http://edamontology.org/topic_0621","http://edamontology.org/topic_0622","http://edamontology.org/topic_0194","http://edamontology.org/topic_0623"],"primary_publication":["10.1093/nar/gks1156"],"operating_system":[],"tool_credit":[{"type_role":["Support"],"name":null,"email":"genomicus-web@ens.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":null,"note":null},{"type_role":["Primary contact"],"name":"Hugues Roest Crollius","email":"hrc@ens.fr","url":"http://www.ibens.ens.fr/?rubrique43","orcidid":"http://orcid.org/0000-0002-8209-173X","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":"Alexandra Louis","email":"alouis@biologie.ens.fr","url":"http://www.ibens.ens.fr/spip.php?article182","orcidid":"http://orcid.org/0000-0001-7032-5650","gridid":null,"typeEntity":"Person","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":["PB-IBENS"],"source_repository":null},{"id":96,"name":"GINsim","description":"Computer tool for the modeling and simulation of genetic regulatory networks.","homepage":"http://ginsim.org/","biotoolsID":"ginsim","biotoolsCURIE":"biotools:ginsim","tool_type":["Desktop application"],"collection":["elixir-fr-sdp-2019","FR","EBI Training Tools","PerMedCoE"],"scientific_topics":["http://edamontology.org/topic_0204","http://edamontology.org/topic_2259","http://edamontology.org/topic_0602"],"primary_publication":[],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Support","Developer"],"name":null,"email":null,"url":"http://ginsim.org/contact","orcidid":null,"gridid":null,"typeEntity":"Project","note":null}],"tool_licence":"GPL-3.0","documentation":"http://ginsim.org/documentation","maturity":"Mature","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2024-11-24T20:09:51.625867Z","teams":[],"source_repository":"http://ginsim.org/models_repository"},{"id":175,"name":"Logol","description":"Pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic).","homepage":"http://logol.genouest.org","biotoolsID":"logol","biotoolsCURIE":"biotools:logol","tool_type":["Web application","Command-line tool"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0160"],"primary_publication":["10.1007/978-3-319-09192-1_4"],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":"GenOuest","email":"support@genouest.org","url":"http://www.genouest.org","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":"CECILL-2.0","documentation":"http://training.genouest.org/claroline/claroline/learnPath/learningPathList.php?cidReset=true&cidReq=LOGOL","maturity":"Emerging","cost":"Free of charge","unique_visits":0,"citations":null,"annual_visits":0,"last_update":"2018-12-10T12:58:34Z","teams":["GenOuest"],"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":122,"name":"microSysMics","description":"This workflow provides an automated microbiome data analysis, starting with sequenced taxonomic markers (such as 16SrRNA) and using the standard QIIME2 toolbox to produce an abundance table and preliminary diversity, phylogeny and taxonomy analysis.","homepage":"https://gitlab.univ-nantes.fr/bird_pipeline_registry/microSysMics","biotoolsID":"microSysMics","biotoolsCURIE":"biotools:microSysMics","tool_type":["Workflow"],"collection":[],"scientific_topics":["http://edamontology.org/topic_3697"],"primary_publication":[],"operating_system":["Linux","Mac"],"tool_credit":[{"type_role":["Provider"],"name":"BiRD bioinformatics facility","email":"pf-bird@univ-nantes.fr","url":"http://pf-bird.univ-nantes.fr","orcidid":null,"gridid":null,"typeEntity":"Division","note":null},{"type_role":["Primary contact"],"name":"Samuel Chaffron","email":"samuel.chaffron@univ-nantes.fr","url":null,"orcidid":"https://orcid.org/0000-0001-5903-617X","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Developer"],"name":"Erwan Delage","email":"erwan.delage@univ-nantes.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Provider"],"name":"BiRD","email":"pf-bird@univ-nantes.fr","url":"http://pf-bird.univ-nantes.fr","orcidid":null,"gridid":null,"typeEntity":"Division","note":null},{"type_role":["Maintainer","Contributor"],"name":"Damien Vintache","email":"Damien.Vintache@univ-nantes.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Provider"],"name":"TENS","email":null,"url":"https://www.inserm-tens.com/","orcidid":null,"gridid":null,"typeEntity":"Institute","note":null},{"type_role":[],"name":"Michel Neunlist","email":"michel.neunlist@univ-nantes.fr","url":null,"orcidid":"https://orcid.org/0000-0003-1892-5071","gridid":null,"typeEntity":null,"note":null},{"type_role":["Provider"],"name":"LS2N","email":null,"url":"http://www.ls2n.fr","orcidid":null,"gridid":null,"typeEntity":"Institute","note":null},{"type_role":["Primary contact","Contributor"],"name":"Audrey Bihouée","email":"audrey.bihouee@univ-nantes.fr","url":null,"orcidid":"https://orcid.org/0000-0002-8689-2083","gridid":null,"typeEntity":"Person","note":null}],"tool_licence":"Other","documentation":null,"maturity":"Emerging","cost":"Free of charge","unique_visits":0,"citations":null,"annual_visits":0,"last_update":"2023-09-19T15:06:56.878425Z","teams":["BiRD"],"source_repository":null}]}