{"count":233,"next":"https://catalogue.france-bioinformatique.fr/api/tool/?format=json&limit=20&offset=200&ordering=-biotoolsID","previous":"https://catalogue.france-bioinformatique.fr/api/tool/?format=json&limit=20&offset=160&ordering=-biotoolsID","results":[{"id":180,"name":"Assemble2","description":"Design your RNA 2D structure interactively and to create and assemble the corresponding RNA 3D modules directly in UCSF Chimera.","homepage":"http://bioinformatics.org/assemble/","biotoolsID":"assemble2","biotoolsCURIE":"biotools:assemble2","tool_type":["Web API"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0097"],"primary_publication":["10.1093/bioinformatics/btq321"],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":null,"email":null,"url":"http://www.bioinformatics.org/assemble/contacts.html","orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Documentor"],"name":"BioCatalogue","email":null,"url":"https://www.biocatalogue.org","orcidid":null,"gridid":null,"typeEntity":"Project","note":null}],"tool_licence":null,"documentation":"http://bioinformatics.org/assemble/","maturity":null,"cost":null,"unique_visits":0,"citations":null,"annual_visits":0,"last_update":"2024-11-25T15:45:38.090886Z","teams":["BiGEst"],"source_repository":null},{"id":135,"name":"Askomics","description":"AskOmics is a visual SPARQL query interface supporting both intuitive data integration and querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL","homepage":"https://github.com/askomics","biotoolsID":"askomics","biotoolsCURIE":"biotools:askomics","tool_type":["Desktop application"],"collection":[],"scientific_topics":["http://edamontology.org/topic_3366"],"primary_publication":[],"operating_system":["Linux","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":"Olivier Dameron","email":"olivier.dameron@irisa.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Developer"],"name":"Olivier Filangi","email":"olivier.filangi@inra.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":"Anthony Bretaudeau","email":"anthony.bretaudeau@irisa.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null}],"tool_licence":"AGPL-3.0","documentation":"https://github.com/askomics/askomics","maturity":"Mature","cost":"Free of charge","unique_visits":0,"citations":null,"annual_visits":0,"last_update":"2025-06-09T11:52:30.706337Z","teams":["GenOuest"],"source_repository":null},{"id":85,"name":"ARIA","description":"A software for automated NOE assignment and NMR structure calculation.","homepage":"http://aria.pasteur.fr/","biotoolsID":"aria","biotoolsCURIE":"biotools:aria","tool_type":["Command-line tool"],"collection":["elixir-fr-sdp-2019","Institut Pasteur","FR"],"scientific_topics":["http://edamontology.org/topic_1317","http://edamontology.org/topic_0176","http://edamontology.org/topic_3306","http://edamontology.org/topic_3332","http://edamontology.org/topic_2275","http://edamontology.org/topic_0081","http://edamontology.org/topic_0078","http://edamontology.org/topic_0593"],"primary_publication":["10.1093/bioinformatics/btl589"],"operating_system":["Linux","Mac"],"tool_credit":[{"type_role":["Provider"],"name":"Institut Pasteur","email":null,"url":"http://aria.pasteur.fr/contact-info","orcidid":null,"gridid":null,"typeEntity":"Institute","note":null},{"type_role":["Primary contact"],"name":"Michael Nilges","email":"michael.nilges@pasteur.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Developer"],"name":"Benjamin Bardiaux","email":"benjamin.bardiaux@pasteur.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null}],"tool_licence":"MIT","documentation":"http://aria.pasteur.fr/documentation","maturity":"Mature","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2024-11-24T20:37:34.670261Z","teams":[],"source_repository":null},{"id":54,"name":"AphidBase","description":"An aphid genome database.","homepage":"http://aphidbase.com/","biotoolsID":"aphidbase","biotoolsCURIE":"biotools:aphidbase","tool_type":["Database portal"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0622"],"primary_publication":["10.1111/j.1365-2583.2009.00930.x"],"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/aphidbase/","maturity":null,"cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2018-12-10T12:58:49Z","teams":["GenOuest"],"source_repository":null},{"id":57,"name":"AnnotQTL","description":"Tool designed to gather the functional annotation of genes from several institutional databases for a specific chromosomal region.","homepage":"http://annotqtl.genouest.org/","biotoolsID":"annotqtl","biotoolsCURIE":"biotools:annotqtl","tool_type":["Database portal","Web application"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0085"],"primary_publication":["10.1093/nar/gkr361"],"operating_system":["Linux","Windows","Mac"],"tool_credit":[{"type_role":["Primary contact"],"name":"GenOuest","email":"support@genouest.org","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":"http://annotqtl.genouest.org/tutorial","maturity":"Mature","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2024-11-25T16:06:26.428724Z","teams":[],"source_repository":null},{"id":104,"name":"ANISEED","description":"ANISEED is the main model organism database for the worldwide community of scientists working on tunicates (sister-group of vertebrates). It integrates for each species: \ni) a main knowledge base with extended functional, gene expression, phenotyping, anatomical and phylogenetic information; \nii) A multispecies genomic browser; \niii) a Genomicus gene synteny browser.","homepage":"https://www.aniseed.fr","biotoolsID":"ANISEED","biotoolsCURIE":"biotools:ANISEED","tool_type":["Database portal","Web API","Web application","Ontology"],"collection":["elixir-fr-sdp-2019"],"scientific_topics":["http://edamontology.org/topic_3065","http://edamontology.org/topic_3383","http://edamontology.org/topic_3679","http://edamontology.org/topic_0085","http://edamontology.org/topic_0084","http://edamontology.org/topic_0219","http://edamontology.org/topic_2229","http://edamontology.org/topic_0194","http://edamontology.org/topic_3064","http://edamontology.org/topic_0089","http://edamontology.org/topic_3308"],"primary_publication":["10.1016/j.cub.2005.12.044","10.1093/nar/gkz955","10.1093/nar/gkx1108","10.1101/gr.108175.110","10.1093/nar/gkv966"],"operating_system":["Linux"],"tool_credit":[{"type_role":["Support"],"name":null,"email":"contact@aniseed.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":null,"note":null},{"type_role":["Support"],"name":null,"email":"contact@aniseed.cnrs.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":null,"note":null},{"type_role":["Primary contact"],"name":"Patrick Lemaire","email":"patrick.lemaire@crbm.cnrs.fr","url":"http://www.crbm.cnrs.fr/en/team/lemaire/","orcidid":"https://orcid.org/0000-0003-4925-2009","gridid":null,"typeEntity":"Person","note":null},{"type_role":["Primary contact"],"name":"Christelle Dantec","email":"christelle.dantec@crbm.cnrs.fr","url":"http://www.crbm.cnrs.fr/en/team/lemaire/","orcidid":"https://orcid.org/0000-0001-7247-6460","gridid":null,"typeEntity":"Person","note":null}],"tool_licence":"GPL-3.0","documentation":"https://www.aniseed.fr/api","maturity":"Mature","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2023-09-25T14:25:18.910230Z","teams":[],"source_repository":null},{"id":5,"name":"AgroLD","description":"The RDF Knowledge-based Database for plant molecular networks.","homepage":"http://agrold.southgreen.fr/agrold/","biotoolsID":"AgroLD","biotoolsCURIE":"biotools:AgroLD","tool_type":["Database portal"],"collection":[],"scientific_topics":["http://edamontology.org/topic_0602","http://edamontology.org/topic_3810"],"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":"2019-11-05T14:52:28Z","teams":["South Green"],"source_repository":null},{"id":239,"name":"ACDtool","description":"Web-server for the generic analysis of large data sets of counts.","homepage":"https://www.igs.cnrs-mrs.fr/acdtool/","biotoolsID":"acdtool","biotoolsCURIE":"biotools:acdtool","tool_type":["Web application"],"collection":[],"scientific_topics":["http://edamontology.org/topic_2269"],"primary_publication":[],"operating_system":[],"tool_credit":[],"tool_licence":null,"documentation":null,"maturity":null,"cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2025-12-10T09:25:24.490675Z","teams":["PACA-Bioinfo"],"source_repository":null},{"id":283,"name":"3SRP","description":"A Snakemake-based pipeline for 3' sequencing RNA profiling data analysis.  This 3’ Digital gene expression sequencing technique allows a precise and low-cost transcriptome profiling.\n\nThe main steps of the pipeline are:\n- Samples demultiplexing transform the raw paired-end fastq files into a single-end fastq file for each sample.\n- Alignment on refseq reference transcriptome is performed using bwa.\n- Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix.\nIf secondary analysis has been asked (providing a comparisons file), the expression matrix is normalized and differentially expressed genes (DEG) are searched using deseq2.\n- If DEG are found, annotation is performed using the database GO and KEGG.\n- A report is provided listing the main quality controls performed and the results found.\n\nCite : https://dx.doi.org/10.21203/rs.3.pex-1336/v1","homepage":"https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline","biotoolsID":"3SRP","biotoolsCURIE":"biotools:3SRP","tool_type":["Workflow"],"collection":[],"scientific_topics":["http://edamontology.org/topic_3308"],"primary_publication":["10.1038/s41598-017-14892-x"],"operating_system":["Linux"],"tool_credit":[{"type_role":["Developer"],"name":"Dimitri MEISTERMANN","email":"dimitri.meistermann@univ-nantes.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Developer"],"name":"Philippe Bordron","email":"philippe.bordron@univ-nantes.fr","url":null,"orcidid":null,"gridid":null,"typeEntity":"Person","note":null},{"type_role":["Provider","Support"],"name":"BiRD bioinformatics facility","email":"pf-bird@univ-nantes.fr","url":"https://pf-bird.univ-nantes.fr","orcidid":null,"gridid":null,"typeEntity":"Division","note":null},{"type_role":["Primary contact","Developer","Support"],"name":"Eric Charpentier","email":"eric.charpentier@univ-nantes.fr","url":"https://pf-bird.univ-nantes.fr/about-us/members/","orcidid":"https://orcid.org/0000-0002-8571-7603","gridid":null,"typeEntity":"Person","note":null},{"type_role":[],"name":"Broad Institute","email":null,"url":null,"orcidid":null,"gridid":null,"typeEntity":"Institute","note":"Some scripts of the pipeline regarding sample demultiplexing and UMI counting have been adapated and modified from this paper:\nXiong, Y., Soumillon, M., Wu, J. et al. A Comparison of mRNA Sequencing with Random Primed and 3′-Directed Libraries. Sci Rep 7, 14626 (2017)."},{"type_role":["Developer"],"name":"Solenne Dumont","email":"solenne.dumont@univ-nantes.fr","url":"https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/","orcidid":"https://orcid.org/0000-0003-3237-7382","gridid":null,"typeEntity":"Person","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":null,"documentation":"https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/wikis/home","maturity":"Emerging","cost":"Free of charge","unique_visits":null,"citations":null,"annual_visits":null,"last_update":"2024-11-24T14:40:06.421826Z","teams":["BiRD"],"source_repository":null},{"id":6,"name":"SNiPlay","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":79,"name":"CRISPRdb ","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":78,"name":"tandemRepeat","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":77,"name":"Podospora ","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":76,"name":"Bacterial Genotyping ","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":74,"name":"ORENZA","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":70,"name":"GnplS","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":["URGI"],"source_repository":null},{"id":67,"name":"PlantRNA","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":["BiGEst"],"source_repository":null},{"id":66,"name":"CYPedia ","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":64,"name":"EvoluCode ","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":63,"name":"BAliBASE","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}]}