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{ "count": 369, "next": "?page=2", "previous": null, "list": [ { "name": "GRNsight", "description": "Web application and service for visualizing small- to medium-scale models of gene regulatory networks. It automatically lays out either an unweighted or weighted network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges and has general applicability.", "homepage": "http://dondi.github.io/GRNsight/", "biotoolsID": "grnsight", "biotoolsCURIE": "biotools:grnsight", "version": [ "6.0.7" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_1781", "term": "Gene regulatory network analysis" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" } ], "input": [], "output": [], "note": "GRNsight automatically lays out a network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. When a user uploads a spreadsheet with an unweighted adjacency matrix, GRNsight automatically lays out the graph using black lines and pointed arrowheads. When a user uploads a spreadsheet with a weighted adjacency matrix, GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (positive for activation or negative for repression) and magnitude of the weight parameter. Nodes are rectangular and support gene labels of up to 12 characters. The edges are arcs, which become straight lines when the nodes are close together. Self-regulatory edges are indicated by a loop on the lower-right side of a node. Visualizations can be modified by sliders that adjust D3.js's force graph layout parameters and through manual node dragging.", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0204", "term": "Gene regulation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/dondi/GRNsight", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/dondi/GRNsight/archive/master.zip", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://dondi.github.io/GRNsight/documentation.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.7717/peerj-cs.85", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "GRNsight: A web application and service for visualizing models of small-to medium-scale gene regulatory networks", "abstract": "GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. The original motivation came from our efforts to perform parameter estimation and forward simulation of the dynamics of a differential equations model of a small GRN with 21 nodes and 31 edges. We wanted a quick and easy way to visualize the weight parameters from the model which represent the direction and magnitude of the influence of a transcription factor on its target gene, so we created GRNsight. GRNsight automatically lays out either an unweighted or weighted network graph based on an Excel spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows, a Simple Interaction Format (SIF) text file, or a GraphML XML file. When a user uploads an input file specifying an unweighted network, GRNsight automatically lays out the graph using black lines and pointed arrowheads. For a weighted network, GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (positive for activation or negative for repression) and magnitude of the weight parameter. GRNsight is written in JavaScript, with diagrams facilitated by D3.js, a data visualization library. Node.js and the Express framework handle server-side functions. GRNsight's diagrams are based on D3.js's force graph layout algorithm, which was then extensively customized to support the specific needs of GRNs. Nodes are rectangular and support gene labels of up to 12 characters. The edges are arcs, which become straight lines when the nodes are close together. Self-regulatory edges are indicated by a loop.When a user mouses over an edge, the numerical value of the weight parameter is displayed. Visualizations can be modified by sliders that adjust the force graph layout parameters and through manual node dragging. GRNsight is best-suited for visualizing networks of fewer than 35 nodes and 70 edges, although it accepts networks of up to 75 nodes or 150 edges. GRNsight has general applicability for displaying any small, unweighted or weighted network with directed edges for systems biology or other application domains. GRNsight serves as an example of following and teaching best practices for scientific computing and complying with FAIR principles, using an open and test-driven development model with rigorous documentation of requirements and issues on GitHub. An exhaustive unit testing framework using Mocha and the Chai assertion library consists of around 160 automated unit tests that examine nearly 530 test files to ensure that the program is running as expected. The GRNsight application (http://dondi.github.io/ GRNsight/) and code (https://github.com/dondi/GRNsight) are available under the open source BSD license.", "date": "2016-01-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Dahlquist K.D." }, { "name": "Dionisio J.D.N." }, { "name": "Fitzpatrick B.G." }, { "name": "Anguiano N.A." }, { "name": "Varshneya A." }, { "name": "Southwick B.J." }, { "name": "Samdarshi M." } ], "journal": "PeerJ Computer Science" } }, { "doi": "10.5281/zenodo.7411630", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Ona O. Igbinedion", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Ahmad R. Mersaghian", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Ian M. Green", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Lauren L. Amparo", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Alexia M. Filler", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Kevin B. Patterson", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "John L. Lopez", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Justin Kyle T. Torres", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Eileen Choe", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jen Shin", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Mihir Samdarshi", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Anindita Varshneya", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Nicole A. Anguiano", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Britain J. Southwick", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "John David N. Dionisio", "email": "dondi@lmu.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Kam D. Dahlquist", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Ben G. Fitzpatrick", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Loyola Marymount University", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "NSF award 0921038; LMU Rains Research Assistant Program; LMU Summer Undergraduate Research Program", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "lmu.edu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Kam D. Dahlquist", "email": "kdahlquist@lmu.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "Kam D. Dahlquist", "email": "kdahlquist@lmu.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "John David N. Dionisio", "email": "dondi@lmu.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "dondi@lmu.edu", "additionDate": "2016-08-13T19:15:03Z", "lastUpdate": "2023-08-29T16:51:15.145002Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CarveMe", "description": "CarveMe is a python-based automated tool used for top-down genome-scale metabolic model reconstruction. It can predict an organism's uptake and secretion capabilities without requiring gap-filling, although gap-filling is also supported. Additionally, CarveMe allows the generation of microbial community models by merging single species models. The tool offers advanced features such as manual adjustment of blasting options, an orthology-based search using eggNOG-mapper (kegg-bigg branch), the ability to provide a custom media library for gap-filling, and the generation of models compatible with various SBML formats. Furthermore, CarveMe supports ensemble modeling, which helps explore how different alternative solutions can lead to diverse network structures and predict various phenotypes. During the model carving process, users can select from provided templates or create their own customized universe model to suit their specific needs.", "homepage": "https://github.com/cdanielmachado/carveme", "biotoolsID": "carveme", "biotoolsCURIE": "biotools:carveme", "version": [ "1.0.0", "1.1.0", "1.2.0", "1.3.0", "1.4.0 - 1.4.1", "1.5.0 - 1.5.2" ], "otherID": [], "relation": [ { "biotoolsID": "bigg_models", "type": "uses" }, { "biotoolsID": "diamond", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3660", "term": "Metabolic network modelling" }, { "uri": "http://edamontology.org/operation_3663", "term": "Homology-based gene prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2787", "term": "NCBI genome accession" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2984", "term": "Pathway or network report" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_2585", "term": "SBML" } ] } ], "note": "Homology-based search is default using diamond. Orthology-based search can be performed with eggNOG-mapper (kegg-bigg branch).", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3217", "term": "Scaffold gap completion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2787", "term": "NCBI genome accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2984", "term": "Pathway or network report" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] }, { "data": { "uri": "http://edamontology.org/data_3724", "term": "Cultivation parameter" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2984", "term": "Pathway or network report" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_2585", "term": "SBML" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2984", "term": "Pathway or network report" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2984", "term": "Pathway or network report" }, "format": [ { "uri": "http://edamontology.org/format_2585", "term": "SBML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "ELIXIR-NO", "ELIXIR-Norway", "NTNU tools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Norway" ], "elixirCommunity": [ "Marine Metagenomics", "Metabolomics", "Microbial Biotechnology", "Proteomics" ], "link": [ { "url": "https://github.com/cdanielmachado/carveme", "type": [ "Repository", "Issue tracker" ], "note": null }, { "url": "https://elixir.no/helpdesk", "type": [ "Helpdesk" ], "note": "Helpdesk and support for ELIXIR Norway services" } ], "download": [ { "url": "https://github.com/cdanielmachado/carveme/releases/tag/1.5.2", "type": "Source code", "note": "Latest release as of 3 August 2023", "version": "1.5.2" }, { "url": "https://github.com/cdanielmachado/carveme/releases", "type": "Source code", "note": null, "version": "All" } ], "documentation": [ { "url": "https://carveme.readthedocs.io/en/latest/index.html", "type": [ "General", "Installation instructions", "Quick start guide", "Command-line options", "User manual" ], "note": null }, { "url": "https://github.com/cdanielmachado/carveme#readme", "type": [ "Citation instructions" ], "note": null }, { "url": "https://github.com/cdanielmachado/carveme/releases", "type": [ "Release notes" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gky537", "pmid": "30192979", "pmcid": "PMC6125623", "type": [ "Primary" ], "version": "1.0.0", "note": null, "metadata": { "title": "Fast automated reconstruction of genome-scale metabolic models for microbial species and communities", "abstract": "Genome-scale metabolic models are instrumental in uncovering operating principles of cellular metabolism, for model-guided re-engineering, and unraveling cross-feeding in microbial communities. Yet, the application of genome-scale models, especially to microbial communities, is lagging behind the availability of sequenced genomes. This is largely due to the time-consuming steps of manual curation required to obtain good quality models. Here, we present an automated tool, CarveMe, for reconstruction of species and community level metabolic models. We introduce the concept of a universal model, which is manually curated and simulation ready. Starting with this universal model and annotated genome sequences, CarveMe uses a topdown approach to build single-species and community models in a fast and scalable manner. We show that CarveMe models perform closely to manually curated models in reproducing experimental phenotypes (substrate utilization and gene essentiality). Additionally, we build a collection of 74 models for human gut bacteria and test their ability to reproduce growth on a set of experimentally defined media. Finally, we create a database of 5587 bacterial models and demonstrate its potential for fast generation of microbial community models. Overall, CarveMe provides an open-source and user-friendly tool towards broadening the use of metabolic modeling in studying microbial species and communities.", "date": "2018-09-06T00:00:00Z", "citationCount": 239, "authors": [ { "name": "Machado D." }, { "name": "Andrejev S." }, { "name": "Tramontano M." }, { "name": "Patil K.R." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1038/s41559-022-01939-0", "pmid": "36471121", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Reply to: Erroneous predictions of auxotrophies by CarveMe", "abstract": "", "date": "2023-02-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Machado D." }, { "name": "Patil K.R." } ], "journal": "Nature Ecology and Evolution" } } ], "credit": [ { "name": "Daniel Machado", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-2063-5383", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk", "email": "support@elixir.no", "url": "https://elixir.no/helpdesk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Support" ], "note": null }, { "name": "Sergej Andrejev", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-7875-0261", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Melanie Tramontano", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-6407-527X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Kiran Raosaheb Patil", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6166-8640", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "NTNU", "email": null, "url": "http://www.ntnu.edu", "orcidid": null, "gridid": "grid.5947.f", "rorid": "05xg72x27", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": "Developed at NTNU 2020-present" }, { "name": "European Molecular Biology Laboratory (EMBL)", "email": null, "url": "http://embl.org/", "orcidid": null, "gridid": "grid.4709.a", "rorid": "03mstc592", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": "Developed at EMBL 2017-2019" }, { "name": "European Union's Horizon 2020", "email": null, "url": "https://doi.org/10.3030/686070", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "Erin Calhoun", "email": "erin.calhoun@uit.no", "url": null, "orcidid": "https://orcid.org/0009-0003-3752-7156", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": "Curation of bio.tools profile - contact me with updates/corrections." } ], "community": null, "owner": "dmachado", "additionDate": "2021-02-18T12:08:51Z", "lastUpdate": "2023-08-15T10:51:32.592010Z", "editPermission": { "type": "group", "authors": [ "eca008" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "omnipy", "description": "Omnipy is a Python library for type-driven data wrangling and scalable data flow orchestration. 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Envisioned as a community effort, omnipy aims to offer various import formats and data models (both hierarchical and tabular representations), as well as ontology mapping and semiautomatic data cleaning.", "homepage": "https://fairtracks.net/fair/#fair-07-transformation", "biotoolsID": "omnipy", "biotoolsCURIE": "biotools:omnipy", "version": [ "0.10.4" ], "otherID": [], "relation": [ { "biotoolsID": "pandas", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3763", "term": "Service invocation" }, { "uri": "http://edamontology.org/operation_2429", "term": "Mapping" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2093", "term": "Data reference" }, "format": [ { "uri": "http://edamontology.org/format_3996", "term": "Python script" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "Import diverse data from API endpoints (JSON) and relational databases. 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These profiles are stored as position frequency matrices (PFMs), which can be transformed into models to predict TF binding sites (TFBS) in DNA sequences. The database collects motifs both internally, analyzing sequences using a custom motif discovery pipeline, and externally from publications and other resources. All selected motifs are manually curated for quality and supporting evidence. JASPAR now offers a tool for TFBS enrichment analysis in user-provided genomic regions. 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"General", "Governance" ], "note": null }, { "url": "http://jaspar.genereg.net/faq/", "type": [ "FAQ" ], "note": null }, { "url": "http://jaspar.genereg.net/api/v1/docs/", "type": [ "API documentation" ], "note": null }, { "url": "https://pyjaspar.readthedocs.io/en/latest/", "type": [ "Citation instructions", "Command-line options", "Installation instructions", "User manual" ], "note": "Documentation for pyJASPAR" }, { "url": "https://bioconductor.org/packages/release/data/annotation/vignettes/JASPAR2022/inst/doc/JASPAR2022.html", "type": [ "Command-line options", "User manual" ], "note": "Documentation for the Bioconductor package" } ], "publication": [ { "doi": "10.1093/nar/gkab1113", "pmid": "34850907", "pmcid": "PMC8728201", "type": [ "Primary" ], "version": "9", "note": null, "metadata": { "title": "JASPAR 2022: The 9th release of the open-access database of transcription factor binding profiles", "abstract": "JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.", "date": "2022-01-07T00:00:00Z", "citationCount": 356, "authors": [ { "name": "Castro-Mondragon J.A." }, { "name": "Riudavets-Puig R." }, { "name": "Rauluseviciute I." }, { "name": "Berhanu Lemma R." }, { "name": "Turchi L." }, { "name": "Blanc-Mathieu R." }, { "name": "Lucas J." }, { "name": "Boddie P." }, { "name": "Khan A." }, { "name": "Perez N.M." }, { "name": "Fornes O." }, { "name": "Leung T.Y." }, { "name": "Aguirre A." }, { "name": "Hammal F." }, { "name": "Schmelter D." }, { "name": "Baranasic D." }, { "name": "Ballester B." }, { "name": "Sandelin A." }, { "name": "Lenhard B." }, { "name": "Vandepoele K." }, { "name": "Wasserman W.W." }, { "name": "Parcy F." }, { "name": "Mathelier A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkz1001", "pmid": "31701148", "pmcid": "PMC7145627", "type": [ "Primary" ], "version": "8", "note": null, "metadata": { "title": "JASPAR 2020: Update of the open-Access database of transcription factor binding profiles", "abstract": "JASPAR (http://jaspar.genereg.net) is an open-Access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). These new profiles represent an 18% expansion compared to the previous release. JASPAR 2020 comes with a novel collection of unvalidated TF-binding profiles for which our curators did not find orthogonal supporting evidence in the literature. This collection has a dedicated web form to engage the community in the curation of unvalidated TF-binding profiles. Moreover, we created a Q&A forum to ease the communication between the user community and JASPAR curators. Finally, we updated the genomic tracks, inference tool, and TF-binding profile similarity clusters. All the data is available through the JASPAR website, its associated RESTful API, and through the JASPAR2020 R/Bioconductor package.", "date": "2020-01-01T00:00:00Z", "citationCount": 996, "authors": [ { "name": "Fornes O." }, { "name": "Castro-Mondragon J.A." }, { "name": "Khan A." }, { "name": "Van Der Lee R." }, { "name": "Zhang X." }, { "name": "Richmond P.A." }, { "name": "Modi B.P." }, { "name": "Correard S." }, { "name": "Gheorghe M." }, { "name": "Baranasic D." }, { "name": "Santana-Garcia W." }, { "name": "Tan G." }, { "name": "Cheneby J." }, { "name": "Ballester B." }, { "name": "Parcy F." }, { "name": "Sandelin A." }, { "name": "Lenhard B." }, { "name": "Wasserman W.W." }, { "name": "Mathelier A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkx1126", "pmid": "29140473", "pmcid": "PMC5753243", "type": [ "Primary" ], "version": "2018", "note": null, "metadata": { "title": "JASPAR 2018: Update of the open-access database of transcription factor binding profiles and its web framework", "abstract": "JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package.", "date": "2018-01-01T00:00:00Z", "citationCount": 879, "authors": [ { "name": "Khan A." }, { "name": "Fornes O." }, { "name": "Stigliani A." }, { "name": "Gheorghe M." }, { "name": "Castro-Mondragon J.A." }, { "name": "Van Der Lee R." }, { "name": "Bessy A." }, { "name": "Cheneby J." }, { "name": "Kulkarni S.R." }, { "name": "Tan G." }, { "name": "Baranasic D." }, { "name": "Arenillas D.J." }, { "name": "Sandelin A." }, { "name": "Vandepoele K." }, { "name": "Lenhard B." }, { "name": "Ballester B." }, { "name": "Wasserman W.W." }, { "name": "Parcy F." }, { "name": "Mathelier A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/bioinformatics/btx804", "pmid": "29253085", "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "JASPAR RESTful API: Accessing JASPAR data from any programming language", "abstract": "JASPAR is a widely used open-access database of curated, non-redundant transcription factor binding profiles. Currently, data from JASPAR can be retrieved as flat files or by using programming language-specific interfaces. Here, we present a programming language-independent application programming interface (API) to access JASPAR data using the Representational State Transfer (REST) architecture. The REST API enables programmatic access to JASPAR by most programming languages and returns data in eight widely used formats. Several endpoints are available to access the data and an endpoint is available to infer the TF binding profile(s) likely bound by a given DNA binding domain protein sequence. Additionally, it provides an interactive browsable interface for bioinformatics tool developers. Availability and implementation This REST API is implemented in Python using the Django REST Framework. It is accessible at http://jaspar.genereg.net/api/ and the source code is freely available at https://bitbucket.org/CBGR/jaspar under GPL v3 license. Contact aziz.khan@ncmm.uio.no or anthony.mathelier@ncmm.uio.no Supplementary informationSupplementary dataare available at Bioinformatics online.", "date": "2018-05-01T00:00:00Z", "citationCount": 11, "authors": [ { "name": "Khan A." }, { "name": "Mathelier A." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/nar/gkv1176", "pmid": "26531826", "pmcid": null, "type": [ "Primary" ], "version": "2016", "note": null, "metadata": { "title": "JASPAR 2016: A major expansion and update of the open-access database of transcription factor binding profiles", "abstract": "JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release.", "date": "2016-01-01T00:00:00Z", "citationCount": 717, "authors": [ { "name": "Mathelier A." }, { "name": "Fornes O." }, { "name": "Arenillas D.J." }, { "name": "Chen C.-Y." }, { "name": "Denay G." }, { "name": "Lee J." }, { "name": "Shi W." }, { "name": "Shyr C." }, { "name": "Tan G." }, { "name": "Worsley-Hunt R." }, { "name": "Zhang A.W." }, { "name": "Parcy F." }, { "name": "Lenhard B." }, { "name": "Sandelin A." }, { "name": "Wasserman W.W." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkt997", "pmid": "24194598", "pmcid": null, "type": [ "Primary" ], "version": "5.0_ALPHA", "note": null, "metadata": { "title": "JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles", "abstract": "JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR - the JASPAR CORE subcollection, which contains curated, non-redundant profiles - with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in D. melanogaster and 4 in A. thaliana; a 9% update in total). The new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. In addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. Finally, the new JASPAR release is accompanied by a new BioPython package, a new R tool package and a new R/Bioconductor data package to facilitate access for both manual and automated methods. © 2013 The Author(s). Published by Oxford University Press.", "date": "2014-01-01T00:00:00Z", "citationCount": 789, "authors": [ { "name": "Mathelier A." }, { "name": "Zhao X." }, { "name": "Zhang A.W." }, { "name": "Parcy F." }, { "name": "Worsley-Hunt R." }, { "name": "Arenillas D.J." }, { "name": "Buchman S." }, { "name": "Chen C.-Y." }, { "name": "Chou A." }, { "name": "Ienasescu H." }, { "name": "Lim J." }, { "name": "Shyr C." }, { "name": "Tan G." }, { "name": "Zhou M." }, { "name": "Lenhard B." }, { "name": "Sandelin A." }, { "name": "Wasserman W.W." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkp950", "pmid": "19906716", "pmcid": null, "type": [ "Primary" ], "version": "4", "note": null, "metadata": { "title": "JASPAR 2010: The greatly expanded open-access database of transcription factor binding profiles", "abstract": "JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database to date: the database now holds 457 non-redundant, curated profiles. The new entries include the first batch of profiles derived from ChIP-seq and ChIP-chip whole-genome binding experiments, and 177 yeast TF binding profiles. The introduction of a yeast division brings the convenience of JASPAR to an active research community. As binding models are refined by newer data, the JASPAR database now uses versioning of matrices: in this release, 12% of the older models were updated to improved versions. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature. A curated catalog of mammalian TFs is provided, extending the use of the JASPAR profiles to additional TFs belonging to the same structural family. The changes in the database set the system ready for more rapid acquisition of new high-throughput data sources. Additionally, three new special collections provide matrix profile data produced by recent alternative high-throughput approaches. © The Author(s) 2009. Published by Oxford University Press.", "date": "2009-11-10T00:00:00Z", "citationCount": 478, "authors": [ { "name": "Portales-Casamar E." }, { "name": "Thongjuea S." }, { "name": "Kwon A.T." }, { "name": "Arenillas D." }, { "name": "Zhao X." }, { "name": "Valen E." }, { "name": "Yusuf D." }, { "name": "Lenhard B." }, { "name": "Wasserman W.W." }, { "name": "Sandelin A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkm955", "pmid": "18006571", "pmcid": null, "type": [ "Primary" ], "version": "3", "note": null, "metadata": { "title": "JASPAR, the open access database of transcription factor-binding profiles: New content and tools in the 2008 update", "abstract": "JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR database - the JASPAR CORE sub-database - has increased by 12% in size, and three new specialized sub-databases have been added. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. JASPAR is available at http://jaspar.genereg.net. © 2007 The Author(s).", "date": "2008-01-01T00:00:00Z", "citationCount": 550, "authors": [ { "name": "Bryne J.C." }, { "name": "Valen E." }, { "name": "Tang M.-H.E." }, { "name": "Marstrand T." }, { "name": "Winther O." }, { "name": "Da piedade I." }, { "name": "Krogh A." }, { "name": "Lenhard B." }, { "name": "Sandelin A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkj115", "pmid": "16381983", "pmcid": null, "type": [ "Primary" ], "version": "2", "note": null, "metadata": null }, { "doi": "10.1093/nar/gkh012", "pmid": "14681366", "pmcid": null, "type": [ "Primary" ], "version": "1", "note": null, "metadata": null } ], "credit": [ { "name": "Albin Sandelin", "email": "albin@binf.ku.dk", "url": "https://albinsandelin.wixsite.com/sandelinlab", "orcidid": "http://orcid.org/0000-0002-7109-7378", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Boris Lenhard", "email": "b.lenhard@imperial.ac.uk", "url": "https://lms.mrc.ac.uk/research-group/computational-regulatory-genomics/", "orcidid": "http://orcid.org/0000-0002-1114-1509", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Wyeth Wasserman", "email": "wyeth@cmmt.ubc.ca", "url": "https://cmmt.ubc.ca/wasserman-lab/", "orcidid": "http://orcid.org/0000-0001-6098-6412", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "François Parcy", "email": "francois.parcy@cea.fr", "url": "https://www.lpcv.fr/en/Pages/Flo_Re/Presentation.aspx", "orcidid": "https://orcid.org/0000-0003-2191-500X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Anthony Mathelier", "email": "anthony.mathelier@ncmm.uio.no", "url": 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The latest release of CHOPCHOP (version 3) includes many new features and visualization options, supporting over 200 genomes with whole-gene targeting and versatile search modes. The tool now enables precise RNA targeting with Cas13, supporting alternative transcript isoforms and predicting RNA accessibility using ViennaRNA's RNAfold. The update also introduces new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. For larger queries or handling unsupported genomes, a command-line version is available with additional functionalities. 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The technology was initially developed to induce targeted mutations in DNA, but CRISPR-Cas has now been adapted to target nucleic acids for a range of purposes. CHOPCHOP is a web tool for identifying CRISPR-Cas single guide RNA (sgRNA) targets. In this major update of CHOPCHOP, we expand our toolbox beyond knockouts. We introduce functionality for targeting RNA with Cas13, which includes support for alternative transcript isoforms and RNA accessibility predictions. We incorporate new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. Finally, we expand our results page visualization to reveal alternative isoforms and downstream ATG sites, which will aid users in avoiding the expression of truncated proteins. The CHOPCHOP web tool now supports over 200 genomes and we have released a command-line script for running larger jobs and handling unsupported genomes. CHOPCHOP v3 can be found at https://chopchop.cbu.uib.no", "date": "2019-07-01T00:00:00Z", "citationCount": 600, "authors": [ { "name": "Labun K." }, { "name": "Montague T.G." }, { "name": "Krause M." }, { "name": "Torres Cleuren Y.N." }, { "name": "Tjeldnes H." }, { "name": "Valen E." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1002/cpz1.46", "pmid": "33905612", "pmcid": null, "type": [ "Usage" ], "version": "3", "note": null, "metadata": { "title": "CRISPR Genome Editing Made Easy Through the CHOPCHOP Website", "abstract": "The design of optimal guide RNA (gRNA) sequences for CRISPR systems is challenged by the need to achieve highly efficient editing at the desired location (on-target editing) with minimal editing at unintended locations (off-target editing). Although laboratory validation should ideally be used to detect off-target activity, computational predictions are almost always preferred in practice due to their speed and low cost. Several studies have therefore explored gRNA-DNA interactions in order to understand how CRISPR complexes select their genomic targets. CHOPCHOP (https://chopchop.cbu.uib.no/) leverages these developments to build a user-friendly web interface that helps users design optimal gRNAs. CHOPCHOP supports a wide range of CRISPR applications, including gene knock-out, sequence knock-in, and RNA knock-down. Furthermore, CHOPCHOP offers visualization that enables an informed choice of gRNAs and supports experimental validation. In these protocols, we describe the best practices for gRNA design using CHOPCHOP. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Design of gRNAs for gene knock-out. Alternate Protocol 1: Design of gRNAs for dCas9 fusion/effector targeting. Support Protocol: Design of gRNAs for targeting transgenic or plasmid sequences. Basic Protocol 2: Design of gRNAs for RNA targeting. Basic Protocol 3: Design of gRNAs for sequence knock-in. Alternate Protocol 2: Design of gRNAs for knock-in using non-homologous end joining. Basic Protocol 4: Design of gRNAs for knock-in using Cas9 nickases.", "date": "2021-04-01T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Labun K." }, { "name": "Krause M." }, { "name": "Torres Cleuren Y." }, { "name": "Valen E." } ], "journal": "Current Protocols" } }, { "doi": "10.1093/nar/gkw398", "pmid": "27185894", "pmcid": "PMC4987937", "type": [ "Primary" ], "version": "2", "note": null, "metadata": { "title": "CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering", "abstract": "In just 3 years CRISPR genome editing has transformed biology, and its popularity and potency continue to grow. New CRISPR effectors and rules for locating optimum targets continue to be reported, highlighting the need for computational CRISPR targeting tools to compile these rules and facilitate target selection and design. CHOPCHOP is one of the most widely used web tools for CRISPR- and TALEN-based genome editing. Its overarching principle is to provide an intuitive and powerful tool that can serve both novice and experienced users. In this major update we introduce tools for the next generation of CRISPR advances, including Cpf1 and Cas9 nickases. We support a number of new features that improve the targeting power, usability and efficiency of CHOPCHOP. To increase targeting range and specificity we provide support for custom length sgRNAs, and we evaluate the sequence composition of the whole sgRNA and its surrounding region using models compiled from multiple large-scale studies. These and other new features, coupled with an updated interface for increased usability and support for a continually growing list of organisms, maintain CHOPCHOP as one of the leading tools for CRISPR genome editing. CHOPCHOP v2 can be found at http://chopchop.cbu.uib.no.", "date": "2016-07-08T00:00:00Z", "citationCount": 552, "authors": [ { "name": "Labun K." }, { "name": "Montague T.G." }, { "name": "Gagnon J.A." }, { "name": "Thyme S.B." }, { "name": "Valen E." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gku410", "pmid": "24861617", "pmcid": "PMC4086086", "type": [ "Primary" ], "version": "1", "note": null, "metadata": { "title": "CHOPCHOP: A CRISPR/Cas9 and TALEN web tool for genome editing", "abstract": "Major advances in genome editing have recently been made possible with the development of the TALEN and CRISPR/Cas9 methods. The speed and ease of implementing these technologies has led to an explosion of mutant and transgenic organisms. A rate-limiting step in efficiently applying TALEN and CRISPR/Cas9 methods is the selection and design of targeting constructs. We have developed an online tool, CHOPCHOP (https://chopchop.rc.fas.harvard.edu), to expedite the design process. CHOPCHOP accepts a wide range of inputs (gene identifiers, genomic regions or pasted sequences) and provides an array of advanced options for target selection. It uses efficient sequence alignment algorithms to minimize search times, and rigorously predicts off-target binding of single-guide RNAs (sgRNAs) and TALENs. Each query produces an interactive visualization of the gene with candidate target sites displayed at their genomic positions and color-coded according to quality scores. In addition, for each possible target site, restriction sites and primer candidates are visualized, facilitating a streamlined pipeline of mutant generation and validation. The ease-of-use and speed of CHOPCHOP make it a valuable tool for genome engineering. © 2014 The Author(s).", "date": "2014-07-01T00:00:00Z", "citationCount": 736, "authors": [ { "name": "Montague T.G." }, { "name": "Cruz J.M." }, { "name": "Gagnon J.A." }, { "name": "Church G.M." }, { "name": "Valen E." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Kornel Labun", "email": "kornel.labun@uib.no", "url": null, "orcidid": "https://orcid.org/0000-0002-1262-2611", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer", "Support" ], "note": null }, { "name": "Tessa Montague", "email": "tessa.chopchop@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0002-5918-6327", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Contributor", "Support" ], "note": null }, { "name": "Valen Group (Computational Biology Unit)", "email": null, "url": "https://www.cbu.uib.no/valen/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Developer", "Maintainer", "Support" ], "note": null }, { "name": "The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk", "email": "support@elixir.no", "url": "https://elixir.no/helpdesk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Support" ], "note": "Helpdesk and support for ELIXIR Norway services" }, { "name": "University of Bergen", "email": null, "url": "https://www.uib.no/en", "orcidid": null, "gridid": "grid.7914.b", "rorid": "03zga2b32", "fundrefid": "10.13039/501100005036", "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "James Graham", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-8639-7592", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Recommendations on the long-read enrichment mode" }, { "name": "Bergen Research Foundation", "email": null, "url": "https://mohnfoundation.no/en/about/", "orcidid": null, "gridid": "grid.478482.5", "rorid": "04efaep75", "fundrefid": "10.13039/501100006475", "typeEntity": "Funding agency", "typeRole": [], "note": "Now part of the Trond Mohn Foundation" }, { "name": "University of Bergen", "email": null, "url": "https://www.uib.no/en", "orcidid": null, "gridid": "grid.7914.b", "rorid": "03zga2b32", "fundrefid": "10.13039/501100005036", "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "The Research Council of Norway", "email": null, "url": "http://www.forskningsradet.no/en/Home_page/1177315753906", "orcidid": null, "gridid": "grid.13985.36", "rorid": "00epmv149", "fundrefid": "10.13039/501100005416", "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "Erin Calhoun", "email": "erin.calhoun@uit.no", "url": null, "orcidid": "https://orcid.org/0009-0003-3752-7156", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": "Curation of bio.tools profile - contact me with updates/corrections." } ], "community": null, "owner": "edv", "additionDate": "2016-03-11T10:35:00Z", "lastUpdate": "2023-08-03T13:19:40.201053Z", "editPermission": { "type": "group", "authors": [ "eca008" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "The Genomic HyperBrowser", "description": "A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets.", "homepage": "https://hyperbrowser.uio.no", "biotoolsID": "the_genomic_hyperbrowser", "biotoolsCURIE": "biotools:the_genomic_hyperbrowser", "version": [ "1.6" ], "otherID": [], "relation": [ { "biotoolsID": "gsuite_hyperbrowser", "type": "hasNewVersion" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3194", "term": "Genome feature comparison" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" }, { "uri": "http://edamontology.org/operation_3463", "term": "Gene expression correlation" }, { "uri": "http://edamontology.org/operation_0531", "term": "Heat map generation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3003", "term": "BED" }, { "uri": "http://edamontology.org/format_3005", "term": "WIG" }, { "uri": "http://edamontology.org/format_3164", "term": "GTrack" } ] }, { "data": { "uri": "http://edamontology.org/data_3108", "term": "Experimental measurement" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3003", "term": "BED" }, { "uri": "http://edamontology.org/format_3005", "term": "WIG" }, { "uri": "http://edamontology.org/format_3164", "term": "GTrack" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" }, { "uri": "http://edamontology.org/topic_3173", "term": "Epigenomics" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Norway" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://genomebiology.com/content/11/12/R121", "type": [ "Citation instructions" ], "note": null }, { "url": "https://sites.google.com/site/hyperbrowserhelp/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/gb-2010-11-12-r121", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The Genomic HyperBrowser: Inferential genomics at the sequence level", "abstract": "The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical analysis of sequence-level genomic information. We provide a growing collection of generic biological investigations that query pairwise relations between tracks, represented as mathematical objects, along the genome. The Genomic HyperBrowser implements the approach and is available at http://hyperbrowser.uio.no.© 2010 Sandve et al.; licensee BioMed Central Ltd.", "date": "2010-12-23T00:00:00Z", "citationCount": 67, "authors": [ { "name": "Sandve G.K." }, { "name": "Gundersen S." }, { "name": "Rydbeck H." }, { "name": "Glad I.K." }, { "name": "Holden L." }, { "name": "Holden M." }, { "name": "Liestol K." }, { "name": "Clancy T." }, { "name": "Ferkingstad E." }, { "name": "Johansen M." }, { "name": "Nygaard V." }, { "name": "Tostesen E." }, { "name": "Frigessi A." }, { "name": "Hovig E." } ], "journal": "Genome Biology" } }, { "doi": "10.1186/gb-2010-11-8-r86", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", "abstract": "Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis. © 2010 Goecks et al.; licensee BioMed Central Ltd.", "date": "2010-08-25T00:00:00Z", "citationCount": 2716, "authors": [ { "name": "Goecks J." }, { "name": "Nekrutenko A." }, { "name": "Taylor J." }, { "name": "Afgan E." }, { "name": "Ananda G." }, { "name": "Baker D." }, { "name": "Blankenberg D." }, { "name": "Chakrabarty R." }, { "name": "Coraor N." }, { "name": "Von Kuster G." }, { "name": "Lazarus R." }, { "name": "Li K." }, { "name": "Taylor J." }, { "name": "Vincent K." } ], "journal": "Genome Biology" } }, { "doi": "10.1186/1471-2105-12-494", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Identifying elemental genomic track types and representing them uniformly", "abstract": "Background: With the recent advances and availability of various high-throughput sequencing technologies, data on many molecular aspects, such as gene regulation, chromatin dynamics, and the three-dimensional organization of DNA, are rapidly being generated in an increasing number of laboratories. The variation in biological context, and the increasingly dispersed mode of data generation, imply a need for precise, interoperable and flexible representations of genomic features through formats that are easy to parse. A host of alternative formats are currently available and in use, complicating analysis and tool development. The issue of whether and how the multitude of formats reflects varying underlying characteristics of data has to our knowledge not previously been systematically treated.Results: We here identify intrinsic distinctions between genomic features, and argue that the distinctions imply that a certain variation in the representation of features as genomic tracks is warranted. Four core informational properties of tracks are discussed: gaps, lengths, values and interconnections. From this we delineate fifteen generic track types. Based on the track type distinctions, we characterize major existing representational formats and find that the track types are not adequately supported by any single format. We also find, in contrast to the XML formats, that none of the existing tabular formats are conveniently extendable to support all track types. We thus propose two unified formats for track data, an improved XML format, BioXSD 1.1, and a new tabular format, GTrack 1.0.Conclusions: The defined track types are shown to capture relevant distinctions between genomic annotation tracks, resulting in varying representational needs and analysis possibilities. The proposed formats, GTrack 1.0 and BioXSD 1.1, cater to the identified track distinctions and emphasize preciseness, flexibility and parsing convenience. © 2011 Gundersen et al; licensee BioMed Central Ltd.", "date": "2011-12-30T00:00:00Z", "citationCount": 15, "authors": [ { "name": "Gundersen S." }, { "name": "Kalas M." }, { "name": "Abul O." }, { "name": "Frigessi A." }, { "name": "Hovig E." }, { "name": "Sandve G.K." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1093/nar/gkt342", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Genomic HyperBrowser: an analysis web server for genome-scale data.", "abstract": "The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable biological questions. With this opportunity, however, researchers are faced with the challenge of how to best analyze and interpret their genome-scale datasets. A powerful way of representing genome-scale data is as feature-specific coordinates relative to reference genome assemblies, i.e. as genomic tracks. The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web server for the analysis of genomic track data. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome.", "date": "2013-01-01T00:00:00Z", "citationCount": 28, "authors": [ { "name": "Sandve G.K." }, { "name": "Gundersen S." }, { "name": "Johansen M." }, { "name": "Glad I.K." }, { "name": "Gunathasan K." }, { "name": "Holden L." }, { "name": "Holden M." }, { "name": "Liestol K." }, { "name": "Nygard S." }, { "name": "Nygaard V." }, { "name": "Paulsen J." }, { "name": "Rydbeck H." }, { "name": "Trengereid K." }, { "name": "Clancy T." }, { "name": "Drablos F." }, { "name": "Ferkingstad E." }, { "name": "Kalas M." }, { "name": "Lien T." }, { "name": "Rye M.B." }, { "name": "Frigessi A." }, { "name": "Hovig E." } ], "journal": "Nucleic acids research" } } ], "credit": [ { "name": "University Of Oslo", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Galaxy", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "Oslo University Hospital", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "EMBIO", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "University Of Oslo", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Statistics for Innovation", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Helse Sør-Øst", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "UiO", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "hyperbrowser-requests@usit.uio.no", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "UiO", "additionDate": "2016-03-07T16:53:56Z", "lastUpdate": "2023-08-02T07:58:55.646223Z", "editPermission": { "type": "group", "authors": [ "eca008" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Training Infrastructure as a Service (TIaaS)", "description": "Originally developed by Galaxy Europe and the Gallantries project, together with the Galaxy community we have created \"Training Infrastructure-as-a-Service\" (TIaaS), aimed at providing user-friendly training infrastructure to the global training community. TIaaS provides dedicated training resources for Galaxy-based courses and events. Event organisers register their course, after which trainees are transparently placed in a private queue on the compute infrastructure, which ensures jobs complete quickly, even when the main queue is experiencing high wait times. A built-in dashboard allows instructors to monitor student progress.\n\nTraining Infrastructure as a Service (TIaaS) has been in development since 21 June 2018, and three days later became a production service at Galaxy Europe on 24 June. As of June 7th, 2023 is has supported 504 training events with over 24000 learners have used this infrastructure for Galaxy training.", "homepage": "https://github.com/galaxyproject/tiaas2", "biotoolsID": "tiaas", "biotoolsCURIE": "biotools:tiaas", "version": [ "2.1.0" ], "otherID": [ { "value": "RRID:SCR_023200", "type": "rrid", "version": null } ], "relation": [ { "biotoolsID": "galaxy", "type": "uses" }, { "biotoolsID": "galaxy", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3760", "term": "Service management" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0605", "term": "Informatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "AGPL-3.0", "collectionID": [ "Galaxy" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Training", "Compute" ], "elixirNode": [ "Netherlands", "Germany", "France" ], "elixirCommunity": [ "Galaxy" ], "link": [ { "url": "https://github.com/galaxyproject/tiaas2/", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/galaxyproject/ansible-tiaas2", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/galaxyproject/tiaas2/issues/", "type": [ "Issue tracker", "Helpdesk" ], "note": null }, { "url": "https://usegalaxy.eu/tiaas/", "type": [ "Service" ], "note": null }, { "url": "https://usegalaxy.org.au/tiaas/", "type": [ "Service" ], "note": null }, { "url": "https://usegalaxy.org/tiaas/", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://github.com/galaxyproject/tiaas2/archive/refs/tags/2.1.0", "type": "Software package", "note": null, "version": "2.1.0" }, { "url": "https://github.com/galaxyproject/ansible-tiaas2/releases/tag/2.2.0", "type": "Other", "note": "Ansible role for TIaaS installation", "version": "2.2.0 (ansible)" } ], "documentation": [ { "url": "https://training.galaxyproject.org/training-material/topics/admin/tutorials/tiaas/tutorial.html", "type": [ "Installation instructions", "Training material" ], "note": null }, { "url": "https://github.com/galaxyproject/tiaas2/blob/main/CODE_OF_CONDUCT.md", "type": [ "Code of conduct" ], "note": null }, { "url": "https://training.galaxyproject.org/training-material/topics/teaching/tutorials/setup-tiaas-for-training/tutorial.html", "type": [ "Training material", "User manual" ], "note": null }, { "url": "https://usegalaxy.eu/tiaas/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/2020.08.23.263509", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "This is a preprint", "metadata": null }, { "doi": "10.1093/gigascience/giad048", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Helena Rasche", "email": "helena.rasche@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0001-9760-8992", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer", "Support" ], "note": null }, { "name": "Bundesministerium für Bildung und Forschung", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": "10.13039/501100002347", "typeEntity": "Funding agency", "typeRole": [], "note": "grants 031 A538A/A538C RBC and 031L0101B/031L0101C de.NBI-epi" }, { "name": "National Human Genome Research Institute", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": "10.13039/100000051", "typeEntity": "Funding agency", "typeRole": [], "note": "grant 2U24HG006620" }, { "name": "Cameron Hyde", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-5913-9766", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "John Davis", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-1363-1245", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Simon Gladman", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6100-4385", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "In loving memory of Simon Gladman (1970-2022) beloved mentor and system administrator, who was instrumental in getting the second TIaaS deployment running at Galaxy Australia, proving its generalisability." }, { "name": "Nate Coraor", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-8083-2963", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Provider" ], "note": null }, { "name": "Anthony Bretaudeau", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0914-2470", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Provider" ], "note": null }, { "name": "Gianmauro Cuccuru", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-5335-545X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Wendi Bacon", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-8170-8806", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null }, { "name": "Beatriz García-Jiménez", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-5862-6132", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider", "Support" ], "note": null }, { "name": "Jennifer Hillman-Jackson", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-4012-8116", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider", "Support" ], "note": null }, { "name": "Saskia Hiltemann", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3803-468X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Documentor" ], "note": null }, { "name": "Miaomiao Zhou", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-4426-1758", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null }, { "name": "Björn Grüning", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-3079-6586", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support", "Provider", "Contributor" ], "note": null }, { "name": "Andrew Stubbs", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-9817-9982", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Erasmus+ Programme", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": "10.13039/100001501", "typeEntity": "Funding agency", "typeRole": [ "Support" ], "note": "Grant 2020-1-NL01-KA203-064717" } ], "community": null, "owner": "hexylena", "additionDate": "2021-01-18T10:21:30Z", "lastUpdate": "2023-07-04T13:36:19.654323Z", "editPermission": { "type": "group", "authors": [ "hexylena" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "APPRIS", "description": "Annotates variants with biological data such as protein structural information, functionally important residues, conservation of functional domains and evidence of cross-species conservation.", "homepage": "https://appris.bioinfo.cnio.es", "biotoolsID": "appris", "biotoolsCURIE": "biotools:appris", "version": [ "2022_07.v47" ], "otherID": [], "relation": [ { "biotoolsID": "firestar", "type": "includes" }, { "biotoolsID": "firestar_ws", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0361", "term": "Sequence annotation" }, { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3320", "term": "RNA splicing" }, { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "IMPaCT-Data" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/appris/appris", "type": [ "Repository" ], "note": null }, { "url": "https://appris.bioinfo.cnio.es/#/downloads", "type": [ "Other" ], "note": "Access annotations for the species annotated in the database via gene name or Ensembl id." }, { "url": "https://appris.bioinfo.cnio.es/#/server", "type": [ "Other" ], "note": "Annotate splice isoforms for vertebrate genes that are not in the APPRIS Database" }, { "url": "http://apprisws.bioinfo.cnio.es/apidoc/", "type": [ "Other" ], "note": "Annotate genes and transcripts automatically and access queries through RESTful web services." } ], "download": [ { "url": "https://appris.bioinfo.cnio.es/#/downloads", "type": "Downloads page", "note": "The annotations of the following species are available.", "version": null } ], "documentation": [ { "url": "https://appris.bioinfo.cnio.es/#/help/intro", "type": [ "General" ], "note": null }, { "url": "http://apprisws.bioinfo.cnio.es/apidoc/", "type": [ "Command-line options" ], "note": "The APPRIS WebServices make use of standard HTTP method calls (often termed RESTful services), and the HTTP request methods GET and POST can be used to send and receive queries and data. APPRIS Database and APPRIS WebServer can be accessed through these RESTful web services.\n\nIn this API Interface, the APPRIS Web Services are described and you can interact with them. Try it Out!!" } ], "publication": [ { "doi": "10.1093/nar/gks1058", "pmid": "23161672", "pmcid": null, "type": [ "Primary" ], "version": null, "note": "APPRIS: annotation of principal and alternative splice isoforms.\nRodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A and Tress ML. Nucleic acids research 2013;41;Database issue;D110-7", "metadata": { "title": "APPRIS: Annotation of principal and alternative splice isoforms", "abstract": "Here, we present APPRIS (http://appris.bioinfo.cnio.es), a database that houses annotations of human splice isoforms. APPRIS has been designed to provide value to manual annotations of the human genome by adding reliable protein structural and functional data and information from cross-species conservation. The visual representation of the annotations provided by APPRIS for each gene allows annotators and researchers alike to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, APPRIS also selects a single reference sequence for each gene, here termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. APPRIS identifies a principal isoform for 85% of the protein-coding genes in the GENCODE 7 release for ENSEMBL. Analysis of the APPRIS data shows that at least 70% of the alternative (non-principal) variants would lose important functional or structural information relative to the principal isoform. © The Author(s) 2012.", "date": "2013-01-01T00:00:00Z", "citationCount": 128, "authors": [ { "name": "Rodriguez J.M." }, { "name": "Maietta P." }, { "name": "Ezkurdia I." }, { "name": "Pietrelli A." }, { "name": "Wesselink J.J." }, { "name": "Lopez G." }, { "name": "Valencia A." }, { "name": "Tress M.L." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkv512", "pmid": "25990727", "pmcid": null, "type": [ "Primary" ], "version": null, "note": "APPRIS WebServer and WebServices.\nRodriguez JM, Carro A, Valencia A, and Tress ML.\nNucleic Acids Res. 2015 May 18.", "metadata": { "title": "APPRIS WebServer and WebServices", "abstract": "© 2015 The Author(s).This paper introduces the APPRIS WebServer (http://appris.bioinfo.cnio.es) and WebServices (http://apprisws.bioinfo.cnio.es). Both the web servers and the web services are based around the APPRIS Database, a database that presently houses annotations of splice isoforms for five different vertebrate genomes. The APPRIS WebServer and WebServices provide access to the computational methods implemented in the APPRIS Database, while the APPRIS WebServices also allows retrieval of the annotations. The APPRIS WebServer and WebServices annotate splice isoforms with protein structural and functional features, and with data from cross-species alignments. In addition they can use the annotations of structure, function and conservation to select a single reference isoform for each protein-coding gene (the principal protein isoform). APPRIS principal isoforms have been shown to agree overwhelmingly with the main protein isoform detected in proteomics experiments. The APPRIS WebServer allows for the annotation of splice isoforms for individual genes, and provides a range of visual representations and tools to allow researchers to identify the likely effect of splicing events. The APPRIS WebServices permit users to generate annotations automatically in high throughput mode and to interrogate the annotations in the APPRIS Database. The APPRIS WebServices have been implemented using REST architecture to be flexible, modular and automatic.", "date": "2015-01-01T00:00:00Z", "citationCount": 16, "authors": [ { "name": "Rodriguez J.M." }, { "name": "Carro A." }, { "name": "Valencia A." }, { "name": "Tress M.L." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkx997", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": "APPRIS 2017: principal isoforms for multiple gene sets.\nRodriguez JM, Rodriguez-Rivas J, Domenico TD, Vázquez J, Valencia A, and Tress ML.\nNucleic Acids Res. Database issue; 2017 Oct 23.", "metadata": { "title": "APPRIS 2017: Principal isoforms for multiple gene sets", "abstract": "© 2017 The Author(s).The APPRIS database (http://appris-tools.org) uses protein structural and functional features and information from cross-species conservation to annotate splice isoforms in protein-coding genes. APPRIS selects a single protein isoform, the 'principal' isoform, as the reference for each gene based on these annotations. A single main splice isoform reflects the biological reality for most protein coding genes and APPRIS principal isoforms are the best predictors of these main proteins isoforms. Here, we present the updates to the database, new developments that include the addition of three new species (chimpanzee, Drosophila melangaster and Caenorhabditis elegans), the expansion of APPRIS to cover the RefSeq gene set and the UniProtKB proteome for six species and refinements in the core methods that make up the annotation pipeline. In addition APPRIS now provides a measure of reliability for individual principal isoforms and updates with each release of the GENCODE/Ensembl and RefSeq reference sets. The individual GENCODE/Ensembl, RefSeq and UniProtKB reference gene sets for six organisms have been merged to produce common sets of splice variants.", "date": "2018-01-01T00:00:00Z", "citationCount": 69, "authors": [ { "name": "Rodriguez J.M." }, { "name": "Rodriguez-Rivas J." }, { "name": "Di Domenico T." }, { "name": "Vazquez J." }, { "name": "Valencia A." }, { "name": "Tress M.L." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkab1058", "pmid": "34755885", "pmcid": "PMC8728124", "type": [ "Primary" ], "version": null, "note": "Rodriguez JM, Pozo F, Cerdán-Vélez D, Di Domenico T, Vázquez J, Tress ML. APPRIS: selecting functionally important isoforms. Nucleic Acids Res. 2022;50(D1):D54-D59.", "metadata": { "title": "APPRIS: Selecting functionally important isoforms", "abstract": "© 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.APPRIS (https://appris.bioinfo.cnio.es) is a well-established database housing annotations for protein isoforms for a range of species. APPRIS selects principal isoforms based on protein structure and function features and on cross-species conservation. Most coding genes produce a single main protein isoform and the principal isoforms chosen by the APPRIS database best represent this main cellular isoform. Human genetic data, experimental protein evidence and the distribution of clinical variants all support the relevance of APPRIS principal isoforms. APPRIS annotations and principal isoforms have now been expanded to 10 model organisms. In this paper we highlight the most recent updates to the database. APPRIS annotations have been generated for two new species, cow and chicken, the protein structural information has been augmented with reliable models from the EMBL-EBI AlphaFold database, and we have substantially expanded the confirmatory proteomics evidence available for the human genome. The most significant change in APPRIS has been the implementation of TRIFID functional isoform scores. TRIFID functional scores are assigned to all splice isoforms, and APPRIS uses the TRIFID functional scores and proteomics evidence to determine principal isoforms when core methods cannot.", "date": "2022-01-07T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Rodriguez J.M." }, { "name": "Pozo F." }, { "name": "Cerdan-Velez D." }, { "name": "Di Domenico T." }, { "name": "Vazquez J." }, { "name": "Tress M.L." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "INB", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "CNIO", "email": null, "url": "https://www.cnio.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ISCIII", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "BU_CNIO", "email": null, "url": "https://bioinformatics.cnio.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null }, { "name": "APPRIS", "email": "appris.cnio@gmail.com", "url": "http://appris.bioinfo.cnio.es/#/about", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "Jose Rodriguez", "email": "jmrodriguezc@cnic.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9948-5073", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Michael Tress", "email": "mtress@cnio.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null } ], "community": null, "owner": "tdido", 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"http://edamontology.org/topic_3303", "term": "Medicine" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Czech Republic", "ELIXIR-CZ" ], "maturity": "Emerging", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Lucie Houdová", "email": "houdina@kky.zcu.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Miloš Fetter", "email": "fetter@kky.zcu.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Daniel Georgiev", "email": "georgiev@kky.zcu.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "University of West Bohemia, Czech Republic", "email": null, "url": "http://ccy.zcu.cz", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": "https://www.elixir-czech.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "TA CR", "email": null, "url": "https://www.tacr.cz/index.php/en/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Daniel Georgiev", "email": "georgiev@ntis.zcu.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "Daniel Georgiev", "email": "georgiev@ntis.zcu.cz", "url": null, "orcidid": null, 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