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{ "count": 2669, "next": "?page=2", "previous": null, "list": [ { "name": "BIGR XNAT", "description": "Imaging platform based on the open source XNAT software. It is used for sharing de-identified medical imaging data, and for data exchange in collaborative research projects. The data is served in a standardized way, with proper access control.", "homepage": "https://bigr-xnat.erasmusmc.nl", "biotoolsID": "bigr_xnat", "biotoolsCURIE": "biotools:bigr_xnat", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3468", "term": "xls" }, { "uri": "http://edamontology.org/format_3550", "term": "mhd" }, { "uri": "http://edamontology.org/format_3551", "term": "nrrd" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] }, { "data": { "uri": "http://edamontology.org/data_3546", "term": "Image metadata" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3468", "term": "xls" }, { "uri": "http://edamontology.org/format_3550", "term": "mhd" }, { "uri": "http://edamontology.org/format_3551", "term": "nrrd" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3468", "term": "xls" }, { "uri": "http://edamontology.org/format_3550", "term": "mhd" }, { "uri": "http://edamontology.org/format_3551", "term": "nrrd" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] }, { "data": { "uri": "http://edamontology.org/data_3546", "term": "Image metadata" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3468", "term": "xls" }, { "uri": "http://edamontology.org/format_3550", "term": "mhd" }, { "uri": "http://edamontology.org/format_3551", "term": "nrrd" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "BioMedBridges Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://xnat.bigr.nl", "type": [ "Helpdesk" ], "note": null } ], "download": [], "documentation": [ { "url": "http://xnat.bigr.nl", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/2043-9113-5-s1-s18", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Erwin Vast", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "NRG Lab, Washington University School of Medicine", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Erasmus MC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "BioMedBridges", "email": null, "url": "http://www.biomedbridges.eu", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Documentor" ], "note": null }, { "name": null, "email": null, "url": "http://xnat.bigr.nl", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Stefan Klein", "email": "s.klein@erasmusmc.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hachterberg", "additionDate": "2015-02-04T09:14:44Z", "lastUpdate": "2025-07-24T22:46:15.794823Z", "editPermission": { "type": "group", "authors": [ "korbinib" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MOCCASIN", "description": "Designed to convert certain basic forms of ODE simulation models written in MATLAB or Octave and translate them into SBML format.", "homepage": "https://github.com/sbmlteam/moccasin", "biotoolsID": "moccasin", "biotoolsCURIE": "biotools:moccasin", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3524", "term": "Simulation experiment" }, { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/moccasin-converting-matlab-ode-models-to-sbml.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/sbmlteam/moccasin/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": null, "pmid": "26861819", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MOCCASIN: Converting MATLAB ODE models to SBML", "abstract": "© 2016 The Author 2016. Published by Oxford University Press.MATLAB is popular in biological research for creating and simulating models that use ordinary differential equations (ODEs). However, sharing or using these models outside of MATLAB is often problematic. A community standard such as Systems Biology Markup Language (SBML) can serve as a neutral exchange format, but translating models from MATLAB to SBML can be challenging - especially for legacy models not written with translation in mind. We developed MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) to help. MOCCASIN can convert ODE-based MATLAB models of biochemical reaction networks into the SBML format.", "date": "2016-06-15T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Gomez H.F." }, { "name": "Hucka M." }, { "name": "Keating S.M." }, { "name": "Nudelman G." }, { "name": "Iber D." }, { "name": "Sealfon S.C." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Michael Hucka,", "email": "mhucka@caltech.edu", "url": "https://github.com/sbmlteam/moccasin", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "frankbergmann", "additionDate": "2017-08-03T18:49:51Z", "lastUpdate": "2025-07-08T14:13:52.296025Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Clotbase", "description": "A curated knowledgebase on the proteins that are involved in the blood coagulation pathway. It contains information on sequence, accession number, source, taxonomy, keywords, function, subcellular location, tissue specificity, associated diseases, mutation and links to external databases.", "homepage": "http://www.clotbase.bicnirrh.res.in/", "biotoolsID": "clotbase", "biotoolsCURIE": "biotools:clotbase", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3202", "term": "Polymorphism detection" }, { "uri": "http://edamontology.org/operation_0331", "term": "Protein modelling (mutation)" }, { "uri": "http://edamontology.org/operation_0478", "term": "Molecular docking" }, { "uri": "http://edamontology.org/operation_0367", "term": "Sequence mutation and randomisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3408", "term": "Haematology" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": null, "pmid": "20688969", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "ClotBase: A knowledgebase on proteins involved in blood coagulation", "abstract": "", "date": "2010-08-05T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Sonawani A." }, { "name": "Nilawe P." }, { "name": "Barai R.S." }, { "name": "Idicula-Thomas S." } ], "journal": "Blood" } } ], "credit": [ { "name": "ClotBase Support", "email": "clotbase@bicnirrh.res.in", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "YthCxz", "additionDate": "2017-03-30T21:27:38Z", "lastUpdate": "2025-05-26T10:48:03.927649Z", "editPermission": { "type": "group", "authors": [ "YthCxz" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PREP Suite", "description": "The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.", "homepage": "http://prep.unl.edu/", "biotoolsID": "prep_suite", "biotoolsCURIE": "biotools:prep_suite", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2489", "term": "Protein subcellular localisation prediction" }, { "uri": "http://edamontology.org/operation_3096", "term": "Editing" }, { "uri": "http://edamontology.org/operation_2454", "term": "Gene prediction" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0099", "term": "RNA" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" }, { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://prep.unl.edu/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": null, "pmid": "19433507", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "The PREP suite: Predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments", "abstract": "RNA editing alters plant mitochondrial and chloroplast transcripts by converting specific cytidines to uridines, which usually results in a change in the amino acid sequence of the translated protein. Systematic studies have experimentally identified sites of RNA editing in organellar transcriptomes from several species, but these analyses have not kept pace with rate of genome sequencing. The PREP (predictive RNA editors for plants) suite was developed to computationally predict sites of RNA editing based on the well-known principle that editing in plant organelles increases the conservation of proteins across species. The PREP suite provides predictive RNA editors for plant mitochondrial genes (PREP-Mt), for chloroplast genes (PREP-Cp), and for alignments submitted by the user (PREP-Aln). These servers require minimal input, are very fast, and are highly accurate on all seed plants examined to date. PREP-Mt has proved useful in several research studies and the newly developed PREP-Cp and PREP-Aln servers should be of further assistance for analyses that require knowledge of the location of sites of RNA editing. The PREP suite is freely available at http://prep.unl.edu/.", "date": "2009-08-04T00:00:00Z", "citationCount": 154, "authors": [ { "name": "Mower J.P." } ], "journal": "Nucleic Acids Research" } }, { "doi": null, "pmid": "15826309", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "PREP-Mt: Predictive RNA editor for plant mitochondrial genes", "abstract": "Background: In plants, RNA editing is a process that converts specific cytidines to uridines and uridines to cytidines in transcripts from virtually all mitochondrial protein-coding genes. There are thousands of plant mitochondrial genes in the sequence databases, but sites of RNA editing have not been determined for most. Accurate methods of RNA editing site prediction will be important in filling in this information gap and could reduce or even eliminate the need for experimental determination of editing sites for many sequences. Because RNA editing tends to increase protein conservation across species by \"correcting\" codons that specify unconserved amino acids, this principle can be used to predict editing sites by identifying positions where an RNA editing event would increase the conservation of a protein to homologues from other plants. PREP-Mt takes this approach to predict editing sites for any protein-coding gene in plant mitochondria. Results: To test the general applicability of the PREP-Mt methodology, RNA editing sites were predicted for 370 full-length or nearly full-length DNA sequences and then compared to the known sites of RNA editing for these sequences. Of 60,263 cytidines in this test set, PREP-Mt correctly classified 58,994 as either an edited or unedited site (accuracy = 97.9%). PREP-Mt properly identified 3,038 of the 3,698 known sites of RNA editing (sensitivity = 82.2%) and 55,956 of the 56,565 known unedited sites (specificity = 98.9%). Accuracy and sensitivity increased to 98.7% and 94.7%, respectively, after excluding the 489 silent editing sites (which have no effect on protein sequence or function) from the test set. Conclusion: These results indicate that PREP-Mt is effective at identifying C to U RNA editing sites in plant mitochondrial protein-coding genes. Thus, PREP-Mt should be useful in predicting protein sequences for use in molecular, biochemical, and phylogenetic analyses. In addition, PREP-Mt could be used to determine functionality of a mitochondrial gene or to identify particular sequences with unusual editing properties. The PREP-Mt methodology should be applicable to any system where RNA editing increases protein conservation across species. © 2005 Mower; licensee BioMed Central Ltd.", "date": "2005-04-12T00:00:00Z", "citationCount": 74, "authors": [ { "name": "Mower J.P." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Jeff Mower", "email": "jmower2@unl.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-02-14T09:35:15Z", "lastUpdate": "2025-01-08T15:03:40.568675Z", "editPermission": { "type": "group", "authors": [ "huahahajjd", "thidasoe" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SwissTargetPrediction", "description": "SwissTargetPrediction is a web server for target prediction of bioactive small molecules. This website allows you to predict the targets of a small molecule. Using a combination of 2D and 3D similarity measures, it compares the query molecule to a library of 280 000 compounds active on more than 2000 targets of 5 different organisms.", "homepage": "http://www.swisstargetprediction.ch", "biotoolsID": "swisstargetprediction", "biotoolsCURIE": "biotools:swisstargetprediction", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2489", "term": "Protein subcellular localisation prediction" }, { "uri": "http://edamontology.org/operation_0478", "term": "Molecular docking" }, { "uri": "http://edamontology.org/operation_2492", "term": "Protein interaction prediction" }, { "uri": "http://edamontology.org/operation_2575", "term": "Protein binding site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0209", "term": "Medicinal chemistry" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" }, { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.swisstargetprediction.ch/help.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gku293", "pmid": "24792161", "pmcid": "PMC4086140", "type": [], "version": null, "note": null, "metadata": { "title": "SwissTargetPrediction: A web server for target prediction of bioactive small molecules", "abstract": "Bioactive small molecules, such as drugs or metabolites, bind to proteins or other macro-molecular targets to modulate their activity, which in turn results in the observed phenotypic effects. For this reason, mapping the targets of bioactive small molecules is a key step toward unraveling the molecular mechanisms underlying their bioactivity and predicting potential side effects or cross-reactivity. Recently, large datasets of protein-small molecule interactions have become available, providing a unique source of information for the development of knowledge-based approaches to computationally identify new targets for uncharacterized molecules or secondary targets for known molecules. Here, we introduce SwissTargetPrediction, a web server to accurately predict the targets of bioactive molecules based on a combination of 2D and 3D similarity measures with known ligands. Predictions can be carried out in five different organisms, and mapping predictions by homology within and between different species is enabled for close paralogs and orthologs. SwissTargetPrediction is accessible free of charge and without login requirement at http://www. swisstargetprediction.ch. © 2014 The Author(s).", "date": "2014-07-01T00:00:00Z", "citationCount": 404, "authors": [ { "name": "Gfeller D." }, { "name": "Grosdidier A." }, { "name": "Wirth M." }, { "name": "Daina A." }, { "name": "Michielin O." }, { "name": "Zoete V." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "SIB Swiss Institute of Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "Contact Form", "email": null, "url": "http://www.swisstargetprediction.ch/contact.php", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mozyme2001", "additionDate": "2017-05-16T13:43:22Z", "lastUpdate": "2024-11-20T17:39:22.939120Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "stringMLST", "description": "stringMLST is a tool for detecting the MLST of an isolate directly from the genome sequencing reads. stringMLST predicts the ST of an isolate in a completely assembly and alignment free manner.", "homepage": "http://jordan.biology.gatech.edu/page/software/stringmlst/index.html", "biotoolsID": "stringmlst", "biotoolsCURIE": "biotools:stringmlst", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0654", "term": "DNA" }, { "uri": "http://edamontology.org/topic_0196", "term": "Assembly" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/stringmlst-an-ultrafast-k-mer-based-mlst-tool.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://jordan.biology.gatech.edu/page/software/stringmlst/README.txt", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btw586", "pmid": "27605103", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "stringMLST: A fast k-mer based tool for multilocus sequence typing", "abstract": "© The Author 2016. Published by Oxford University Press. All rights reserved.Rapid and accurate identification of the sequence type (ST) of bacterial pathogens is critical for epidemiological surveillance and outbreak control. Cheaper and faster next-generation sequencing (NGS) technologies have taken preference over the traditional method of amplicon sequencing for multilocus sequence typing (MLST). But data generated by NGS platforms necessitate quality control, genome assembly and sequence similarity searching before an isolate's ST can be determined. These are computationally intensive and time consuming steps, which are not ideally suited for real-time molecular epidemiology. Here, we present stringMLST, an assembly- and alignment-free, lightweight, platform-independent program capable of rapidly typing bacterial isolates directly from raw sequence reads. The program implements a simple hash table data structure to find exact matches between short sequence strings (k-mers) and an MLST allele library. We show that stringMLST is more accurate, and order of magnitude faster, than its contemporary genome-based ST detection tools.", "date": "2017-01-01T00:00:00Z", "citationCount": 33, "authors": [ { "name": "Gupta A." }, { "name": "Jordan I.K." }, { "name": "Rishishwar L." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Support", "email": "king.jordan@biology.gatech.edu", "url": "http://jordan.biology.gatech.edu/page/index.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-12-18T00:15:41Z", "lastUpdate": "2024-11-07T10:34:19.548191Z", "editPermission": { "type": "group", "authors": [ "rlibouban" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "VelvetOptimiser", "description": "This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.", "homepage": "https://github.com/Slugger70/VelvetOptimiser", "biotoolsID": "velvetoptimiser", "biotoolsCURIE": "biotools:velvetoptimiser", "version": [ "2.2.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2425", "term": "Optimisation and refinement" }, { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": "GPL-2.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/Slugger70/VelvetOptimiser/blob/master/README", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Torsten Seemann", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Simon Gladman", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "University of Melbourne", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "unimelb.edu.au", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Simon Gladman", "email": "simon.gladman@unimelb.edu.au", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Torsten Seemann", "email": "torsten.seemann@unimelb.edu.au", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Australia", "email": null, "url": "https://github.com/tseemann/VelvetOptimiser/issues", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "griffinp@unimelb.edu.au", "additionDate": "2016-09-21T06:49:37Z", "lastUpdate": "2024-11-06T09:50:52.192442Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "rlibouban" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "snippy", "description": "Rapid haploid variant calling and core SNP phylogeny generation.", "homepage": "https://github.com/tseemann/snippy", "biotoolsID": "snippy", "biotoolsCURIE": "biotools:snippy", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0567", "term": "Phylogenetic tree visualisation" }, { "uri": "http://edamontology.org/operation_0323", "term": "Phylogenetic tree generation" }, { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" } ], "input": [], "output": [], "note": "Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can then take a set of Snippy results using the same reference and generate a core SNP alignment (and ultimately a phylogenomic tree).", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/tseemann/snippy/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/tseemann/snippy/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Torsten Seemann", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "University of Melbourne, Australia", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "unimelb.edu.au", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Torsten Seemann", "email": "torsten.seemann@gmail.com", "url": "https://github.com/tseemann/snippy/issues", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Australia", "email": null, "url": "https://github.com/tseemann/snippy/issues", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "griffinp@unimelb.edu.au", "additionDate": "2016-09-02T00:53:09Z", "lastUpdate": "2023-11-02T09:06:08.194721Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "LightDock", "description": "It is a protein-protein docking framework based on the Glowworm Swarm Optimization algorithm.\nThe framework is highly versatile, with many options that can be further developed and optimized by the users: it can accept any user-defined scoring function, can use local gradient-free minimization, the simulation can be restrained from the beginning to focus on user-assigned interacting regions, and it has support for the use of pre-calculated conformers for both receptor and ligand.", "homepage": "https://life.bsc.es/pid/lightdock/", "biotoolsID": "lightdock", "biotoolsCURIE": "biotools:lightdock", "version": [ "0.4.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2464", "term": "Protein-protein interaction prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2877", "term": "Protein complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2877", "term": "Protein complex" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "Other", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/brianjimenez/lightdock", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://readthedocs.org/projects/lightdock/", "type": [ "API documentation" ], "note": null }, { "url": "https://github.com/brianjimenez/lightdock/blob/master/README.md", "type": [ "User manual" ], "note": null }, { "url": "https://github.com/brianjimenez/lightdock/blob/master/LICENSE", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": null, "pmid": "28968719", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "LightDock: A new multi-scale approach to protein-protein docking", "abstract": "© 2017 The Author.Motivation: Computational prediction of protein-protein complex structure by docking can provide structural and mechanistic insights for protein interactions of biomedical interest. However, current methods struggle with difficult cases, such as those involving flexible proteins, low-affinity complexes or transient interactions. A major challenge is how to efficiently sample the structural and energetic landscape of the association at different resolution levels, given that each scoring function is often highly coupled to a specific type of search method. Thus, new methodologies capable of accommodating multi-scale conformational flexibility and scoring are strongly needed. Results: We describe here a new multi-scale protein-protein docking methodology, LightDock, capable of accommodating conformational flexibility and a variety of scoring functions at different resolution levels. Implicit use of normal modes during the search and atomic/coarse-grained combined scoring functions yielded improved predictive results with respect to state-of-the-art rigidbody docking, especially in flexible cases.", "date": "2018-01-01T00:00:00Z", "citationCount": 29, "authors": [ { "name": "Jimenez-Garcia B." }, { "name": "Roel-Touris J." }, { "name": "Romero-Durana M." }, { "name": "Vidal M." }, { "name": "Jimenez-Gonzalez D." }, { "name": "Fernandez-Recio J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Brian Jimenez", "email": "brian.jimenez@bsc.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-11-02T09:30:52Z", "lastUpdate": "2023-10-24T07:35:50.760785Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SwarmDock", "description": "Generating 3D structures of protein-protein complexes. Allows flexible modelling of protein-protein complexes using the SwarmDock algorithm which incorporates a normal modes approach.", "homepage": "http://bmm.cancerresearchuk.org/~SwarmDock/index.html", "biotoolsID": "swarmdock", "biotoolsCURIE": "biotools:swarmdock", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0478", "term": "Protein docking" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/swarmdock-webservice-generating-3d-structures-protein-protein-complexes.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://life.bsc.es/pid/ccharppi/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btt038", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "SwarmDock: A server for flexible protein-protein docking", "abstract": "Protein-protein interactions are central to almost all biological functions, and the atomic details of such interactions can yield insights into the mechanisms that underlie these functions.We present a web server that wraps and extends the SwarmDock flexible protein- protein docking algorithm. After uploading PDB files of the binding partners, the server generates low energy conformations and returns a ranked list of clustered docking poses and their corresponding structures. The user can perform full global docking, or focus on particular residues that are implicated in binding. The server is validated in the CAPRI blind docking experiment, against the most current docking benchmark, and against the ClusPro docking server, the highest performing server currently available. © The Author 2013.", "date": "2013-03-01T00:00:00Z", "citationCount": 165, "authors": [ { "name": "Torchala M." }, { "name": "Moal I.H." }, { "name": "Chaleil R.A.G." }, { "name": "Fernandez-Recio J." }, { "name": "Bates P.A." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": null, "email": null, "url": "http://bmm.cancerresearchuk.org/index.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "xiaobing", "additionDate": "2017-12-18T00:13:22Z", "lastUpdate": "2023-04-19T09:34:03.998128Z", "editPermission": { "type": "group", "authors": [ "xiaobing" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Protein Frustratometer", "description": "The Protein Frustratometer is an energy landscape theory inspired algorithm that aims at quantifying the degree of local frustration manifested in protein molecules. By analyzing protein frustration one can gain insight into protein biological function and how mutations alter this function.", "homepage": "http://lfp.qb.fcen.uba.ar/embnet/charge.php?app=Frustratometer&chains=NO", "biotoolsID": "protein_frustratometer", "biotoolsCURIE": "biotools:protein_frustratometer", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" }, { "uri": "http://edamontology.org/operation_2415", "term": "Protein folding analysis" }, { "uri": "http://edamontology.org/operation_0303", "term": "Protein fold recognition" }, { "uri": "http://edamontology.org/operation_0331", "term": "Protein modelling (mutation)" }, { "uri": "http://edamontology.org/operation_0474", "term": "Protein structure prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": null, "pmid": "22645321", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Protein frustratometer: A tool to localize energetic frustration in protein molecules", "abstract": "The frustratometer is an energy landscape theory-inspired algorithm that aims at quantifying the location of frustration manifested in protein molecules. Frustration is a useful concept for gaining insight to the proteins biological behavior by analyzing how the energy is distributed in protein structures and how mutations or conformational changes shift the energetics. Sites of high local frustration often indicate biologically important regions involved in binding or allostery. In contrast, minimally frustrated linkages comprise a stable folding core of the molecule that is conserved in conformational changes. Here, we describe the implementation of these ideas in a webserver freely available at the National EMBNet node-Argentina, at URL: http://lfp.qb.fcen.uba. ar/embnet/. © 2012 The Author(s).", "date": "2012-07-01T00:00:00Z", "citationCount": 89, "authors": [ { "name": "Jenik M." }, { "name": "Parra R.G." }, { "name": "Radusky L.G." }, { "name": "Turjanski A." }, { "name": "Wolynes P.G." }, { "name": "Ferreiro D.U." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Dr. Ignacio E. Sánchez", "email": "isanchez@qb.fcen.uba.ar", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Dr. Adrián G. Turjanski", "email": "adrian@qb.fcen.uba.ar", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Msc. Leandro G. Radusky", "email": "embnet@qb.fcen.uba.ar", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-03-25T13:09:45Z", "lastUpdate": "2022-11-07T14:53:37.248643Z", "editPermission": { "type": "group", "authors": [ "gparra" ] }, "validated": 1, "homepage_status": 1, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioModels Database Converters", "description": "Set of converters between various modelling formats, there are also some available online to be used directly.", "homepage": "http://www.ebi.ac.uk/compneur-srv/converters/converters", "biotoolsID": "biomodels_database_converters", "biotoolsCURIE": "biotools:biomodels_database_converters", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0950", "term": "Mathematical model" }, "format": [ { "uri": "http://edamontology.org/format_2585", "term": "SBML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0950", "term": "Mathematical model" }, "format": [ { "uri": "http://edamontology.org/format_2585", "term": "SBML" }, { "uri": "http://edamontology.org/format_3156", "term": "BioPAX" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://www.ebi.ac.uk/compneur-srv/sbml/converters/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkv1352", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The European Bioinformatics Institute in 2016: Data growth and integration", "abstract": "© The Author(s) 2015.New technologies are revolutionising biological research and its applications by making it easier and cheaper to generate ever-greater volumes and types of data. In response, the services and infrastructure of the European Bioinformatics Institute (EMBL-EBI, www.ebi.ac.UK) are continually expanding: total disk capacity increases significantly every year to keep pace with demand (75 petabytes as of December 2015), and interoperability between resources remains a strategic priority. Since 2014 we have launched two new resources: the European Variation Archive for genetic variation data and EMPIAR for two-dimensional electron microscopy data, as well as a Resource Description Framework platform. We also launched the Embassy Cloud service, which allows users to run large analyses in a virtual environment next to EMBL-EBI's vast public data resources.", "date": "2016-01-01T00:00:00Z", "citationCount": 78, "authors": [ { "name": "Cook C.E." }, { "name": "Bergman M.T." }, { "name": "Finn R.D." }, { "name": "Cochrane G." }, { "name": "Birney E." }, { "name": "Apweiler R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "BioModels Team", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "biomodels-net-support@lists.sf.net", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Camille Laibe", "email": "laibe@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "rsmsheriff", "additionDate": "2015-01-29T15:46:48Z", "lastUpdate": "2022-08-08T16:44:29.661404Z", "editPermission": { "type": "group", "authors": [ "rsmsheriff" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "bedtools_coveragebed_counts", "description": "Count the number of intervals in a BAM or BED file (the source) that overlap another BED file (the target).", "homepage": "https://github.com/arq5x/bedtools3", "biotoolsID": "bedtools_coveragebed_counts", "biotoolsCURIE": "biotools:bedtools_coveragebed_counts-ip", "version": [ "0.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] }, { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Shell", "Python" ], "license": null, "collectionID": [ "galaxyPasteur", "bedtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/bedtools_pasteur/bedtools_coveragebed_counts/0.1.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "http://quinlanlab.org/tutorials/bedtools/bedtools.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btq033", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "BEDTools: A flexible suite of utilities for comparing genomic features", "abstract": "Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing webbased methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools. Contact: aaronquinlan@gmail.com; imh4y@virginia.edu. Supplementary information: Supplementary data are available at Bioinformatics online. © The Author(s) 2010. Published by Oxford University Press.", "date": "2010-01-28T00:00:00Z", "citationCount": 8825, "authors": [ { "name": "Quinlan A.R." }, { "name": "Hall I.M." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1025, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Von Kuster G." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic acids research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:29:58Z", "lastUpdate": "2022-06-01T04:14:29.977329Z", "editPermission": { "type": "group", "authors": [ "tcollins" ] }, "validated": 1, "homepage_status": 1, "elixir_badge": 0, "confidence_flag": null }, { "name": "GPU-BSM", "description": "GPU-BSM (GPU-BiSulfite reads Mapping) is a GPU-based tool devised to map bisulfite-treated reads.", "homepage": "http://www.itb.cnr.it/web/bioinformatics/gpu-bsm", "biotoolsID": "gpu-bsm", "biotoolsCURIE": "biotools:gpu-bsm", "version": [ "2.7.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2429", "term": "Mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0654", "term": "DNA" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/gpu-bsm-bs-treated-reads-mapping-tool.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "https://www.itb.cnr.it/documents/11811/167605/Manual.pdf/20130bee-621c-4cff-aafe-a34d8426d98b", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": null, "email": null, "url": "http://www.itb.cnr.it/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-12-18T00:06:54Z", "lastUpdate": "2022-05-11T07:20:17.692153Z", "editPermission": { "type": "group", "authors": [ "zyndagj" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "COBRApy", "description": "COnstraints-Based Reconstruction and Analysis for Python.", "homepage": "https://github.com/opencobra/cobrapy", "biotoolsID": "cobrapy", "biotoolsCURIE": "biotools:cobrapy", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3660", "term": "Metabolic network modelling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://cobrapy.readthedocs.io/en/stable/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1752-0509-7-74", "pmid": "23927696", "pmcid": "PMC3751080", "type": [], "version": null, "note": null, "metadata": { "title": "COBRApy: COnstraints-Based Reconstruction and Analysis for Python", "abstract": "Background: COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. Due to the successes with metabolism, there is an increasing effort to apply COBRA methods to reconstruct and analyze integrated models of cellular processes. The COBRA Toolbox for MATLAB is a leading software package for genome-scale analysis of metabolism; however, it was not designed to elegantly capture the complexity inherent in integrated biological networks and lacks an integration framework for the multiomics data used in systems biology. The openCOBRA Project is a community effort to promote constraints-based research through the distribution of freely available software.Results: Here, we describe COBRA for Python (COBRApy), a Python package that provides support for basic COBRA methods. COBRApy is designed in an object-oriented fashion that facilitates the representation of the complex biological processes of metabolism and gene expression. COBRApy does not require MATLAB to function; however, it includes an interface to the COBRA Toolbox for MATLAB to facilitate use of legacy codes. For improved performance, COBRApy includes parallel processing support for computationally intensive processes.Conclusion: COBRApy is an object-oriented framework designed to meet the computational challenges associated with the next generation of stoichiometric constraint-based models and high-density omics data sets. © 2013 Ebrahim et al.; licensee BioMed Central Ltd.", "date": "2013-08-08T00:00:00Z", "citationCount": 380, "authors": [ { "name": "Ebrahim A." }, { "name": "Lerman J.A." }, { "name": "Palsson B.O." }, { "name": "Hyduke D.R." } ], "journal": "BMC Systems Biology" } } ], "credit": [ { "name": "openCOBRA", "email": null, "url": "https://github.com/opencobra", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-04-29T10:20:37Z", "lastUpdate": "2022-05-04T09:45:45.501716Z", "editPermission": { "type": "group", "authors": [ 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}, { "uri": "http://edamontology.org/operation_0438", "term": "Regulatory element prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_0204", "term": "Gene regulation" }, { "uri": "http://edamontology.org/topic_0749", "term": "Transcription factors and regulatory sites" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": null, "pmid": "12824433", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "FootPrinter: A program designed for phylogenetic footprinting", "abstract": "Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of homologous regulatory regions, usually collected from multiple species. It does so by identifying the best conserved motifs in those homologous regions. This note describes web software that has been designed specifically for this purpose, making use of the phylogenetic relationships among the homologous sequences in order to make more accurate predictions. The software is called FootPrinter and is available at http://bio.cs.washington.edu/software.html.", "date": "2003-07-01T00:00:00Z", "citationCount": 136, "authors": [ { "name": "Blanchette M." }, { "name": "Tompa M." } ], "journal": "Nucleic Acids Research" } }, { "doi": null, "pmid": "12015878", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Algorithms for phylogenetic footprinting", "abstract": "Phylogenetic footprinting is a technique that identifies regulatory elements by finding unusually well conserved regions in a set of orthologous noncoding DNA sequences from multiple species. We introduce a new motif-finding problem, the Substring Parsimony Problem, which is a formalization of the ideas behind phylogenetic footprinting, and we present an exact dynamic programming algorithm to solve it. We then present a number of algorithmic optimizations that allow our program to run quickly on most biologically interesting datasets. We show how to handle data sets in which only an unknown subset of the sequences contains the regulatory element. Finally, we describe how to empirically assess the statistical significance of the motifs found. Each technique is implemented and successfully identifies a number of known binding sites, as well as several highly conserved but uncharacterized regions. The program is available at http://bio.cs.washington.edu/software.html.", "date": "2002-06-03T00:00:00Z", "citationCount": 109, "authors": [ { "name": "Blanchette M." }, { "name": "Schwikowski B." }, { "name": "Tompa M." } ], "journal": "Journal of Computational Biology" } }, { "doi": null, "pmid": "16845027", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MicroFootPrinter: A tool for phylogenetic footprinting in prokaryotic genomes", "abstract": "Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of homologous regulatory regions, usually collected from multiple species. It does so by identifying the most conserved motifs in those homologous regions. This note describes web software that has been designed specifically for this purpose in prokaryotic genomes, making use of the phylogenetic relationships among the homologous sequences in order to make more accurate predictions. The software is called MicroFootPrinter and is available at http://bio.cs.washington.edu/software.html. © The Author 2006. Published by Oxford University Press. All rights reserved.", "date": "2006-07-01T00:00:00Z", "citationCount": 22, "authors": [ { "name": "Neph S." }, { "name": "Tompa M." } ], "journal": "Nucleic Acids Research" } }, { "doi": null, "pmid": "11997340", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Discovery of regulatory elements by a computational method for phylogenetic footprinting", "abstract": "Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the phylogenetic relationships among the sequences under study to make more accurate predictions. The program is guaranteed to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phylogenetic tree relating the input species. We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known.", "date": "2002-06-03T00:00:00Z", "citationCount": 239, "authors": [ { "name": "Blanchette M." }, { "name": "Tompa M." } ], "journal": "Genome Research" } } ], "credit": [ { "name": "Martin Tompa", "email": "tompa@cs.washington.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-02-10T14:15:33Z", "lastUpdate": "2022-03-15T10:32:30.884689Z", "editPermission": { "type": "group", "authors": [ "jesalazar" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FNBtools", "description": "Software to Identify Homozygous Lesions in Deletion Mutant Populations.", "homepage": "https://github.com/noble-research-institute/fnbtools", "biotoolsID": "fnbtools", "biotoolsCURIE": "biotools:fnbtools", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/noble-research-institute/fnbtools", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.3389/fpls.2018.00976", "pmid": "30042776", "pmcid": "PMC6048286", "type": [], "version": null, "note": null, "metadata": { "title": "FNBtools: A software to identify homozygous lesions in deletion mutant populations", "abstract": "© 2018 Sun, Ge, Bancroft, Cheng and Wen.Deletion mutagenesis such as fast neutron bombardment (FNB) has been widely used for forward and reverse genetics studies in functional genomics. Traditionally, the time-consuming map-based cloning is used to locate causal deletions in deletion mutants. In recent years, comparative genomic hybridization (CGH) has been used to speed up and scale up the lesion identification process in deletion mutants. However, limitations of low accuracy and sensitivity for small deletions in the CGH approach are apparent. With the next generation sequencing (NGS) becoming affordable for most users, NGS-based bioinformatics tools are more appealing. Although several deletion callers are available, these tools are not efficient in detecting small deletions. Population-scale deletion callers that can identify both small and large deletions are rare. We were motivated to create a population-scale deletion detection tool, called FNBtools, to identify homozygous causal deletions in mutant populations by using NGS data. FNBtools is a tool to call deletions at a population-scale and to achieve high accuracy at different levels of coverage. In addition, FNBtools can detect both small and large deletions with the ability to identify unique deletions in a mutant pool by filtering deletions that exist in a wild-type or control pool. Furthermore, FNBtools is also able to visualize all identified deletions in a genome-wide scope by using Circos. From simulated data analysis, FNBtools outperforms four existing popular deletion callers in detecting small deletions at different coverage levels. To test the usefulness of FNBtools in real biological applications, we used it to analyze a salt-tolerant mutant in Medicago truncatula and identified the unique deletion locus that is tightly linked with this trait. The causal deletion in the mutant was confirmed by PCR amplification, sequencing and genetic linkage analyses. FNBtools can be used for homozygous deletion identification in any species with reference genome sequences. FNBtools is publicly available at: https://github.com/noble-research-institute/fnbtools.", "date": "2018-07-10T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Sun L." }, { "name": "Ge Y." }, { "name": "Bancroft A.C." }, { "name": "Cheng X." }, { "name": "Wen J." } ], "journal": "Frontiers in Plant Science" } } ], "credit": [ { "name": "Liang Sun", "email": "lsun@noble.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Jiangqi Wen", "email": "jwen@noble.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "keke2", "additionDate": "2018-07-29T08:47:59Z", "lastUpdate": "2021-10-14T08:51:40.221506Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DRAR-CPI", "description": "DRAR-CPI is a web server for the identification of drug repositioning and adverse drug reactions using mining of a chemical-protein interactome.", "homepage": "http://cpi.bio-x.cn/drar/", "biotoolsID": "drar-cpi", "biotoolsCURIE": "biotools:drar-cpi", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0478", "term": "Molecular docking" }, { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" }, { "uri": "http://edamontology.org/operation_3280", "term": "Named-entity and concept recognition" }, { "uri": "http://edamontology.org/operation_2436", "term": "Gene-set enrichment analysis" }, { "uri": "http://edamontology.org/operation_2492", "term": "Protein interaction prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3377", "term": "Safety sciences" }, { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" }, { "uri": "http://edamontology.org/topic_3379", "term": "Preclinical and clinical studies" }, { "uri": "http://edamontology.org/topic_3373", "term": "Drug development" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://cpi.bio-x.cn/drar/?page=help", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkr299", "pmid": "21558322", "pmcid": "PMC3125745", "type": [], "version": null, "note": null, "metadata": { "title": "DRAR-CPI: A server for identifying drug repositioning potential and adverse drug reactions via the chemical-protein interactome", "abstract": "Identifying new indications for existing drugs (drug repositioning) is an efficient way of maximizing their potential. Adverse drug reaction (ADR) is one of the leading causes of death among hospitalized patients. As both new indications and ADRs are caused by unexpected chemical-protein interactions on off-targets, it is reasonable to predict these interactions by mining the chemical-protein interactome (CPI). Making such predictions has recently been facilitated by a web server named DRAR-CPI. This server has a representative collection of drug molecules and targetable human proteins built up from our work in drug repositioning and ADR. When a user submits a molecule, the server will give the positive or negative association scores between the user's molecule and our library drugs based on their interaction profiles towards the targets. Users can thus predict the indications or ADRs of their molecule based on the association scores towards our library drugs. We have matched our predictions of drug-drug associations with those predicted via gene-expression profiles, achieving a matching rate as high as 74. We have also successfully predicted the connections between anti-psychotics and anti-infectives, indicating the underlying relevance of anti-psychotics in the potential treatment of infections, vice versa. This server is freely available at http://cpi.bio-x.cn/drar/. © 2011 The Author(s).", "date": "2011-07-01T00:00:00Z", "citationCount": 163, "authors": [ { "name": "Luo H." }, { "name": "Chen J." }, { "name": "Shi L." }, { "name": "Mikailov M." }, { "name": "Zhu H." }, { "name": "Wang K." }, { "name": "He L." }, { "name": "Yang L." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "DRAR-CPI Support", "email": "cpiserver@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-05-16T12:28:08Z", "lastUpdate": "2021-06-09T09:37:58Z", "editPermission": { "type": "group", "authors": [ "CoCo" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GREAT:SCAN:multipatterns", "description": "This tool performs, in a systematic way, an automated analysis of regular arrangements in organisms having multiple chromosomes, for different transcription factors (or regulators, conditions) at the same time. It reports and allows identification of periodic regions of target genes for the different conditions, on each chromosome.", "homepage": "https://absynth.issb.genopole.fr/Bioinformatics/tools/GREAT/index", "biotoolsID": "greatscanmultipatterns", "biotoolsCURIE": "biotools:greatscanmultipatterns", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1893", "term": "Locus ID" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_2755", "term": "Transcription factor name" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_1016", "term": "Sequence position" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "Detection and analysis of periods in the position of the targets of multiple TF/regulators. The targets of the studied transcription factors (or conditions/regulators). Transcriptions factors (or any conditions or regulators). Positions of the targets of the studied transcription factors (or conditions/regulators). Rich and interactive visualisations of the regular patterns found during the analysis. Machine-readable files of the results of each step of the analysis.", "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://absynth.issb.genopole.fr/Bioinformatics/tools/GREAT/help#docker_integrated", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://absynth.issb.genopole.fr/Bioinformatics/tools/GREAT/help#docker_integrated", "type": "Source code", "note": null, "version": null }, { "url": "https://absynth.issb.genopole.fr/Bioinformatics/tools/GREAT/help#docker_integrated", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://absynth.issb.genopole.fr/Bioinformatics/tools/GREAT/help#integrated_help", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkw384", "pmid": null, "pmcid": null, "type": [ "Review" ], "version": null, "note": null, "metadata": { "title": "GREAT: a web portal for Genome Regulatory Architecture Tools", "abstract": "© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.GREAT (Genome REgulatory Architecture Tools) is a novel web portal for tools designed to generate user-friendly and biologically useful analysis of genome architecture and regulation. The online tools of GREAT are freely accessible and compatible with essentially any operating system which runs a modern browser. GREAT is based on the analysis of genome layout -defined as the respective positioning of co-functional genes- and its relation with chromosome architecture and gene expression. GREAT tools allow users to systematically detect regular patterns along co-functional genomic features in an automatic way consisting of three individual steps and respective interactive visualizations. In addition to the complete analysis of regularities, GREAT tools enable the use of periodicity and position information for improving the prediction of transcription factor binding sites using a multi-view machine learning approach. The outcome of this integrative approach features a multivariate analysis of the interplay between the location of a gene and its regulatory sequence. GREAT results are plotted in web interactive graphs and are available for download either as individual plots, self-contained interactive pages or as machine readable tables for downstream analysis. The GREAT portal can be reached at the following URL https://absynth.issb.genopole.fr/GREAT and each individual GREAT tool is available for downloading.", "date": "2016-07-08T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Bouyioukos C." }, { "name": "Bucchini F." }, { "name": "Elati M." }, { "name": "Kepes F." } ], "journal": "Nucleic acids research" } } ], "credit": [ { "name": "François Bucchini", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Institute of Systems and Synthetic Biology", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "issb.genopole.fr", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "MEGA team", "email": null, "url": "https://absynth.issb.genopole.fr/Bioinformatics/tools/GREAT/contact", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "MEGA team", "email": null, "url": "https://absynth.issb.genopole.fr/Bioinformatics/tools/GREAT/contact", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "francois_b", "additionDate": "2016-03-24T22:14:54Z", "lastUpdate": "2021-03-26T08:59:40Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DRAWID", "description": "Chromosome analysis and idiogram construction.", "homepage": "http://www.drawid.xyz/", "biotoolsID": "drawid", "biotoolsCURIE": "biotools:drawid", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.drawid.xyz/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.3897/CompCytogen.v11i4.20830", "pmid": "29302295", "pmcid": "PMC5740402", "type": [], "version": null, "note": null, "metadata": { "title": "DRAWID: User-friendly java software for chromosome measurements and idiogram drawing", "abstract": "© Ilya Kirov et al.An idiogram construction following chromosome measurements is a versatile tool for cytological, cytogenetic and phylogenetic studies. The information on chromosome length, centromere index and position of cytogenetic landmarks along with modern techniques (e.g. genomic and fluorescence in situ hybridization, banding, chromosome painting) can help to shed light on genome constitution, chromosome rearrangements and evolution. While idiogram construction is a routine task there are only few freely available programs that can perform chromosome measurements and no software for simultaneous measuring of chromosome parameters, chromosomal landmark and FISH signal positions and idiogram construction. To fill this gap, we developed DRAWID (DRAWing IDiogram), java-based cross-platforming program for chromosome analysis and idiogram construction. DRAWID has number of advantages including a user-friendly interactive interface, possibility for simultaneous chromosome and FISH/GISH/banding signal measurement and idiogram drawing as well as number of useful functions facilitating the procedure of chromosome analysis. The output of the program is Microsoft XL table and publish-ready idiogram picture. DRAWID and the manual for its use are freely available on the website at: http://www.drawid.xyz.", "date": "2017-01-01T00:00:00Z", "citationCount": 24, "authors": [ { "name": "Kirov I." }, { "name": "Khrustaleva L." }, { "name": "Van Laere K." }, { "name": "Soloviev A." }, { "name": "Meeus S." }, { "name": "Romanov D." }, { "name": "Fesenko I." } ], "journal": "Comparative Cytogenetics" } } ], "credit": [ { "name": "Ilya Kirov", "email": "kirovez@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "SolAcosta", "additionDate": "2018-07-22T08:19:46Z", "lastUpdate": "2020-12-14T08:50:34Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BATEx", "description": "The aim of BATEx is the establishment of a data warehouse for array-based gene expression data of plants to enable experiment-spanning expression data analyses. Therefore, data is integrated from various data sources, such as BarleyBase, AtGenExpress, AFGC, TIGR SGED and IPK’s operational system FLAREX.", "homepage": "http://pgrc.ipk-gatersleben.de/batex/", "biotoolsID": "batex", "biotoolsCURIE": "biotools:batex", "version": [ "0.1.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2495", "term": "Microarray data analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0780", "term": "Plant" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plants" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/batex-0-1-2-data-warehouse-array-based-gene-expression-data-plants.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": null, "email": null, "url": "http://pgrc.ipk-gatersleben.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ipk", "additionDate": "2017-12-18T00:03:51Z", "lastUpdate": "2020-10-15T07:12:34Z", "editPermission": { "type": "group", "authors": [ "ipk" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CleavPredict", "description": "A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events.", "homepage": "http://cleavpredict.sanfordburnham.org/", "biotoolsID": "cleavpredict", "biotoolsCURIE": "biotools:cleavpredict", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0250", "term": "Protein property calculation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3534", "term": "Protein binding sites" }, { "uri": "http://edamontology.org/topic_0821", "term": "Enzymes" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://cleavpredict.sanfordburnham.org/tutorial", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/JOURNAL.PONE.0127877", "pmid": "25996941", "pmcid": "PMC4440711", "type": [], "version": null, "note": null, "metadata": { "title": "CleavPredict: A platform for reasoning about matrix metalloproteinases proteolytic events", "abstract": "© 2015 Kumar et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.CleavPredict (http://cleavpredict.sanfordburnham.org) is a Web server for substrate cleavage prediction for matrix metalloproteinases (MMPs). It is intended as a computational platform aiding the scientific community in reasoning about proteolytic events. CleavPredict offers in silico prediction of cleavage sites specific for 11 human MMPs. The prediction method employs the MMP specific position weight matrices (PWMs) derived from statistical analysis of high-throughput phage display experimental results. To augment the substrate cleavage prediction process, CleavPredict provides information about the structural features of potential cleavage sites that influence proteolysis. These include: secondary structure, disordered regions, transmembrane domains, and solvent accessibility. The server also provides information about subcellular location, co-localization, and co-expression of proteinase and potential substrates, along with experimentally determined positions of single nucleotide polymorphism (SNP), and posttranslational modification (PTM) sites in substrates. All this information will provide the user with perspectives in reasoning about proteolytic events. CleavPredict is freely accessible, and there is no login required.", "date": "2015-05-21T00:00:00Z", "citationCount": 31, "authors": [ { "name": "Kumar S." }, { "name": "Ratnikov B.I." }, { "name": "Kazanov M.D." }, { "name": "Smith J.W." }, { "name": "Cieplak P.C." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "Support", "email": "skumar@sanfordburnham.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Support", "email": "pcieplak@sanfordburnham.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-05-18T14:12:34Z", "lastUpdate": "2020-10-14T07:03:58Z", "editPermission": { "type": "group", "authors": [ "irajab" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "sam_to_bam", "description": "Converts SAM format to BAM format.", "homepage": "http://www.htslib.org/", "biotoolsID": "sam_to_bam", "biotoolsCURIE": "biotools:sam_to_bam-ip", "version": [ "0.1.19" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] }, { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": null, "collectionID": [ "galaxyPasteur", "SAMtools" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/samtobam/sam_to_bam/0.1.19", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.htslib.org/doc/samtools.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp352", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The Sequence Alignment/Map format and SAMtools", "abstract": "Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAM tools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. © 2009 The Author(s).", "date": "2009-08-01T00:00:00Z", "citationCount": 24069, "authors": [ { "name": "Li H." }, { "name": "Handsaker B." }, { "name": "Wysoker A." }, { "name": "Fennell T." }, { "name": "Ruan J." }, { "name": "Homer N." }, { "name": "Marth G." }, { "name": "Abecasis G." }, { "name": "Durbin R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1022, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Von Kuster G." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic acids research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:26:14Z", "lastUpdate": "2020-08-16T18:32:41Z", "editPermission": { "type": "group", "authors": [ "alice" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EOSC pipeline-Reproducibility", "description": "The described pipeline is aimed to replicate data stored at EGA generated by the GoNL consortium", "homepage": "https://github.com/CRG-CNAG/EOSC-Pilot", "biotoolsID": "eosc_pipeline-reproducibility", "biotoolsCURIE": "biotools:eosc_pipeline-reproducibility", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": "Human genome (hg19) fasta retrieval from bundle resource of GATK. Downloaded via command:\nwget -q ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/human_g1k_v37.fasta.gz", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3210", "term": "Genome index" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3210", "term": "Genome index" }, "format": [] } ], "note": "Human genome (hg19) fasta.fai retrieval from bundle resource of GATK. Downloaded via command:\nwget -q ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/human_g1k_v37.fasta.fai.gz", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3210", "term": "Genome index" }, "format": [ { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3210", "term": "Genome index" }, "format": [] } ], "note": "Human genome (hg19) fasta.dict retrieval from bundle resource of GATK. Downloaded via command:\nwget -q ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/human_g1k_v37.dict.gz", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": "dbSNP known variant retrieval from bundle resource of GATK. Downloaded via command:\nwget -q ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.excluding_sites_after_129.vcf.gz", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": "1000Genomes Project known indels retrieval from bundle resource of GATK. Downloaded via command:\nwget -q ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.gz", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": "1000Genomes Project low coverage CEU genotypes retrieval from 1000Genomes Project repository. Downloaded via command:\nwget -q ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_07/low_coverage/snps/CEU.low_coverage.2010_07.genotypes.vcf.gz", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3211", "term": "Genome indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3210", "term": "Genome index" }, "format": [] } ], "note": "Genome indexing obtained using bwa (version 0.5.8c). Used command:\nbwa index -a bwtsw human_g1k_v37.fasta", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3497", "term": "DNA sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [] } ], "note": "Input reads SA coordinates generation using bwa (version 0.5.8c). Used commands:\nbwa aln <genome fasta file> <fastq 1 file> -f \"prefix_1.sai\"\nbwa aln <genome fasta file> <fastq 2 file> -f \"prefix_2.sai\"", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3497", "term": "DNA sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_3497", "term": "DNA sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Read mapping obtained using bwa (version 0.5.8c) and picard tools (version 1.32). Used command:\nbwa sampe -P -p <platform> -i <lane> -m <sample ID> -l <library> <genome fasta file> <prefix_1.sai> <prefix_2.sai> <fastq 1 file> <fastq 2 file> | java -jar -Xmx4g picard-tools/SamFormatConverter.jar INPUT=/dev/stdin OUTPUT=<bam file>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3802", "term": "Sorting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Mapped read sorting using picard tools (version 1.32) based on chromosome order on genome fasta file and coordinate position of mapped reads. Used command:\njava -jar -Xmx4g picard-tools/SortSam.jar INPUT=<bam file> OUTPUT=<sorted bam file> SORT_ORDER=coordinate", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [ { "uri": "http://edamontology.org/format_3327", "term": "BAI" } ] } ], "note": "Indexing of BAM sorted file using picard-tools (version 1.32). Used command:\njava -jar -Xmx4g picard-tools/BuildBamIndex.jar INPUT=<sorted bam file> OUTPUT=<sorted bam index file>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Duplicated reads detection using picard-tools (version 1.32). Used command:\njava -jar -Xmx4g picard-tools/MarkDuplicates.jar INPUT=<sorted bam file> OUTPUT=<No duplicates bam file> METRICS_FILE=<metric file> REMOVE_DUPLICATES=false ASSUME_SORTED=true", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [ { "uri": "http://edamontology.org/format_3327", "term": "BAI" } ] } ], "note": "Indexing of BAM sorted file using picard-tools (version 1.32). Used command:\njava -jar -Xmx4g picard-tools/BuildBamIndex.jar INPUT=<No duplicates bam file> OUTPUT=<No duplicates bam index file>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2089", "term": "Sequence alignment refinement" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] } ], "note": "Identification of suspicious intervals which are likely in need of realignment using GATK (version 1.1). Used command:\njava -Xmx10g -jar GenomeAnalysisTK.jar -l INFO -T RealignerTargetCreator -R <genome fasta file> -I <No duplicates bam file> -o <intervals file>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2089", "term": "Sequence alignment refinement" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Realignment around indels using GATK (version 1.1). Used command:\njava -Xmx10g -jar GenomeAnalysisTK.jar -l INFO -T IndelRealigner -U ALLOW_UNINDEXED_BAM -I <No duplicates bam file> -targetIntervals <intervals file> -R <genome fasta file> -known <dbsnp VCF file> -known <known indels 1000Genomes Project VCF file> -o <realigned bam file> -LOD 0.4 -compress 0", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2089", "term": "Sequence alignment refinement" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Fixing aligned mate pairs using picard tools (version 1.32). Used command:\njava -jar -Xmx4g picard-tools/FixMateInformation.jar INPUT=<realigned bam file> OUTPUT=<mate fixed bam SORT_ORDER=coordinate", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [ { "uri": "http://edamontology.org/format_3327", "term": "BAI" } ] } ], "note": "Indexing of BAM fixed mate file using picard-tools (version 1.32). Used command:\njava -jar -Xmx4g picard-tools/BuildBamIndex.jar INPUT=<mate fixed bam file> OUTPUT=<mate fixed bam index file>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "Building model of covariation based on the data and a set of known variants retrieved from dbSNP and using GATK (version 1.1). Used command:\njava -jar -Xmx4g GenomeAnalysisTK.jar -l INFO -T CountCovariates -U ALLOW_UNINDEXED_BAM -R <genome fasta file> -knownSites <dbsnp VCF file> -I <mate fixed bam file> -cov ReadGroupcovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile <covariates csv table>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2089", "term": "Sequence alignment refinement" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Base recalibration based on model of covariation obtained in the previous step based on the data and a set of known variants using GATK (version 1.1). Used command:\njava -jar -Xmx4g GenomeAnalysisTK.jar -l INFO -T TableRecalibration -U ALLOW_UNINDEXED_BAM -R <genome fasta file> -I <mate fixed bam file> --recal_file <covariates csv table> --out <recalibrated bam>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3802", "term": "Sorting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": "Recalibrated read sorting using picard tools (version 1.32) based on chromosome order on genome fasta file and coordinate position of mapped reads. Used command:\njava -jar -Xmx4g picard-tools/SortSam.jar INPUT=<recalibrated bam> OUTPUT=<sorted recalibrated bam> SORT_ORDER=coordinate", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0955", "term": "Data index" }, "format": [ { "uri": "http://edamontology.org/format_3327", "term": "BAI" } ] } ], "note": "java -jar -Xmx4g picard-tools/BuildBamIndex.jar INPUT=<sorted recalibrated bam> OUTPUT=<sorted recalibrated bam index file>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "Building model of covariation based on the data and a set of known variants retrieved from dbSNP and using GATK (version 1.1). Used command:\njava -jar -Xmx4g GenomeAnalysisTK.jar -l INFO -T CountCovariates -U ALLOW_UNINDEXED_BAM -R <genome fasta file> -knownSites <dbsnp VCF file> -I <sorted recalibrated bam> -cov ReadGroupcovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile <recalibrated covariates csv table>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": "Visualization of covariates computed before the base quality score recalibration using GATK (version 1.1) .Used command:\njava -jar -Xmx4g AnalyzeCovariates.jar -l INFO -resources <R path> --recal_file <mate fixed bam file> -outputDir <before folder>", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": "Visualization of covariates computed after the base quality score recalibration using GATK (version 1.1) .Used command:\njava -jar -Xmx4g AnalyzeCovariates.jar -l INFO -resources <R path> --recal_file <sorted recalibrated bam file> -outputDir <after folder>", "cmd": null } ], "toolType": [ "Workflow", "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": "Apache-1.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/CRG-CNAG/EOSC-Pilot", "type": "Source code", "note": "Repository of EOSC-Reproducibility pipeline", "version": null } ], "documentation": [], "publication": [], "credit": [ { "name": "Nino Spataro", "email": "nino.spataro@crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Paolo Di Tommaso", "email": "paolo.ditommaso@crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "spatariello", "additionDate": "2018-07-03T13:38:14Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "kWIP", "description": "The k-mer weighted inner product (kWIP) is a method for a de novo estimator of genetic similarity without the need of reference genome.", "homepage": "https://github.com/kdmurray91/kwip", "biotoolsID": "kwip", "biotoolsCURIE": "biotools:kwip", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" }, { "uri": "http://edamontology.org/operation_3731", "term": "Sample comparison" }, { "uri": "http://edamontology.org/operation_0289", "term": "Sequence distance matrix generation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0848", "term": "Raw sequence" }, "format": [ { "uri": "http://edamontology.org/format_2571", "term": "Raw sequence format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0870", "term": "Sequence distance matrix" }, "format": [ { "uri": "http://edamontology.org/format_3033", "term": "Matrix format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/kdmurray91/kWIP", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://kwip.readthedocs.io/en/latest/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/JOURNAL.PCBI.1005727", "pmid": "28873405", "pmcid": "PMC5600398", "type": [], "version": null, "note": null, "metadata": { "title": "kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity", "abstract": "© 2017 Murray et al.Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or “samples”) in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include establishing sample identity and detecting mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.", "date": "2017-09-01T00:00:00Z", "citationCount": 19, "authors": [ { "name": "Murray K.D." }, { "name": "Webers C." }, { "name": "Ong C.S." }, { "name": "Borevitz J." }, { "name": "Warthmann N." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Kevin Murray", "email": null, "url": "https://github.com/kdmurray91", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-04-29T10:44:43Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PCSF", "description": "R-Package for network-based interpretation of high-throughput data.", "homepage": "https://github.com/IOR-Bioinformatics/PCSF", "biotoolsID": "pcsf", "biotoolsCURIE": "biotools:pcsf", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3439", "term": "Pathway or network prediction" }, { "uri": "http://edamontology.org/operation_2464", "term": "Protein-protein interaction prediction" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_3617", "term": "Graph format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_3617", "term": "Graph format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_1775", "term": "Function analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R", "C++" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/IOR-Bioinformatics/PCSF", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/IOR-Bioinformatics/PCSF/tree/master/vignettes", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pcbi.1005694", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PCSF: An R-package for network-based interpretation of high-throughput data", "abstract": "© 2017 Akhmedov et al.With the recent technological developments a vast amount of high-throughput data has been profiled to understand the mechanism of complex diseases. The current bioinformatics challenge is to interpret the data and underlying biology, where efficient algorithms for analyzing heterogeneous high-throughput data using biological networks are becoming increasingly valuable. In this paper, we propose a software package based on the Prize-collecting Steiner Forest graph optimization approach. The PCSF package performs fast and user-friendly network analysis of high-throughput data by mapping the data onto a biological networks such as protein-protein interaction, gene-gene interaction or any other correlation or coexpression based networks. Using the interaction networks as a template, it determines high-confidence subnetworks relevant to the data, which potentially leads to predictions of functional units. It also interactively visualizes the resulting subnetwork with functional enrichment analysis.", "date": "2017-07-01T00:00:00Z", "citationCount": 11, "authors": [ { "name": "Akhmedov M." }, { "name": "Kedaigle A." }, { "name": "Chong R.E." }, { "name": "Montemanni R." }, { "name": "Bertoni F." }, { "name": "Fraenkel E." }, { "name": "Kwee I." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Murodzhon Akhmedov", "email": "murodzhon@idsia.ch", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "migle_sur", "additionDate": "2018-06-20T16:01:50Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Mendel,MD", "description": "Online tool created to help doctors and scientists to identify disease causing variants in human exome/genome sequencing data from patients with Mendelian disorders.", "homepage": "https://mendelmd.org/", "biotoolsID": "mendelmd", "biotoolsCURIE": "biotools:mendelmd", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_1775", "term": "Function analysis" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://mendelmd.readthedocs.io/en/latest/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pcbi.1005520", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders", "abstract": "© 2017 G. C. C. L. Cardenas et al.Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human Mendelian disorders. As pangenomic agnostic tests, they are capable of more accurate and agile diagnosis compared to traditional sequencing methods. This article describes new software called Mendel,MD, which combines multiple types of filter options and makes use of regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants for experimental validation and possible diagnosis. This tool offers a user-friendly interface, and leads clinicians through simple steps by limiting the number of candidates to achieve a final diagnosis of a medical genetics case. A useful innovation is the “1-click” method, which enables listing all the relevant variants in genes present at OMIM for perusal by clinicians. Mendel,MD was experimentally validated using clinical cases from the literature and was tested by students at the Universidade Federal de Minas Gerais, at GENE–Núcleo de Genética Médica in Brazil and at the Children’s University Hospital in Dublin, Ireland. We show in this article how it can simplify and increase the speed of identifying the culprit mutation in each of the clinical cases that were received for further investigation. Mendel,MD proved to be a reliable web-based tool, being open-source and time efficient for identifying the culprit mutation in different clinical cases of patients with Mendelian Disorders. It is also freely accessible for academic users on the following URL: https://mendelmd.org.", "date": "2017-06-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "G. C. C. L. Cardenas R." }, { "name": "D. Linhares N." }, { "name": "L. Ferreira R." }, { "name": "Pena S.D.J." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Sérgio D. J. Pena", "email": "spena@dcc.ufmg.br", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "migle_sur", "additionDate": "2018-06-19T19:52:08Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ITSxpress", "description": "ITSxpress: Software to rapidly trim the Internally transcribed spacer (ITS) region of FASTQ files", "homepage": "https://github.com/USDA-ARS-GBRU/itsxpress", "biotoolsID": "itsxpress", "biotoolsCURIE": "biotools:itsxpress", "version": [ "v1.6.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2975", "term": "Nucleic acid sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_2182", "term": "FASTQ-like format (text)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2975", "term": "Nucleic acid sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_2545", "term": "FASTQ-like format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "CC0-1.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/USDA-ARS-GBRU/itsxpress", "type": [ "Repository" ], "note": null }, { "url": "https://pypi.org/project/itsxpress/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Adam Rivers", "email": "adam.rivers@ars.usda.gov", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Adam Rivers", "email": null, "url": "https://tinyecology.com", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "arivers", "additionDate": "2018-07-03T14:53:16Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "q2_ITSxpress", "description": "q2_ITSxpress: a Qiime2 plugin for ITSxpress, software to rapidly trim the Internally transcribed spacer (ITS) region of FASTQ files", "homepage": "https://github.com/USDA-ARS-GBRU/q2_itsxpress", "biotoolsID": "q2_itsxpress", "biotoolsCURIE": "biotools:q2_itsxpress", "version": [ "v1.6.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2975", "term": "Nucleic acid sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_2182", "term": "FASTQ-like format (text)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2975", "term": "Nucleic acid sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_2182", "term": "FASTQ-like format (text)" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "CC0-1.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/USDA-ARS-GBRU/q2_itsxpress", "type": [ "Repository" ], "note": null }, { "url": "https://pypi.org/project/q2_itsxpress/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Adam Rivers", "email": "adam.rivers@ars.usda.gov", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Kyle Weber", "email": "kweber1@uf.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Adam Rivers", "email": null, "url": "https://tinyecology.com", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "arivers", "additionDate": "2018-07-13T20:26:51Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NetControl4BioMed", "description": "The pipeline can be used by researchers for controlling and better understanding of molecular interaction networks through combinatorial multi-drug therapies, for more efficient therapeutic approaches and personalised medicine.", "homepage": "http://combio.abo.fi/research/network-controlability-project/", "biotoolsID": "netcontrol4biomed", "biotoolsCURIE": "biotools:netcontrol4biomed", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2464", "term": "Protein-protein interaction prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Cancer" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "PHP", "Python" ], "license": "BSD-2-Clause-FreeBSD", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://combio.abo.fi/nc/net_control/remote_call.php", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://combio.abo.fi/scm/git/netcontrol", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://combio.abo.fi/nc/net_control/documentation.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-018-2177-3", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "NetControl4BioMed: A pipeline for biomedical data acquisition and analysis of network controllability", "abstract": "© 2018 The Author(s).Background: Network controllability focuses on discovering combinations of external interventions that can drive a biological system to a desired configuration. In practice, this approach translates into finding a combined multi-drug therapy in order to induce a desired response from a cell; this can lead to developments of novel therapeutic approaches for systemic diseases like cancer. Result: We develop a novel bioinformatics data analysis pipeline called NetControl4BioMed based on the concept of target structural control of linear networks. Our pipeline generates novel molecular interaction networks by combining pathway data from various public databases starting from the user's query. The pipeline then identifies a set of nodes that is enough to control a given, user-defined set of disease-specific essential proteins in the network, i.e., it is able to induce a change in their configuration from any initial state to any final state. We provide both the source code of the pipeline as well as an online web-service based on this pipeline http://combio.abo.fi/nc/net_control/remote_call.php. Conclusion: The pipeline can be used by researchers for controlling and better understanding of molecular interaction networks through combinatorial multi-drug therapies, for more efficient therapeutic approaches and personalised medicine.", "date": "2018-07-09T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Kanhaiya K." }, { "name": "Rogojin V." }, { "name": "Kazemi K." }, { "name": "Czeizler E." }, { "name": "Petre I." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Ion Petre", "email": "ipetre@abo.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "shadi.m", "additionDate": "2018-07-29T11:25:53Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FC_analysis", "description": "This open source software package automatically analyses single force curves or entire force volume maps to yield the corresponding elasticity and deformability images. The principal characteristic of the package is a large adaptability to the various experimental setups and to different analysis methodologies.", "homepage": "http://uk.mathworks.com/products/compiler/mcr", "biotoolsID": "fc_analysis", "biotoolsCURIE": "biotools:fc_analysis", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Windows" ], "language": [ "MATLAB" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://static-content.springer.com/esm/art%3A10.1186%2Fs12859-018-2265-4/MediaObjects/12859_2018_2265_MOESM1_ESM.exe", "type": "Software package", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1186/s12859-018-2265-4", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "FC_analysis: A tool for investigating atomic force microscopy maps of force curves", "abstract": "© 2018 The Author(s).Background: The collection and analysis of Atomic Force Microscopy force curves is a well-established procedure to obtain high-resolution information of non-topographic data from any kind of sample, including biological specimens. In particular, these analyses are commonly employed to study elasticity, stiffness or adhesion properties of the samples. Furthermore, the collection of several force curves over an extended area of the specimens allows reconstructing maps, called force volume maps, of the spatial distribution of the mechanical properties. Coupling these maps with the conventional high-resolution topographic reconstruction of the sample's surface, provides a deeper insight on the sample composition from the structural and nanomechanical point of view. Results: In this paper we present the open source software package FC_analysis that automatically analyses single force curves or entire force volume maps to yield the corresponding elasticity and deformability images. The principal characteristic of the FC_analysis is a large adaptability to the various experimental setups and to different analysis methodologies. For instance, the user can provide custom values for the detector sensitivity, scanner-z sensitivity, cantilever's elastic constant and map's acquisition modality and can choose between different analysis methodologies. Furthermore, the software allows the optimization of the fitting parameters and gives direct control on each step of the analysis procedure. Notably, to overcome a limitation common to many other analysis programs, FC_analysis can be applied to a rectangular portion of the image, allowing the analysis of inhomogeneous samples. Finally, the software allows reconstructing a Young's modulus map at different penetration depths, enabling the use of modern investigation tools such as the force tomography. Conclusions: The FC_analysis software aims to become a useful tool for the analysis of force curves maps collected using custom or commercial Atomic Force Microscopes, and is especially useful in those cases for which the producer doesn't release a dedicated software.", "date": "2018-07-06T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Dinarelli S." }, { "name": "Girasole M." }, { "name": "Longo G." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Simone Dinarelli", "email": "simone.dinarelli@ism.cnr.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "shadi.m", "additionDate": "2018-07-29T11:54:35Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ToTem", "description": "Variant calling pipeline optimization.", "homepage": "https://totem.software/login/?backlink=iplpf&_fid=t22e", "biotoolsID": "totem", "biotoolsCURIE": "biotools:totem", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3762", "term": "Service composition" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "PHP", "Java" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://totem.software/login/?backlink=iplpf&_fid=t22e", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-018-2227-x", "pmid": "29940847", "pmcid": "PMC6020218", "type": [], "version": null, "note": null, "metadata": { "title": "ToTem: A tool for variant calling pipeline optimization", "abstract": "© 2018 The Author(s).Background: High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall. Results: Here we introduce ToTem, a tool for automated pipeline optimization. ToTem is a stand-alone web application with a comprehensive graphical user interface (GUI). ToTem is written in Java and PHP with an underlying connection to a MySQL database. Its primary role is to automatically generate, execute and benchmark different variant calling pipeline settings. Our tool allows an analysis to be started from any level of the process and with the possibility of plugging almost any tool or code. To prevent an over-fitting of pipeline parameters, ToTem ensures the reproducibility of these by using cross validation techniques that penalize the final precision, recall and F-measure. The results are interpreted as interactive graphs and tables allowing an optimal pipeline to be selected, based on the user's priorities. Using ToTem, we were able to optimize somatic variant calling from ultra-deep targeted gene sequencing (TGS) data and germline variant detection in whole genome sequencing (WGS) data. Conclusions: ToTem is a tool for automated pipeline optimization which is freely available as a web application at https://totem.software.", "date": "2018-06-26T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Tom N." }, { "name": "Tom O." }, { "name": "Malcikova J." }, { "name": "Pavlova S." }, { "name": "Kubesova B." }, { "name": "Rausch T." }, { "name": "Kolarik M." }, { "name": "Benes V." }, { "name": "Bystry V." }, { "name": "Pospisilova S." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Nikola Tom", "email": "1nikola.tom@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-07-23T18:00:16Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PepBonPred", "description": "PepBindPred is for users interested in identifying peptide binding regions within a protein sequence, which may bind to a know protein structure. PepBindPred was trained on a set of non-redundant protein sequences containing known peptide binding regions sourced from the ELM database.", "homepage": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php", "biotoolsID": "pepbonpred", "biotoolsCURIE": "biotools:pepbonpred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" }, { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0072838", "pmid": "24019881", "pmcid": "PMC3760854", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Predicting Binding within Disordered Protein Regions to Structurally Characterised Peptide-Binding Domains", "abstract": "Disordered regions of proteins often bind to structured domains, mediating interactions within and between proteins. However, it is difficult to identify a priori the short disordered regions involved in binding. We set out to determine if docking such peptide regions to peptide binding domains would assist in these predictions.We assembled a redundancy reduced dataset of SLiM (Short Linear Motif) containing proteins from the ELM database. We selected 84 sequences which had an associated PDB structures showing the SLiM bound to a protein receptor, where the SLiM was found within a 50 residue region of the protein sequence which was predicted to be disordered. First, we investigated the Vina docking scores of overlapping tripeptides from the 50 residue SLiM containing disordered regions of the protein sequence to the corresponding PDB domain. We found only weak discrimination of docking scores between peptides involved in binding and adjacent non-binding peptides in this context (AUC 0.58).Next, we trained a bidirectional recurrent neural network (BRNN) using as input the protein sequence, predicted secondary structure, Vina docking score and predicted disorder score. The results were very promising (AUC 0.72) showing that multiple sources of information can be combined to produce results which are clearly superior to any single source.We conclude that the Vina docking score alone has only modest power to define the location of a peptide within a larger protein region known to contain it. However, combining this information with other knowledge (using machine learning methods) clearly improves the identification of peptide binding regions within a protein sequence. This approach combining docking with machine learning is primarily a predictor of binding to peptide-binding sites, and is not intended as a predictor of specificity of binding to particular receptors. © 2013 Khan et al.", "date": "2013-09-03T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Khan W." }, { "name": "Duffy F." }, { "name": "Pollastri G." }, { "name": "Shields D.C." }, { "name": "Mooney C." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "Prof. Dr. Denis C. Shields", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": null, "email": "waqasnayab@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "WaqasuddinKhan", "additionDate": "2018-08-02T10:04:31Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PepBindPred", "description": "PepBindPred is for users interested in identifying peptide binding regions within a protein sequence, which may bind to a know protein structure. PepBindPred was trained on a set of non-redundant protein sequences containing known peptide binding regions sourced from the ELM database.", "homepage": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php", "biotoolsID": "pepbindpred", "biotoolsCURIE": "biotools:pepbindpred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" }, { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0072838", "pmid": "24019881", "pmcid": "PMC3760854", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Predicting Binding within Disordered Protein Regions to Structurally Characterised Peptide-Binding Domains", "abstract": "Disordered regions of proteins often bind to structured domains, mediating interactions within and between proteins. However, it is difficult to identify a priori the short disordered regions involved in binding. We set out to determine if docking such peptide regions to peptide binding domains would assist in these predictions.We assembled a redundancy reduced dataset of SLiM (Short Linear Motif) containing proteins from the ELM database. We selected 84 sequences which had an associated PDB structures showing the SLiM bound to a protein receptor, where the SLiM was found within a 50 residue region of the protein sequence which was predicted to be disordered. First, we investigated the Vina docking scores of overlapping tripeptides from the 50 residue SLiM containing disordered regions of the protein sequence to the corresponding PDB domain. We found only weak discrimination of docking scores between peptides involved in binding and adjacent non-binding peptides in this context (AUC 0.58).Next, we trained a bidirectional recurrent neural network (BRNN) using as input the protein sequence, predicted secondary structure, Vina docking score and predicted disorder score. The results were very promising (AUC 0.72) showing that multiple sources of information can be combined to produce results which are clearly superior to any single source.We conclude that the Vina docking score alone has only modest power to define the location of a peptide within a larger protein region known to contain it. However, combining this information with other knowledge (using machine learning methods) clearly improves the identification of peptide binding regions within a protein sequence. This approach combining docking with machine learning is primarily a predictor of binding to peptide-binding sites, and is not intended as a predictor of specificity of binding to particular receptors. © 2013 Khan et al.", "date": "2013-09-03T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Khan W." }, { "name": "Duffy F." }, { "name": "Pollastri G." }, { "name": "Shields D.C." }, { "name": "Mooney C." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "Prof. Dr. Denis C. Shields", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": null, "email": "waqasnayab@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "WaqasuddinKhan", "additionDate": "2018-08-02T10:05:27Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MEGADOCK-Web", "description": "It is an integrated database of high-throughput structure-based PPI predictions.", "homepage": "http://www.bi.cs.titech.ac.jp/megadock-web/", "biotoolsID": "megadock-web", "biotoolsCURIE": "biotools:megadock-web", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2464", "term": "Protein-protein interaction prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s12859-018-2073-x", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MEGADOCK-Web: An integrated database of high-throughput structure-based protein-protein interaction predictions", "abstract": "© 2018 The Author(s).Background: Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required. We have developed rapid PPI prediction software based on protein-protein docking, called MEGADOCK. In order to fully utilize the benefits of computational PPI predictions, it is necessary to construct a comprehensive database to gather prediction results and their predicted 3D complex structures and to make them easily accessible. Although several databases exist that provide predicted PPIs, the previous databases do not contain a sufficient number of entries for the purpose of discovering novel PPIs. Results: In this study, we constructed an integrated database of MEGADOCK PPI predictions, named MEGADOCK-Web. MEGADOCK-Web provides more than 10 times the number of PPI predictions than previous databases and enables users to conduct PPI predictions that cannot be found in conventional PPI prediction databases. In MEGADOCK-Web, there are 7528 protein chains and 28,331,628 predicted PPIs from all possible combinations of those proteins. Each protein structure is annotated with PDB ID, chain ID, UniProt AC, related KEGG pathway IDs, and known PPI pairs. Additionally, MEGADOCK-Web provides four powerful functions: 1) searching precalculated PPI predictions, 2) providing annotations for each predicted protein pair with an experimentally known PPI, 3) visualizing candidates that may interact with the query protein on biochemical pathways, and 4) visualizing predicted complex structures through a 3D molecular viewer. Conclusion: MEGADOCK-Web provides a huge amount of comprehensive PPI predictions based on docking calculations with biochemical pathways and enables users to easily and quickly assess PPI feasibilities by archiving PPI predictions. MEGADOCK-Web also promotes the discovery of new PPIs and protein functions and is freely available for use at http://www.bi.cs.titech.ac.jp/megadock-web/.", "date": "2018-05-08T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Hayashi T." }, { "name": "Matsuzaki Y." }, { "name": "Yanagisawa K." }, { "name": "Ohue M." }, { "name": "Akiyama Y." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Masahito Ohue", "email": "ohue@c.titech.ac.jp", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Yutaka Akiyama", "email": "akiyama@c.titech.ac.jp", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "shadi.m", "additionDate": "2018-08-06T13:08:41Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BIP", "description": "Brassica Information Portal.", "homepage": "https://bip.earlham.ac.uk/", "biotoolsID": "bip", "biotoolsCURIE": "biotools:bip", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] } ], "output": [], "note": "crop phenotyping data", "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3298", "term": "Phenomics" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Ruby" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/TGAC/brassica", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://bip.earlham.ac.uk/api_documentation", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.11301.1", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data", "abstract": "© 2017 Eckes AH et al.The Brassica Information Portal (BIP) is a centralised repository for Brassica phenotypic data. Trait data associated with Brassica research and breeding experiments conducted on Brassica crops, used as vegetables, for livestock fodder and biofuels, is hosted on the site, together with information on the experimental plant materials used, as well as trial design. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for scientists and breeders. BIP opens up the opportunity to apply big data analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository.", "date": "2017-01-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Jurkowski W." }, { "name": "Eckes A.H." }, { "name": "Gubala T." }, { "name": "Nowakowski P." }, { "name": "Szymczyszyn T." }, { "name": "Wells R." }, { "name": "Irwin J.A." }, { "name": "Horro C." }, { "name": "Hancock J.M." }, { "name": "King G." }, { "name": "Dyer S.C." } ], "journal": "F1000Research" } } ], "credit": [ { "name": null, "email": "bip@earlham.ac.uk", "url": "https://bip.earlham.ac.uk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": null, "email": "wiktor.jurkowski@earlham.ac.uk", "url": "http://www.earlham.ac.uk/jurkowski-group", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "wjurki", "additionDate": "2017-02-02T14:45:59Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FGMP", "description": "Genome completeness assessment tool focused on Fungi", "homepage": "http://github.com/stajichlab/FGMP", "biotoolsID": "fgmp", "biotoolsCURIE": "biotools:fgmp", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0925", "term": "Sequence assembly" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3181", "term": "Sequence assembly report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/stajichlab/FGMP", "type": [ "Repository" ], "note": "Github repository (main site)" } ], "download": [ { "url": "https://github.com/stajichlab/FGMP/releases", "type": "Source code", "note": "Latest release code available from this URL", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1101/049619", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Ousmane Cissé", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jason Stajich", "email": "jasonstajich.phd@gmail.com", "url": "http://lab.stajich.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Ousmane Cissé", "email": "ousmanecis@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "stajich", "additionDate": "2018-09-22T13:40:35Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "group", "authors": [ "ocisse1" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioExcel Virtual Screening pipeline", "description": "VirtualScreening is a Python package inheriting from pymdsetup to perform virtual screening on a set of predefined targets.", "homepage": "https://github.com/bioexcel/virtualscreening", "biotoolsID": "virtualscreening", "biotoolsCURIE": "biotools:virtualscreening", "version": [ "Alpha" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" }, { "uri": "http://edamontology.org/operation_2425", "term": "Optimisation and refinement" }, { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [ { "uri": "http://edamontology.org/format_3816", "term": "Mol2" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3314", "term": "Chemistry" }, { "uri": "http://edamontology.org/topic_3344", "term": "Biomedical science" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "BioExcel" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bioexcel/virtualscreening", "type": [ "Repository" ], "note": "VirtualScreening is a Python package inheriting from pymdsetup to perform virtual screening on a set of predefined targets" } ], "download": [ { "url": "https://github.com/bioexcel/virtualscreening", "type": "Source code", "note": "VirtualScreening is a Python package inheriting from pymdsetup to perform virtual screening on a set of predefined targets", "version": null } ], "documentation": [ { "url": "https://github.com/bioexcel/virtualscreening/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.5281/zenodo.263965", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "BioExcel Center of Excellence for Computational Biomolecular Research", "email": null, "url": "https://bioexcel.eu", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Pau Andrio", "email": "pau.andrio@bsc.es", "url": "https://github.com/bioexcel/virtualscreening", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "adam.hospital@irbbarcelona.org", "additionDate": "2018-10-18T14:31:58Z", "lastUpdate": "2020-06-16T10:55:21Z", "editPermission": { "type": "group", "authors": [ "gelpi@ub.edu" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DISEASES", "description": "DISEASES is a weekly updated web resource that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. We further unify the evidence by assigning confidence scores that facilitate comparison of the different types and sources of evidence.", "homepage": "https://diseases.jensenlab.org/", "biotoolsID": "diseases", "biotoolsCURIE": "biotools:diseases", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1025", "term": "Gene identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3667", "term": "Disease identifier" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3667", "term": "Disease identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1025", "term": "Gene identifier" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" }, { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "JensenLab" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://diseases.jensenlab.org/Downloads", "type": "Biological data", "note": "Bulk download files in tab-delimited format.", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1016/j.ymeth.2014.11.020", "pmid": "25484339", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "DISEASES: Text mining and data integration of disease-gene associations", "abstract": "© 2014 The Authors.Text mining is a flexible technology that can be applied to numerous different tasks in biology and medicine. We present a system for extracting disease-gene associations from biomedical abstracts. The system consists of a highly efficient dictionary-based tagger for named entity recognition of human genes and diseases, which we combine with a scoring scheme that takes into account co-occurrences both within and between sentences. We show that this approach is able to extract half of all manually curated associations with a false positive rate of only 0.16%. Nonetheless, text mining should not stand alone, but be combined with other types of evidence. For this reason, we have developed the DISEASES resource, which integrates the results from text mining with manually curated disease-gene associations, cancer mutation data, and genome-wide association studies from existing databases. The DISEASES resource is accessible through a web interface at http://diseases.jensenlab.org/, where the text-mining software and all associations are also freely available for download.", "date": "2015-03-01T00:00:00Z", "citationCount": 248, "authors": [ { "name": "Pletscher-Frankild S." }, { "name": "Palleja A." }, { "name": "Tsafou K." }, { "name": "Binder J.X." }, { "name": "Jensen L.J." } ], "journal": "Methods" } } ], "credit": [ { "name": "Lars Juhl Jensen", "email": "lars.juhl.jensen@cpr.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "larsjuhljensen", "additionDate": "2018-02-23T09:36:20Z", "lastUpdate": "2020-06-16T10:55:20Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "COMPARTMENTS", "description": "COMPARTMENTS is a weekly updated web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. We map all evidence to common protein identifiers and Gene Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence and visualize these scores on a schematic cell.", "homepage": "https://compartments.jensenlab.org/", "biotoolsID": "compartments", "biotoolsCURIE": "biotools:compartments", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1025", "term": "Gene identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1176", "term": "GO concept ID" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0140", "term": "Protein targeting and localisation" }, { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "JensenLab" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://compartments.jensenlab.org/Downloads", "type": "Biological data", "note": "Bulk download files in tab-delimited format.", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1093/database/bau012", "pmid": "24573882", "pmcid": "PMC3935310", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "COMPARTMENTS: Unification and visualization of protein subcellular localization evidence", "abstract": "© The Author(s) 2014.Information on protein subcellular localization is important to understand the cellular functions of proteins. Currently, such information is manually curated from the literature, obtained from high-throughput microscopy-based screens and predicted from primary sequence. To get a comprehensive view of the localization of a protein, it is thus necessary to consult multiple databases and prediction tools. To address this, we present the COMPARTMENTS resource, which integrates all sources listed above as well as the results of automatic text mining. The resource is automatically kept up to date with source databases, and all localization evidence is mapped onto common protein identifiers and Gene Ontology terms. We further assign confidence scores to the localization evidence to facilitate comparison of different types and sources of evidence. To further improve the comparability, we assign confidence scores based on the type and source of the localization evidence. Finally, we visualize the unified localization evidence for a protein on a schematic cell to provide a simple overview.", "date": "2014-01-01T00:00:00Z", "citationCount": 221, "authors": [ { "name": "Binder J.X." }, { "name": "Pletscher-Frankild S." }, { "name": "Tsafou K." }, { "name": "Stolte C." }, { "name": "O'Donoghue S.I." }, { "name": "Schneider R." }, { "name": "Jensen L.J." } ], "journal": "Database" } } ], "credit": [ { "name": "Lars Juhl Jensen", "email": "lars.juhl.jensen@cpr.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "larsjuhljensen", "additionDate": "2018-02-23T10:16:53Z", "lastUpdate": "2020-06-16T10:55:20Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ORGANISMS", "description": "ORGANISMS is a weekly updated web resource that facilitates taxonomy-aware search and retrieval of articles. To this end, the the resource performs named entity recognition of terms from the NCBI Taxonomy on PubMed abstracts. The resource further provides download files of organism-disease and organism-tissue associations extracted through automatic text mining.", "homepage": "https://organisms.jensenlab.org/", "biotoolsID": "organisms", "biotoolsCURIE": "biotools:organisms", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0305", "term": "Literature search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1869", "term": "Organism identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1187", "term": "PubMed ID" }, "format": [ { "uri": "http://edamontology.org/format_2020", "term": "Article format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "JensenLab" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://organisms.jensenlab.org/Downloads", "type": "Biological data", "note": "Bulk download files in tab-delimited format.", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1371/journal.pone.0065390", "pmid": "23823062", "pmcid": "PMC3688812", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text", "abstract": "The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus of 800 abstracts, which were manually annotated after the development of the tool. The corpus comprises abstracts from journals selected to represent many taxonomic groups, which gives insights into which types of organism names are hard to detect and which are easy. Finally, we have tagged organism names in the entire Medline database and developed a web resource, ORGANISMS, that makes the results accessible to the broad community of biologists. The SPECIES software is open source and can be downloaded from http://species.jensenlab.org along with dictionary files and the manually annotated gold-standard corpus. The ORGANISMS web resource can be found at http://organisms.jensenlab.org. © 2013 Pafilis et al.", "date": "2013-06-18T00:00:00Z", "citationCount": 55, "authors": [ { "name": "Pafilis E." }, { "name": "Frankild S.P." }, { "name": "Fanini L." }, { "name": "Faulwetter S." }, { "name": "Pavloudi C." }, { "name": "Vasileiadou A." }, { "name": "Arvanitidis C." }, { "name": "Jensen L.J." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "Lars Juhl Jensen", "email": "lars.juhl.jensen@cpr.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "larsjuhljensen", "additionDate": "2018-02-25T10:17:45Z", "lastUpdate": "2020-06-16T10:55:20Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "TriFusion", "description": "Modern GUI and command line application designed to make the life of anyone with proteome and/or alignment sequence data easier and more pleasurable. 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Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.", "homepage": "https://github.com/GATB/simka", "biotoolsID": "simka", "biotoolsCURIE": "biotools:simka", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0289", "term": "Sequence distance matrix generation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2975", "term": "Nucleic acid sequence (raw)" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0870", "term": "Sequence distance matrix" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "C++" ], "license": "AGPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://gatb.inria.fr/software/simka/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/GATB/simka", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.7717/peerj-cs.94", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Multiple comparative metagenomics using multiset k-mer counting", "abstract": "© 2016 Benoit et al.Background. Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can be associated to known organisms. On the other hand, de novo methods, that compare the whole sets of sequences, either do not scale up on ambitious metagenomic projects or do not provide precise and exhaustive results. Methods. These limitations motivated the development of a new de novo metagenomic comparative method, called Simka. This method computes a large collection of standard ecological distances by replacing species counts by k-mer counts. Simka scales-up today's metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets. Results. Experiments on public Human Microbiome Project datasets demonstrate that Simka captures the essential underlying biological structure. Simka was able to compute in a few hours both qualitative and quantitative ecological distances on hundreds of metagenomic samples (690 samples, 32 billions of reads). We also demonstrate that analyzing metagenomes at the k-mer level is highly correlated with extremely precise de novo comparison techniques which rely on all-versus-all sequences alignment strategy or which are based on taxonomic profiling.", "date": "2016-01-01T00:00:00Z", "citationCount": 37, "authors": [ { "name": "Benoit G." }, { "name": "Peterlongo P." }, { "name": "Mariadassou M." }, { "name": "Drezen E." }, { "name": "Schbath S." }, { "name": "Lavenier D." }, { "name": "Lemaitre C." } ], "journal": "PeerJ Computer Science" } } ], "credit": [ { "name": null, "email": "Claire.Lemaitre@inria.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "olivier.collin@irisa.fr", "additionDate": "2018-03-05T15:06:35Z", "lastUpdate": "2020-06-16T10:55:20Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "roi_filter", "description": "Filter ROI files.", "homepage": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_filter/0.2.2", "biotoolsID": "roi_filter", "biotoolsCURIE": "biotools:roi_filter-ip", "version": [ "0.2.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_filter/0.2.2", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Fscreno%2Fngs_roi2%2Froi_filter%2F0.2.2", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1025, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Von Kuster G." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic acids research" } } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", 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