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{ "count": 521, "next": "?page=2", "previous": null, "list": [ { "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": "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": [ "ArnauMontagud" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "cusp", "description": "Create a codon usage table from nucleotide sequence(s).", "homepage": "http://emboss.open-bio.org/rel/rel6/apps/cusp.html", "biotoolsID": "cusp", "biotoolsCURIE": "biotools:cusp", "version": [ "r6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0284", "term": "Codon usage table generation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2887", "term": "Nucleic acid sequence record" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1597", "term": "Codon usage table" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": "GPL-3.0", "collectionID": [ "EMBOSS" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://emboss.open-bio.org/html/adm/ch01s01.html", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "http://emboss.open-bio.org/html/adm/ch01s01.html", "type": "Source code", "note": null, "version": null }, { "url": "http://emboss.open-bio.org/html/adm/ch01s01.html", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "http://emboss.open-bio.org/html/dev/ch01s01.html", "type": [ "Terms of use" ], "note": null }, { "url": "http://emboss.open-bio.org/html/use/pr02s04.html", "type": [ "Citation instructions" ], "note": null }, { "url": "http://emboss.open-bio.org/rel/rel6/apps/cusp.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/S0168-9525(00)02024-2", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "EMBOSS: The European Molecular Biology Open Software Suite", "abstract": "", "date": "2000-06-01T00:00:00Z", "citationCount": 5826, "authors": [ { "name": "Rice P." }, { "name": "Longden L." }, { "name": "Bleasby A." } ], "journal": "Trends in Genetics" } }, { "doi": "10.1017/CBO9781139151399", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1017/CBO9781139151405", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "EMBOSS Contributors", "email": null, "url": "http://emboss.open-bio.org/html/use/pr01s01.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "UK MRC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Wellcome Trust", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "UK BBSRC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "EMBOSS", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "EMBOSS", "email": "emboss@emboss.open-bio.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": null, "email": "emboss@emboss.open-bio.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": null, "email": "emboss-bug@emboss.open-bio.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Luisma71", "additionDate": "2015-11-08T14:39:41Z", "lastUpdate": "2022-04-27T08:46:41.312776Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "cai", "description": "Calculate codon adaptation index.", "homepage": "http://emboss.open-bio.org/rel/rel6/apps/cai.html", "biotoolsID": "cai", "biotoolsCURIE": "biotools:cai", "version": [ "r6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0286", "term": "Codon usage analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2887", "term": "Nucleic acid sequence record" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1597", "term": "Codon usage table" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2865", "term": "Codon usage bias" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": "GPL-3.0", "collectionID": [ "EMBOSS" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://emboss.open-bio.org/html/adm/ch01s01.html", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "http://emboss.open-bio.org/html/adm/ch01s01.html", "type": "Source code", "note": null, "version": null }, { "url": "http://emboss.open-bio.org/html/adm/ch01s01.html", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "http://emboss.open-bio.org/html/dev/ch01s01.html", "type": [ "Terms of use" ], "note": null }, { "url": "http://emboss.open-bio.org/html/use/pr02s04.html", "type": [ "Citation instructions" ], "note": null }, { "url": "http://emboss.open-bio.org/rel/rel6/apps/cai.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/S0168-9525(00)02024-2", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "EMBOSS: The European Molecular Biology Open Software Suite", "abstract": "", "date": "2000-06-01T00:00:00Z", "citationCount": 5834, "authors": [ { "name": "Rice P." }, { "name": "Longden L." }, { "name": "Bleasby A." } ], "journal": "Trends in Genetics" } }, { "doi": "10.1017/CBO9781139151399", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1017/CBO9781139151405", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "EMBOSS Contributors", "email": null, "url": "http://emboss.open-bio.org/html/use/pr01s01.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "UK MRC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Wellcome Trust", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "UK BBSRC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "EMBOSS", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "EMBOSS", "email": "emboss@emboss.open-bio.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": null, "email": "emboss@emboss.open-bio.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": null, "email": "emboss-bug@emboss.open-bio.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Luisma71", "additionDate": "2015-11-08T14:39:21Z", "lastUpdate": "2022-04-27T08:40:25.770144Z", "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": "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": "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": "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. It allows user to process their data through three independent modules: (i) Search and explore orthologs across multiple proteomes; (ii) Convert, concatenate, collapse, filter and perform many other manipulations of thousands sequence alignments files. 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Future versions will use NeXML as the output format instead.", "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://bioinfweb.info/Code/sventon/repos/AlignmentComparator/list/", "type": [ "Repository" ], "note": null }, { "url": "http://twitter.com/bioinfweb", "type": [ "Social media" ], "note": null }, { "url": "https://github.com/bioinfweb/AlignmentComparator", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "http://bioinfweb.info/AlignmentComparator/Download", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "http://bioinfweb.info/AlignmentComparator/License", "type": [ "Terms of use" ], "note": null } ], "publication": [], "credit": [ { "name": "Ben Stöver", "email": null, "url": "http://bioinfweb.info/People/Stoever", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Kai Müller", "email": null, "url": "http://bioinfweb.info/People/Mueller", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "bioinfweb", "email": null, "url": "http://bioinfweb.info/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Ben Stöver", "email": null, "url": "http://bioinfweb.info/People/Stoever", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "BenStoever", "additionDate": "2017-04-06T17:04:07Z", "lastUpdate": "2020-06-16T10:55:20Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "gsrc", "description": "Genome Structure Rearrangement Calling in Genomes with High Synteny.", "homepage": "https://github.com/grafab/gsrc", "biotoolsID": "gsrc", "biotoolsCURIE": "biotools:gsrc", "version": [ "1.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_2495", "term": "Gene expression analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1714", "term": "Microarray spots image" }, "format": [ { "uri": "http://edamontology.org/format_3578", "term": "IDAT" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0122", "term": "Structural genomics" }, { "uri": "http://edamontology.org/topic_3360", "term": "Biomarkers" }, { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://CRAN.R-project.org/package=gsrc", "type": [ "Repository" ], "note": "Release version, see development versions on github for bugfixes" } ], "download": [], "documentation": [ { "url": "https://cran.r-project.org/web/packages/gsrc/vignettes/introduction.html", "type": [ "User manual" ], "note": "Manual on how to use the package" }, { "url": "https://cran.r-project.org/web/packages/gsrc/vignettes/synteny.html", "type": [ "User manual" ], "note": "Manual on calculation of synteny blocks" } ], "publication": [ { "doi": "10.1093/bioinformatics/btw648", "pmid": "27797758", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Gsrc: An R package for genome structure rearrangement calling", "abstract": "© 2017 The Author.Genome structure rearrangements are a common phenomenon in allopolyploid species. Deletions, duplications and homeologous non-reciprocal translocations (HNRT) between the highly similar subgenomes can be observed, which are known to have a large impact on phenotypic traits. Current research is limited because these rearrangements can be located genome wide only by cost intensive sequencing approaches and not reliably in high-density array genotyping data. We developed gsrc, an R-package to detect genome structure rearrangements from genotyping data in allopolyploid species including exchanges between subgenomes. We exemplarily apply gsrc to a publicly available Brassica napus dataset.", "date": "2017-02-15T00:00:00Z", "citationCount": 9, "authors": [ { "name": "Grandke F." }, { "name": "Snowdon R." }, { "name": "Samans B." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Fabian Grandke", "email": null, "url": "https://github.com/grafab/gsrc/issues", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "grafab", "additionDate": "2017-01-30T09:14:43Z", "lastUpdate": "2020-06-16T10:55:20Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "S2P", "description": "S2P is an open source application for fast and accurate processing of 2D-gel and MALDI-based mass spectrometry protein data.", "homepage": "http://sing-group.org/s2p", "biotoolsID": "s2p", "biotoolsCURIE": "biotools:s2p", "version": [ "1.2.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0108", "term": "Protein expression" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://sing-group.org/s2p/download.html", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/sing-group/s2p", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://sing.ei.uvigo.es/s2p/tutorial.html", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-319-60816-7", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "SING Research Group", "email": null, "url": "http://sing-group.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Bioscope Research Group", "email": null, "url": "http://www.bioscopegroup.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "S2P", "email": "s2p@sing.ei.uvigo.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hlfernandez@uvigo.es", "additionDate": "2017-01-10T17:25:15Z", "lastUpdate": "2020-06-16T10:55:19Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Scoary", "description": "Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.", "homepage": "https://github.com/AdmiralenOla/Scoary", "biotoolsID": "scoary", "biotoolsCURIE": "biotools:scoary", "version": [ "1.6.11" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0916", "term": "Gene report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1669", "term": "P-value" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "Scoary correlates the genes of an accessory genome to an observed phenotype (e.g. resistance towards a certain antibiotic compound, a particular pathotype etc.). It is thus a quick way of establishing possible genetic mechanisms of an expressed trait, not unlike a GWAS, but with the entire pan-genome rather than a core set of mutations. Scoary works on both bacteria, Archea and (in theory at least) viruses.", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/AdmiralenOla/Scoary", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/AdmiralenOla/Scoary/archive/master.zip", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/AdmiralenOla/Scoary/blob/master/LICENSE", "type": [ "Terms of use" ], "note": null }, { "url": "https://github.com/AdmiralenOla/Scoary", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s13059-016-1108-8", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary", "abstract": "© 2016 The Author(s).Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS. Scoary is implemented in Python and is available under an open source GPLv3 license at https://github.com/AdmiralenOla/Scoary.", "date": "2016-11-25T00:00:00Z", "citationCount": 154, "authors": [ { "name": "Brynildsrud O." }, { "name": "Bohlin J." }, { "name": "Scheffer L." }, { "name": "Eldholm V." } ], "journal": "Genome Biology" } } ], "credit": [ { "name": "Ola Brynildsrud", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Vegard Eldholm", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Norwegian Institute of Public Health", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "UiO", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Ola Brynildsrud", "email": "ola.brynildsrud@fhi.no", "url": "https://github.com/AdmiralenOla", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "UiO", "additionDate": "2016-09-12T15:20:53Z", "lastUpdate": "2020-06-16T10:55:18Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "meneco", "description": "Topological gap-filling of genome-scale draft metabolic networks.", "homepage": "https://bioasp.github.io/meneco/", "biotoolsID": "meneco", "biotoolsCURIE": "biotools:meneco", "version": [ "1.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3660", "term": "Metabolic network modelling" }, { "uri": "http://edamontology.org/operation_3715", "term": "Metabolic labeling" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://codeload.github.com/bioasp/meneco/zip/meneco-1.5.2", "type": "Source code", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1371/JOURNAL.PCBI.1005276", "pmid": "28129330", "pmcid": "PMC5302834", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks", "abstract": "© 2017 Prigent et al.Increasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system.", "date": "2017-01-01T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Prigent S." }, { "name": "Frioux C." }, { "name": "Dittami S.M." }, { "name": "Thiele S." }, { "name": "Larhlimi A." }, { "name": "Collet G." }, { "name": "Gutknecht F." }, { "name": "Got J." }, { "name": "Eveillard D." }, { "name": "Bourdon J." }, { "name": "Plewniak F." }, { "name": "Tonon T." }, { "name": "Siegel A." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Anne Siegel", "email": "anne.siegel@irisa.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Sylvain Prigent", "email": "prigent@chalmers.se", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "jgot", "additionDate": "2018-10-22T10:48:35Z", "lastUpdate": "2019-12-14T20:34:14Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GNAT", "description": "Software package intended primarily for the processing of multicomponent high resolution NMR datasets such as those acquired in diffusion, relaxation and kinetic experiments.", "homepage": "https://www.nmr.chemistry.manchester.ac.uk/?q=node/430", "biotoolsID": "gnat_nmr", "biotoolsCURIE": "biotools:gnat_nmr", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3214", "term": "Spectral analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0593", "term": "NMR" }, { "uri": "http://edamontology.org/topic_0176", "term": "Molecular dynamics" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "MATLAB" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.nmr.chemistry.manchester.ac.uk/sites/default/files/README_1_0.txt", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/mrc.4717", "pmid": "29396867", "pmcid": "PMC6001793", "type": [], "version": null, "note": null, "metadata": { "title": "The GNAT: A new tool for processing NMR data", "abstract": "© 2018 The Authors Magnetic Resonance in Chemistry Published by John Wiley & Sons Ltd.The GNAT (General NMR Analysis Toolbox) is a free and open-source software package for processing, visualising, and analysing NMR data. It supersedes the popular DOSY Toolbox, which has a narrower focus on diffusion NMR. Data import of most common formats from the major NMR platforms is supported, as well as a GNAT generic format. Key basic processing of NMR data (e.g., Fourier transformation, baseline correction, and phasing) is catered for within the program, as well as more advanced techniques (e.g., reference deconvolution and pure shift FID reconstruction). Analysis tools include DOSY and SCORE for diffusion data, ROSY T1/T2 estimation for relaxation data, and PARAFAC for multilinear analysis. The GNAT is written for the MATLAB® language and comes with a user-friendly graphical user interface. The standard version is intended to run with a MATLAB installation, but completely free-standing compiled versions for Windows, Mac, and Linux are also freely available.", "date": "2018-06-01T00:00:00Z", "citationCount": 32, "authors": [ { "name": "Castanar L." }, { "name": "Poggetto G.D." }, { "name": "Colbourne A.A." }, { "name": "Morris G.A." }, { "name": "Nilsson M." } ], "journal": "Magnetic Resonance in Chemistry" } } ], "credit": [ { "name": "Mathias Nilsson", "email": "mathias.nilsson@manchester.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-08-05T09:12:36Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OCTOPUS-toolkit", "description": "Retrieve and process large sets of next-generation sequencing (NGS) data with a single step. Automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, bwtool, Samtools FastQC, Trimmomatic, HISAT2, STAR, and HOMER applications.", "homepage": "http://octopus-toolkit2.readthedocs.io/en/latest/", "biotoolsID": "octopus-toolkit", "biotoolsCURIE": "biotools:octopus-toolkit", "version": [ "2.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0239", "term": "Sequence motif recognition" }, { "uri": "http://edamontology.org/operation_2575", "term": "Protein binding site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R", "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://octopus-toolkit2.readthedocs.io/en/latest/guide.html", "type": [ "General" ], "note": null }, { "url": "http://octopus-toolkit2.readthedocs.io/en/latest/tutorial.html", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gky083", "pmid": "29420797", "pmcid": "PMC5961211", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Octopus-toolkit: A workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data", "abstract": "© The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.Octopus-toolkit is a stand-alone application for retrieving and processing large sets of next-generation sequencing (NGS) data with a single step. Octopus-toolkit is an automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER applications. All the applications are installed on the user’s computer when the program starts. Upon the installation, it can automatically retrieve original files of various epigenomic and transcriptomic data sets, including ChIP-seq, ATAC-seq, DNase-seq, MeDIP-seq, MNase-seq and RNA-seq, from the gene expression omnibus data repository. The downloaded files can then be sequentially processed to generate BAM and BigWig files, which are used for advanced analyses and visualization. Currently, it can process NGS data from popular model genomes such as, human (Homo sapiens), mouse (Mus musculus), dog (Canis lupus familiaris), plant (Arabidopsis thaliana), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), worm (Caenorhabditis elegans), and budding yeast (Saccharomyces cerevisiae) genomes. With the processed files from Octopus-toolkit, the meta-analysis of various data sets, motif searches for DNA-binding proteins, and the identification of differentially expressed genes and/or protein-binding sites can be easily conducted with few commands by users. Overall, Octopus-toolkit facilitates the systematic and integrative analysis of available epigenomic and transcriptomic NGS big data.", "date": "2018-05-01T00:00:00Z", "citationCount": 25, "authors": [ { "name": "Kim T." }, { "name": "Seo H.D." }, { "name": "Hennighausen L." }, { "name": "Lee D." }, { "name": "Kang K." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": null, "email": "Octopustoolkit@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-06T14:31:33Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SigTree", "description": "Provides tools to identify and visualize branches in a phylogenetic tree that are significantly responsive to some intervention, taking as primary inputs a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip (OTU) labels and p-values.", "homepage": "https://cran.r-project.org/web/packages/SigTree/index.html", "biotoolsID": "sigtree", "biotoolsCURIE": "biotools:sigtree", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0324", "term": "Phylogenetic tree analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3056", "term": "Population genetics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://cran.r-project.org/web/packages/SigTree/SigTree.pdf", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.csbj.2017.06.002", "pmid": "28748045", "pmcid": "PMC5512180", "type": [], "version": null, "note": null, "metadata": { "title": "SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree", "abstract": "© 2017 The AuthorsMicrobial community analysis experiments to assess the effect of a treatment intervention (or environmental change) on the relative abundance levels of multiple related microbial species (or operational taxonomic units) simultaneously using high throughput genomics are becoming increasingly common. Within the framework of the evolutionary phylogeny of all species considered in the experiment, this translates to a statistical need to identify the phylogenetic branches that exhibit a significant consensus response (in terms of operational taxonomic unit abundance) to the intervention. We present the R software package SigTree, a collection of flexible tools that make use of meta-analysis methods and regular expressions to identify and visualize significantly responsive branches in a phylogenetic tree, while appropriately adjusting for multiple comparisons.", "date": "2017-01-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Stevens J.R." }, { "name": "Jones T.R." }, { "name": "Lefevre M." }, { "name": "Ganesan B." }, { "name": "Weimer B.C." } ], "journal": "Computational and Structural Biotechnology Journal" } } ], "credit": [ { "name": "John R. Stevens", "email": "john.r.stevens@usu.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-08-06T15:10:45Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MiSTIC", "description": "Integrated platform for the analysis of heterogeneity in large tumour transcriptome datasets.", "homepage": "https://github.com/iric-soft/MiSTIC", "biotoolsID": "mistic-tumour", "biotoolsCURIE": "biotools:mistic-tumour", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "C++", "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/iric-soft/MiSTIC", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkx338", "pmid": "28472340", "pmcid": "PMC5570030", "type": [], "version": null, "note": null, "metadata": { "title": "MiSTIC, an integrated platform for the analysis of heterogeneity in large tumour transcriptome datasets", "abstract": "© The Author(s) 2017.Genome-wide transcriptome profiling has enabled non-supervised classification of tumours, revealing different sub-groups characterized by specific gene expression features. However, the biological significance of these subtypes remains for the most part unclear. We describe herein an interactive platform, Minimum Spanning Trees Inferred Clustering (MiSTIC), that integrates the direct visualization and comparison of the gene correlation structure between datasets, the analysis of the molecular causes underlying co-variations in gene expression in cancer samples, and the clinical annotation of tumour sets defined by the combined expression of selected biomarkers. We have used MiSTIC to highlight the roles of specific transcription factors in breast cancer subtype specification, to compare the aspects of tumour heterogeneity targeted by different prognostic signatures, and to highlight biomarker interactions in AML. A version of MiSTIC preloaded with datasets described herein can be accessed through a public web server (http://mistic.iric.ca) in addition, the MiSTIC software package can be obtained (github.com/iric-soft/MiSTIC) for local use with personalized datasets.", "date": "2017-07-01T00:00:00Z", "citationCount": 11, "authors": [ { "name": "Lemieux S." }, { "name": "Sargeant T." }, { "name": "Laperriere D." }, { "name": "Ismail H." }, { "name": "Boucher G." }, { "name": "Rozendaal M." }, { "name": "Lavallee V.-P." }, { "name": "Ashton-Beaucage D." }, { "name": "Wilhelm B." }, { "name": "Hebert J." }, { "name": "Hilton D.J." }, { "name": "Mader S." }, { "name": "Sauvageau G." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Sylvie Mader", "email": "sylvie.mader@umontreal.ca", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-08-07T09:03:13Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MINTmap", "description": "Generate tRF profiles from short RNA-Seq datasets.", "homepage": "https://cm.jefferson.edu/MINTcodes/", "biotoolsID": "mintmap", "biotoolsCURIE": "biotools:mintmap", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2995", "term": "Sequence classification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-seq" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" } ], "operatingSystem": [ "Linux" ], "language": [ "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/TJU-CMC-Org/MINTmap/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/srep41184", "pmid": "28220888", "pmcid": "PMC5318995", "type": [], "version": null, "note": null, "metadata": { "title": "MINTmap: Fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data", "abstract": "© The Author(s) 2017.Transfer RNA fragments (tRFs) are an established class of constitutive regulatory molecules that arise from precursor and mature tRNAs. RNA deep sequencing (RNA-seq) has greatly facilitated the study of tRFs. However, the repeat nature of the tRNA templates and the idiosyncrasies of tRNA sequences necessitate the development and use of methodologies that differ markedly from those used to analyze RNA-seq data when studying microRNAs (miRNAs) or messenger RNAs (mRNAs). Here we present MINTmap (for MItochondrial and Nuclear TRF mapping), a method and a software package that was developed specifically for the quick, deterministic and exhaustive identification of tRFs in short RNA-seq datasets. In addition to identifying them, MINTmap is able to unambiguously calculate and report both raw and normalized abundances for the discovered tRFs. Furthermore, to ensure specificity, MINTmap identifies the subset of discovered tRFs that could be originating outside of tRNA space and flags them as candidate false positives. Our comparative analysis shows that MINTmap exhibits superior sensitivity and specificity to other available methods while also being exceptionally fast. The MINTmap codes are available through https://github.com/TJU-CMC-Org/MINTmap/ under an open source GNU GPL v3.0 license.", "date": "2017-02-21T00:00:00Z", "citationCount": 53, "authors": [ { "name": "Loher P." }, { "name": "Telonis A.G." }, { "name": "Rigoutsos I." } ], "journal": "Scientific Reports" } } ], "credit": [ { "name": "Isidore Rigoutsos", "email": "isidore.rigoutsos@jefferson.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-08-07T09:24:02Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EpiLog", "description": "Logical modelling of Epithelial dynamics. Definition, simulation and visualisation of qualitative models for epithelial pattern formation.", "homepage": "http://epilog-tool.org/", "biotoolsID": "epilog", "biotoolsCURIE": "biotools:epilog", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/epilog-tool/epilog", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "http://epilog-tool.org/documentation", "type": "Biological data", "note": null, "version": null }, { "url": "http://epilog-tool.org/downloads", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "http://epilog-tool.org/documentation", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.15613.1", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Epilog: A software for the logical modelling of epithelial dynamics", "abstract": "© 2018 Varela PL et al.Cellular responses are governed by regulatory networks subject to external signals from surrounding cells and to other micro-environmental cues. The logical (Boolean or multi-valued) framework proved well suited to study such processes at the cellular level, by specifying qualitative models of involved signalling pathways and gene regulatory networks. Here, we describe and illustrate the main features of EpiLog, a computational tool that implements an extension of the logical framework to the tissue level. EpiLog defines a collection of hexagonal cells over a 2D grid, which embodies a mono-layer epithelium. Basically, it defines a cellular automaton in which cell behaviours are driven by associated logical models subject to external signals. EpiLog is freely available on the web at http://epilog-tool.org. It is implemented in Java (version ≥1.7 required) and the source code is provided at https://github.com/epilog-tool/epilog under a GNU General Public License v3.0.", "date": "2018-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Varela P.L." }, { "name": "Ramos C.V." }, { "name": "Monteiro P.T." }, { "name": "Chaouiya C." } ], "journal": "F1000Research" } } ], "credit": [ { "name": null, "email": "support@epilog-tool.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-09T10:56:18Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BED", "description": "Biological Entity Dictionary. Get and explore mapping between identifiers of biological entities. It provides a way to connect to a BED Neo4j database in which the relationships between the identifiers from different sources are recorded.", "homepage": "https://github.com/patzaw/BED", "biotoolsID": "bed", "biotoolsCURIE": "biotools:bed", "version": [ "1.1.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3282", "term": "ID mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3345", "term": "Data identity and mapping" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://hub.docker.com/r/patzaw/bed-ucb-human/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/patzaw/BED/blob/master/README.md", "type": [ "General" ], "note": null }, { "url": "https://github.com/patzaw/BED/blob/master/vignettes/BED.Rmd", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.13925.3", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Patrice Godard", "email": "patrice.godard@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-09T11:08:22Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ISVASE", "description": "Identification of sequence variant associated with splicing event using RNA-seq data.", "homepage": "https://sourceforge.net/projects/isvase/", "biotoolsID": "isvase", "biotoolsCURIE": "biotools:isvase", "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_3170", "term": "RNA-seq" }, { "uri": "http://edamontology.org/topic_3320", "term": "RNA splicing" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R", "Perl" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://sourceforge.net/projects/isvase/files/README.txt/download", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-017-1732-7", "pmid": "28659141", "pmcid": "PMC5490186", "type": [], "version": null, "note": null, "metadata": { "title": "ISVASE: Identification of sequence variant associated with splicing event using RNA-seq data", "abstract": "© 2017 The Author(s).Background: Exon recognition and splicing precisely and efficiently by spliceosome is the key to generate mature mRNAs. About one third or a half of disease-related mutations affect RNA splicing. Software PVAAS has been developed to identify variants associated with aberrant splicing by directly using RNA-seq data. However, it bases on the assumption that annotated splicing site is normal splicing, which is not true in fact. Results: We develop the ISVASE, a tool for specifically identifying sequence variants associated with splicing events (SVASE) by using RNA-seq data. Comparing with PVAAS, our tool has several advantages, such as multi-pass stringent rule-dependent filters and statistical filters, only using split-reads, independent sequence variant identification in each part of splicing (junction), sequence variant detection for both of known and novel splicing event, additional exon-exon junction shift event detection if known splicing events provided, splicing signal evaluation, known DNA mutation and/or RNA editing data supported, higher precision and consistency, and short running time. Using a realistic RNA-seq dataset, we performed a case study to illustrate the functionality and effectiveness of our method. Moreover, the output of SVASEs can be used for downstream analysis such as splicing regulatory element study and sequence variant functional analysis. Conclusions: ISVASE is useful for researchers interested in sequence variants (DNA mutation and/or RNA editing) associated with splicing events. The package is freely available at https://sourceforge.net/projects/isvase/.", "date": "2017-06-28T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Aljohi H.A." }, { "name": "Liu W." }, { "name": "Lin Q." }, { "name": "Yu J." }, { "name": "Hu S." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Hasan Awad Aljohi", "email": "haljohi@kacst.edu.sa", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-08-09T16:33:25Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SubVis", "description": "Visual Exploration of Protein Alignments Resulting from Multiple Substitution Matrices.", "homepage": "https://cran.r-project.org/web/packages/SubVis/", "biotoolsID": "subvis", "biotoolsCURIE": "biotools:subvis", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "CRAN" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://cran.r-project.org/web/packages/SubVis/SubVis.pdf", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.7717/peerj.3492", "pmid": "28674656", "pmcid": "PMC5490468", "type": [], "version": null, "note": null, "metadata": { "title": "SubVis: An interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment", "abstract": "© 2017 Barlowe et al.Understanding how proteins mutate is critical to solving a host of biological problems. Mutations occur when an amino acid is substituted for another in a protein sequence. The set of likelihoods for amino acid substitutions is stored in a matrix and input to alignment algorithms. The quality of the resulting alignment is used to assess the similarity of two or more sequences and can vary according to assumptions modeled by the substitution matrix. Substitution strategies with minor parameter variations are often grouped together in families. For example, theBLOSUMandPAMmatrix families are commonly used because they provide a standard, predefined way of modeling substitutions. However, researchers often do not know if a given matrix family or any individual matrix within a family is the most suitable. Furthermore, predefined matrix families may inaccurately reflect a particular hypothesis that a researcher wishes to model or otherwise result in unsatisfactory alignments. In these cases, the ability to compare the effects of one or more custom matrices may be needed. This laborious process is often performed manually because the ability to simultaneously load multiple matrices and then compare their effects on alignments is not readily available in current software tools. This paper presents SubVis, an interactive R package for loading and applying multiple substitution matrices to pairwise alignments. Users can simultaneously explore alignments resulting from multiple predefined and custom substitution matrices. SubVis utilizes several of the alignment functions found in R, a common language among protein scientists. Functions are tied together with the Shiny platform which allows the modification of input parameters. Information regarding alignment quality and individual amino acid substitutions is displayed with the JavaScript language which provides interactive visualizations for revealing both high-level and low-level alignment information.", "date": "2017-01-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Barlowe S." }, { "name": "Coan H.B." }, { "name": "Youker R.T." } ], "journal": "PeerJ" } } ], "credit": [ { "name": "Scott Barlowe", "email": "sabarlowe@email.wcu.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-08-09T16:37:20Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "flippant", "description": "Automated analysis of dithionite scramblase assays.", "homepage": "https://bitbucket.org/graumannlabtools/flippant", "biotoolsID": "flippant", "biotoolsCURIE": "biotools:flippant", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2414", "term": "Protein function analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://bitbucket.org/graumannlabtools/flippant", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-017-1542-y", "pmid": "28253836", "pmcid": "PMC5335725", "type": [], "version": null, "note": null, "metadata": { "title": "flippant-An R package for the automated analysis of fluorescence-based scramblase assays", "abstract": "© 2017 The Author(s).Background: The lipid scrambling activity of protein extracts and purified scramblases is typically measured using a fluorescence-based assay. While the assay has yielded insight into the scramblase activity in crude membrane preparations, functional validation of candidate scramblases, stoichiometry of scramblase complexes as well as ATP-dependence of flippases, data analysis in its context has remained a task involving many manual steps. Results: With the extension package \"flippant\" to R, a free software environment for statistical computing and graphics, we introduce an integrated solution for the analysis and publication-grade graphical presentation of dithionite scramblase assays and demonstrate its utility in revisiting an originally manual analysis from the publication record, closely reproducing the reported results. Conclusions: \"flippant\" allows for quick, reproducible data analysis of scramblase activity assays and provides a platform for review, dissemination and extension of the strategies it employs.", "date": "2017-03-03T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Cotton R.J." }, { "name": "Ploier B." }, { "name": "Goren M.A." }, { "name": "Menon A.K." }, { "name": "Graumann J." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Richard J. Cotton", "email": "richierocks@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-08-10T12:38:43Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ANOCVA", "description": "A Non-Parametric Statistical Test to Compare Clustering Structures.", "homepage": "https://cran.r-project.org/web/packages/anocva/index.html", "biotoolsID": "anocva", "biotoolsCURIE": "biotools:anocva", "version": [ "0.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" }, { "uri": "http://edamontology.org/topic_3334", "term": "Neurology" }, { "uri": "http://edamontology.org/topic_3300", "term": "Physiology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://cran.r-project.org/web/packages/anocva/anocva.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.3389/fnins.2017.00016", "pmid": "28174516", "pmcid": "PMC5258722", "type": [], "version": null, "note": null, "metadata": { "title": "ANOCVA in R: A software to compare clusters between groups and its application to the study of autism spectrum disorder", "abstract": "Understanding how brain activities cluster can help in the diagnosis of neuropsychological disorders. Thus, it is important to be able to identify alterations in the clustering structure of functional brain networks. Here, we provide an R implementation of Analysis of Cluster Variability (ANOCVA), which statistically tests (1) whether a set of brain regions of interest (ROI) are equally clustered between two or more populations and (2) whether the contribution of each ROI to the differences in clustering is significant. To illustrate the usefulness of our method and software, we apply the R package in a large functional magnetic resonance imaging (fMRI) dataset composed of 896 individuals (529 controls and 285 diagnosed with ASD-autism spectrum disorder) collected by the ABIDE (The Autism Brain Imaging Data Exchange) Consortium. Our analysis show that the clustering structure of controls and ASD subjects are different (p < 0.001) and that specific brain regions distributed in the frontotemporal, sensorimotor, visual, cerebellar, and brainstem systems significantly contributed (p < 0.05) to this differential clustering. These findings suggest an atypical organization of domain-specific function brain modules in ASD.", "date": "2017-01-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Vidal M.C." }, { "name": "Sato J.R." }, { "name": "Balardin J.B." }, { "name": "Takahashi D.Y." }, { "name": "Fujita A." } ], "journal": "Frontiers in Neuroscience" } } ], "credit": [ { "name": "Maciel C. Vidal", "email": "calebe@ime.usp.br", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-08-11T08:55:01Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "freesurfer", "description": "Wrapper functions that interface with 'Freesurfer', a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'Freesurfer' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'Freesurfer' command and returns an R object of class 'nifti' or necessary output.", "homepage": "https://cran.r-project.org/web/packages/freesurfer/index.html", "biotoolsID": "freesurfer", "biotoolsCURIE": "biotools:freesurfer", "version": [ "1.6.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3763", "term": "Service invocation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "Neuroconductor", "CRAN" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/muschellij2/freesurfer", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://cran.r-project.org/src/contrib/freesurfer_1.6.1.tar.gz", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://cran.r-project.org/web/packages/freesurfer/freesurfer.pdf", "type": [ "User manual" ], "note": null }, { "url": "https://cran.r-project.org/web/packages/freesurfer/vignettes/exploring_included_data.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.14361.1", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Freesurfer: Connecting the Freesurfer software with R [version 1; referees: 2 approved]", "abstract": "© 2018 Muschelli J et al.We present the package freesurfer, a set of R functions that interface with Freesurfer, a commonly-used open-source software package for processing and analyzing structural neuroimaging data, specifically T1-weighted images. The freesurfer package performs operations on nifti image objects in R using command-line functions from Freesurfer, and returns R objects back to the user. freesurfer allows users to process neuroanatomical images and provides functionality to convert and read the output of the Freesurfer pipelines more easily, including brain images, brain surfaces, and Freesurfer output tables.", "date": "2018-01-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Muschelli J." }, { "name": "Sweeney E." }, { "name": "Crainiceanu C.M." } ], "journal": "F1000Research" } } ], "credit": [ { "name": "John Muschelli", "email": "muschellij2@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-11T11:28:06Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ShinyDiversity", "description": "Interactive application to explore various ecological diversity metrics", "homepage": "https://erictleung.shinyapps.io/shinydiversity", "biotoolsID": "shinydiversity", "biotoolsCURIE": "biotools:shinydiversity", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3056", "term": "Population genetics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/erictleung/shinydiversity", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.12688/f1000research.14217.1", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Shinydiversity - Understanding alpha and beta diversity through interactive visualizations [version 1; peer review: 1 approved, 1 approved with reservations]", "abstract": "© 2018 Leung ET et al.In the past few decades, ecologists have developed many diversity indices to describe within and between sample diversity. Consequently, it can be difficult to determine which index to choose and how the distribution of microbial communities affect these indices. We’ve developed an interactive application, ShinyDiversity, that dynamically visualizes different alpha or beta diversity indices. In enabling users to select and simultaneously visualize different indices, our application aims to facilitate understanding of how the microbial data affects selected indices.", "date": "2018-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Leung E.T." }, { "name": "Noronha R." }, { "name": "Mirza A." }, { "name": "Shenwai R." }, { "name": "Mpatziakas A." } ], "journal": "F1000Research" } } ], "credit": [ { "name": null, "email": null, "url": "https://github.com/erictleung/shinydiversity/issues", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-12T21:49:34Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RSEQREP", "description": "Cloud-enabled framework that allows users to execute start-to-end gene-level RNA-Seq analysis. It works with unstranded, stranded, and paired-end sequence FASTQ files. It automatically executes a series of customizable steps including reference alignment, CRAM compression, reference alignment QC, data normalization, multivariate data visualization, identification of differentially expressed genes, heatmaps, co-expressed gene clusters, enriched pathways, and a series of custom visualizations.", "homepage": "https://github.com/emmesgit/RSEQREP", "biotoolsID": "rseqrep", "biotoolsCURIE": "biotools:rseqrep", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" }, { "uri": "http://edamontology.org/operation_0571", "term": "Expression data visualisation" }, { "uri": "http://edamontology.org/operation_0313", "term": "Expression profile clustering" }, { "uri": "http://edamontology.org/operation_3439", "term": "Pathway or network prediction" }, { "uri": "http://edamontology.org/operation_3218", "term": "Sequencing quality control" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1636", "term": "Heat map" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_0928", "term": "Gene expression profile" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3170", "term": "RNA-seq" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Shell", "R", "Perl", "SQL" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://hub.docker.com/r/emmesdock/rseqrep/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/emmesgit/RSEQREP/wiki", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.13049.2", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting", "abstract": "© 2018 Jensen TL et al.RNA-Seq is increasingly being used to measure human RNA expression on a genome-wide scale. Expression profiles can be interrogated to identify and functionally characterize treatment-responsive genes. Ultimately, such controlled studies promise to reveal insights into molecular mechanisms of treatment effects, identify biomarkers, and realize personalized medicine. RNA-Seq Reports (RSEQREP) is a new open-source cloud-enabled framework that allows users to execute start-to-end gene-level RNA-Seq analysis on a preconfigured RSEQREP Amazon Virtual Machine Image (AMI) hosted by AWS or on their own Ubuntu Linux machine via a Docker container or installation script. The framework works with unstranded, stranded, and paired-end sequence FASTQ files stored locally, on Amazon Simple Storage Service (S3), or at the Sequence Read Archive (SRA). RSEQREP automatically executes a series of customizable steps including reference alignment, CRAM compression, reference alignment QC, data normalization, multivariate data visualization, identification of differentially expressed genes, heatmaps, co-expressed gene clusters, enriched pathways, and a series of custom visualizations. The framework outputs a file collection that includes a dynamically generated PDF report using R, knitr, and LaTeX, as well as publication-ready table and figure files. A user-friendly configuration file handles sample metadata entry, processing, analysis, and reporting options. The configuration supports time series RNA-Seq experimental designs with at least one pre- and one post-treatment sample for each subject, as well as multiple treatment groups and specimen types. All RSEQREP analyses components are built using open-source R code and R/Bioconductor packages allowing for further customization. As a use case, we provide RSEQREP results for a trivalent influenza vaccine (TIV) RNA-Seq study that collected 1 pre-TIV and 10 post-TIV vaccination samples (days 1-10) for 5 subjects and two specimen types (peripheral blood mononuclear cells and B-cells).", "date": "2018-01-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Goll J.B." }, { "name": "Jensen T.L." }, { "name": "Frasketi M." }, { "name": "Conway K." }, { "name": "Villarroel L." }, { "name": "Hill H." }, { "name": "Krampis K." } ], "journal": "F1000Research" } } ], "credit": [ { "name": null, "email": null, "url": "https://github.com/emmesgit/RSEQREP/issues", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-12T22:09:11Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "seqfam", "description": "Analysis of next generation sequencing (NGS) DNA data from families with known pedigree information in order to identify rare variants that are potentially causal of a disease/trait of interest. It can be used to verify pedigree information, to perform Monte Carlo gene dropping, to undertake regression-based gene burden testing, and to identify variants which segregate by affection status in families via user-defined pattern of occurrence rules.", "homepage": "https://github.com/mframpton/seqfam", "biotoolsID": "seqfam", "biotoolsCURIE": "biotools:seqfam", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" }, { "uri": "http://edamontology.org/operation_2520", "term": "DNA mapping" }, { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0654", "term": "DNA" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://seqfam.readthedocs.io/en/latest/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.13930.1", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Seqfam: A python package for analysis of next generation sequencing DNA data in families [version 1; peer review: 1 approved with reservations, 1 not approved]", "abstract": "© 2018 Frampton M et al.This article introduces seqfam, a python package which is primarily designed for analysing next generation sequencing (NGS) DNA data from families with known pedigree information in order to identify rare variants that are potentially causal of a disease/trait of interest. It uses the popular and versatile Pandas library, and can be straightforwardly integrated into existing analysis code/pipelines. Seqfam can be used to verify pedigree information, to perform Monte Carlo gene dropping, to undertake regression-based gene burden testing, and to identify variants which segregate by affection status in families via user-defined pattern of occurrence rules. Additionally, it can generate scripts for running analyses in a ‘MapReduce pattern’ on a computer cluster, something which is usually desirable in NGS data analysis and indeed ‘big data’ analysis in general. This article summarises how seqfam’s main user functions work and motivates their use. It also provides explanatory context for example scripts and data included in the package which demonstrate use cases. With respect to verifying pedigree information, software exists for efficiently calculating kinship coefficients, so seqfam performs the necessary extra steps of mapping pedigrees and kinship coefficients to expected and observed degrees of relationship respectively. Gene dropping and the application of variant pattern of occurrence rules in families can provide evidence for a variant being causal. The authors are unaware of other software which performs these tasks in familial cohorts, so seqfam fulfils this need. Gene burden rather than single marker tests are often used to detect rare causal variants due to greater power. Seqfam may be an attractive alternative to existing gene burden testing software due to its flexibility, particularly in grouping and aggregating variants.", "date": "2018-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Frampton M." }, { "name": "Schiff E.R." }, { "name": "Pontikos N." }, { "name": "Segal A.W." }, { "name": "Levine A.P." } ], "journal": "F1000Research" } } ], "credit": [ { "name": null, "email": null, "url": "https://github.com/mframpton/seqfam/issues", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-13T10:08:35Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Breathe Easy EDA", "description": "Easy and reliable identification of respiration-related artifacts in EDA data (data inspection and cleaning).", "homepage": "https://github.com/johnksander/BreatheEasyEDA", "biotoolsID": "breathe_easy_eda", "biotoolsCURIE": "biotools:breathe_easy_eda", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3303", "term": "Medicine" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "MATLAB" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/johnksander/BEEDA_sample_data", "type": "Biological data", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/johnksander/BreatheEasyEDA/blob/master/documentaton/BEEDA_user_guide.pdf", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.13849.1", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Breathe Easy EDA: A MATLAB toolbox for psychophysiology data management, cleaning, and analysis", "abstract": "Electrodermal activity (EDA) recordings are widely used in experimental psychology to measure skin conductance responses (SCRs) that reflect sympathetic nervous system arousal. However, irregular respiration patterns and deep breaths can cause EDA fluctuations that are difficult to distinguish from genuine arousal-related SCRs, presenting a methodological challenge that increases the likelihood of false positives in SCR analyses. Thus, it is crucial to identify respiration-related artifacts in EDA data. Here we developed a novel and freely distributed MATLAB toolbox, Breathe Easy EDA (BEEDA). BEEDA is a flexible toolbox that facilitates EDA visual inspection, allowing users to identify and eliminate respiration artifacts. BEEDA further includes functionality for EDA data analyses (measuring tonic and phasic EDA components) and reliability analyses for artifact identification. The toolbox is suitable for any experiment recording both EDA and respiration data, and flexibly adjusts to experiment-specific parameters (e.g., trial structure and analysis parameters).", "date": "2018-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Ksander J.C." }, { "name": "Kark S.M." }, { "name": "Madan C.R." } ], "journal": "F1000Research" } } ], "credit": [ { "name": null, "email": "jksander@brandeis.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-13T10:29:48Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GAC", "description": "Gene Associations with Clinical. One-stop shop for conducting statistical analysis to identify and visualize the association between a clinical outcome of interest and high-dimensional data types.", "homepage": "http://bbisr.shinyapps.winship.emory.edu/GAC/", "biotoolsID": "gac", "biotoolsCURIE": "biotools:gac", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2939", "term": "Principal component plotting" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3303", "term": "Medicine" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/manalirupji/GAC", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "http://bbisr.shinyapps.winship.emory.edu/GAC/#tab-3626-6", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.11840.4", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "GAC: Gene Associations with Clinical, a web based application", "abstract": "© 2018 Zhang X et al.We present GAC, a shiny R based tool for interactive visualization of clinical associations based on high-dimensional data. The tool provides a web-based suite to perform supervised principal component analysis (SuperPC), an approach that uses both high-dimensional data, such as gene expression, combined with clinical data to infer clinical associations. We extended the approach to address binary outcomes, in addition to continuous and time-to-event data in our package, thereby increasing the use and flexibility of SuperPC. Additionally, the tool provides an interactive visualization for summarizing results based on a forest plot for both binary and time-to-event data. In summary, the GAC suite of tools provide a one stop shop for conducting statistical analysis to identify and visualize the association between a clinical outcome of interest and high-dimensional data types, such as genomic data. Our GAC package has been implemented in R and is available via http://shinygispa.winship.emory.edu/GAC/. The developmental repository is available at https://github.com/manalirupji/GAC.", "date": "2018-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Kowalski J." }, { "name": "Zhang X." }, { "name": "Rupji M." } ], "journal": "F1000Research" } } ], "credit": [ { "name": null, "email": "manali.rupji@emory.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-13T10:40:03Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CellMap", "description": "Visualize protein-protein interaction (PPI) networks in the context of subcellular localization.", "homepage": "https://github.com/sacdallago/cellmap", "biotoolsID": "cellmap", "biotoolsCURIE": "biotools:cellmap", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" } ], "operatingSystem": [], "language": [ "JavaScript" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.12688/f1000research.12707.2", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "CellMap visualizes protein-protein interactions and subcellular localization", "abstract": "© 2018 Dallago C et al.Many tools visualize protein-protein interaction (PPI) networks. The tool introduced here, CellMap, adds one crucial novelty by visualizing PPI networks in the context of subcellular localization, i.e. the location in the cell or cellular component in which a PPI happens. Users can upload images of cells and define areas of interest against which PPIs for selected proteins are displayed (by default on a cartoon of a cell). Annotations of localization are provided by the user or through our in-house database. The visualizer and server are written in JavaScript, making CellMap easy to customize and to extend by researchers and developers.", "date": "2018-01-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Dallago C." }, { "name": "Goldberg T." }, { "name": "Andrade-Navarro M.A." }, { "name": "Alanis-Lobato G." }, { "name": "Rost B." } ], "journal": "F1000Research" } } ], "credit": [ { "name": null, "email": null, "url": "https://github.com/sacdallago/cellmap/issues", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-13T10:51:58Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "miRcomp-Shiny", "description": "Interactive assessment of qPCR-based microRNA quantification and quality control algorithms. Read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves.", "homepage": "https://laurenkemperman.shinyapps.io/mircomp/", "biotoolsID": "mircomp-shiny", "biotoolsCURIE": "biotools:mircomp-shiny", "version": [ "1.10.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2428", "term": "Validation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_3519", "term": "PCR experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "Bioconductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://bioconductor.org/packages/release/bioc/html/miRcomp.html", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "http://bioconductor.org/packages/release/bioc/src/contrib/miRcomp_1.10.0.tar.gz", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/vignettes/miRcomp/inst/doc/miRcomp.html", "type": [ "General" ], "note": null }, { "url": "http://bioconductor.org/packages/release/bioc/manuals/miRcomp/man/miRcomp.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.13098.1", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Matthew N. McCall", "email": "mccallm@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-13T11:10:28Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DROIDS", "description": "DROIDS (Detecting Relative Outlier Impacts in Dynamic Simulations), works in conjunction with existing molecular modeling software to convert any Linux gaming personal computer into a “comparative computational microscope” for observing the biophysical effects of mutations and other chemical changes in proteins.", "homepage": "https://github.com/gbabbitt/DROIDS-1.0---free-software-project-for-comparative-protein-dynamics", "biotoolsID": "droids", "biotoolsCURIE": "biotools:droids", "version": [ "1.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2476", "term": "Molecular dynamics" }, { "uri": "http://edamontology.org/operation_1777", "term": "Protein function prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0176", "term": "Molecular dynamics" } ], "operatingSystem": [ "Linux" ], "language": [ "Perl", "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/gbabbitt/DROIDS-1.0---free-software-project-for-comparative-protein-dynamics/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/gbabbitt/DROIDS-1.0---free-software-project-for-comparative-protein-dynamics/blob/master/DROIDS%201.20%20USER%20MANUAL.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.bpj.2018.01.020", "pmid": "29539389", "pmcid": "PMC5883555", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "DROIDS 1.20: A GUI-Based Pipeline for GPU-Accelerated Comparative Protein Dynamics", "abstract": "© 2018 Biophysical SocietyTraditional informatics in comparative genomics work only with static representations of biomolecules (i.e., sequence and structure), thereby ignoring the molecular dynamics (MD) of proteins that define function in the cell. A comparative approach applied to MD would connect this very short timescale process, defined in femtoseconds, to one of the longest in the universe: molecular evolution measured in millions of years. Here, we leverage advances in graphics-processing-unit-accelerated MD simulation software to develop a comparative method of MD analysis and visualization that can be applied to any two homologous Protein Data Bank structures. Our open-source pipeline, DROIDS (Detecting Relative Outlier Impacts in Dynamic Simulations), works in conjunction with existing molecular modeling software to convert any Linux gaming personal computer into a “comparative computational microscope” for observing the biophysical effects of mutations and other chemical changes in proteins. DROIDS implements structural alignment and Benjamini-Hochberg-corrected Kolmogorov-Smirnov statistics to compare nanosecond-scale atom bond fluctuations on the protein backbone, color mapping the significant differences identified in protein MD with single-amino-acid resolution. DROIDS is simple to use, incorporating graphical user interface control for Amber16 MD simulations, cpptraj analysis, and the final statistical and visual representations in R graphics and UCSF Chimera. We demonstrate that DROIDS can be utilized to visually investigate molecular evolution and disease-related functional changes in MD due to genetic mutation and epigenetic modification. DROIDS can also be used to potentially investigate binding interactions of pharmaceuticals, toxins, or other biomolecules in a functional evolutionary context as well.", "date": "2018-03-13T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Babbitt G.A." }, { "name": "Mortensen J.S." }, { "name": "Coppola E.E." }, { "name": "Adams L.E." }, { "name": "Liao J.K." } ], "journal": "Biophysical Journal" } } ], "credit": [ { "name": "Gregory A Babbitt", "email": "gabsbi@rit.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "daniel_stefan", "additionDate": "2018-08-14T01:15:13Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PROBer", "description": "PROBer is a program to quantify chemical modification profiles for a general set of sequencing-based ‘toeprinting’ assays, which aim at probing RNA structures (DMS/SHAPE-seq), detecting RNA modifications (Pseudo-seq), and investigating RNA-protein interactions (iCLIP).", "homepage": "http://pachterlab.github.io/PROBer/", "biotoolsID": "prober-chem", "biotoolsCURIE": "biotools:prober-chem", "version": [ "0.3.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3258", "term": "Transcriptome assembly" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R", "Perl", "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://pachterlab.github.io/PROBer/manual/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.cels.2017.04.007", "pmid": "28501650", "pmcid": "PMC5758053", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays", "abstract": "© 2017 Elsevier Inc.A number of sequencing-based transcriptase drop-off assays have recently been developed to probe post-transcriptional dynamics of RNA-protein interaction, RNA structure, and RNA modification. Although these assays survey a diverse set of epitranscriptomic marks, we use the term toeprinting assays since they share methodological similarities. Their interpretation is predicated on addressing a similar computational challenge: how to learn isoform-specific chemical modification profiles in the face of complex read multi-mapping. We introduce PROBer, a statistical model and associated software, that addresses this challenge for the analysis of toeprinting assays. PROBer takes sequencing data as input and outputs estimated transcript abundances and isoform-specific modification profiles. Results on both simulated and biological data demonstrate that PROBer significantly outperforms individual methods tailored for specific toeprinting assays. Since the space of toeprinting assays is ever expanding and these assays are likely to be performed and analyzed together, we believe PROBer's unified data analysis solution will be valuable to the RNA community.", "date": "2017-05-24T00:00:00Z", "citationCount": 10, "authors": [ { "name": "Li B." }, { "name": "Tambe A." }, { "name": "Aviran S." }, { "name": "Pachter L." } ], "journal": "Cell Systems" } } ], "credit": [ { "name": "Lior Pachter", "email": "lpachter@caltech.edu", "url": "http://pachterlab.github.io/PROBer/contact/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "daniel_stefan", "additionDate": "2018-08-14T01:48:59Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BlobTools", "description": "Visualisation, quality control and taxonomic partitioning of genome datasets.", "homepage": "https://github.com/DRL/blobtools", "biotoolsID": "blobtools", "biotoolsCURIE": "biotools:blobtools", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3184", "term": "Sequence assembly visualisation" }, { "uri": "http://edamontology.org/operation_3218", "term": "Sequencing quality control" }, { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [], "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" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux" ], "language": [ "R", "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.12688/f1000research.12232.1", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": null, "email": null, "url": "https://github.com/DRL/blobtools/pulls", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-17T09:48:07Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "YODEL", "description": "Peak caller for HITS-CLIP data.", "homepage": "https://github.com/LancePalmerStJude/YODEL/", "biotoolsID": "yodel", "biotoolsCURIE": "biotools:yodel", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3222", "term": "Peak calling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3656", "term": "Immunoprecipitation experiment" } ], "operatingSystem": [], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.12688/f1000research.11861.1", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": null, "email": null, "url": "https://github.com/LancePalmerStJude/YODEL/pulls", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-17T10:01:27Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "TIDDIT", "description": "Efficient and comprehensive structural variant caller for massive parallel sequencing data. Identify chromosomal rearrangements using Mate Pair or Paired End sequencing data. It allows identification of intra and inter-chromosomal translocations, deletions, tandem-duplications and inversions, using supplementary alignments as well as discordant pairs.", "homepage": "https://github.com/J35P312/TIDDIT", "biotoolsID": "tiddit", "biotoolsCURIE": "biotools:tiddit", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" }, { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" }, { "uri": "http://edamontology.org/operation_3228", "term": "Structural variation detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_3676", "term": "Exome sequencing" }, { "uri": "http://edamontology.org/topic_3175", "term": "DNA structural variation" } ], "operatingSystem": [], "language": [ "C++", "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.12688/f1000research.11168.2", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data", "abstract": "© 2017 Eisfeldt J et al.Reliable detection of large structural variation ( > 1000 bp) is important in both rare and common genetic disorders. Whole genome sequencing (WGS) is a technology that may be used to identify a large proportion of the genomic structural variants (SVs) in an individual in a single experiment. Even though SV callers have been extensively used in research to detect mutations, the potential usage of SV callers within routine clinical diagnostics is still limited. One well known, but not well-addressed problem is the large number of benign variants and reference errors present in the human genome that further complicates analysis. Even though there is a wide range of SV-callers available, the number of callers that allow detection of the entire spectra of SV at a low computational cost is still relatively limited.", "date": "2017-01-01T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Lindstrand A." }, { "name": "Eisfeldt J." }, { "name": "Vezzi F." }, { "name": "Olason P." }, { "name": "Nilsson D." } ], "journal": "F1000Research" } } ], "credit": [ { "name": "Francesco Vezzi", "email": "francesco.vezzi@scilifelab.se", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Jesper Eisfeldt", "email": "jesper.eisfeldt@scilifelab.se", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-21T09:48:33Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ogttMetrics", "description": "Management and analysis of large numbers of oral glucose tolerance test series. Computes diverse measures of glucose metabolism derived from oral glucose tolerance tests (OGTTs).", "homepage": "https://github.com/vjcitn/ogttMetrics", "biotoolsID": "ogttmetrics", "biotoolsCURIE": "biotools:ogttmetrics", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" }, { "uri": "http://edamontology.org/topic_3379", "term": "Preclinical and clinical studies" }, { "uri": "http://edamontology.org/topic_3360", "term": "Biomarkers" }, { "uri": "http://edamontology.org/topic_0152", "term": "Carbohydrates" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.12688/f1000research.11317.1", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ogttMetrics: Data structures and algorithms for oral glucose tolerance tests", "abstract": "© 2017 Stubbs BJ et al.We describe an open source software package, ogttMetrics, to compute diverse measures of glucose metabolism derived from oral glucose tolerance tests (OGTTs). Tools are provided to organize, visualize and compare OGTT data from large cohorts. Numerical difficulties in estimation of parameters of the Bergman minimal model are described, and in one large clinical trial, the simpler closed form index of Matsuda is observed to lead to similar rankings of individuals with respect to insulin sensitivity, and similar inferences concerning effects of modifications to carbohydrate content and glycemic index of experimental diets.", "date": "2017-01-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Stubbs B.J." }, { "name": "Frankston K." }, { "name": "Ramos M." }, { "name": "Laranjo N." }, { "name": "Sacks F.M." }, { "name": "Carey V.J." } ], "journal": "F1000Research" } } ], "credit": [ { "name": "VJ Carey", "email": "stvjc@channing.harvard.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-21T10:12:37Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "haploR", "description": "Query web based genome annotation tools HaploReg and RegulomeDB. It gathers information in a data frame which is suitable for downstream bioinformatic analyses. This will facilitate post-genome wide association studies streamline analysis for rapid discovery and interpretation of genetic associations.", "homepage": "https://github.com/izhbannikov/haploR", "biotoolsID": "haplor", "biotoolsCURIE": "biotools:haplor", "version": [ "2.0.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_0306", "term": "Text mining" }, { "uri": "http://edamontology.org/operation_3232", "term": "Gene expression QTL analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "CRAN" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://cran.r-project.org/web/packages/haploR/index.html", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://cran.r-project.org/src/contrib/haploR_2.0.6.tar.gz", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://cran.r-project.org/web/packages/haploR/vignettes/haplor-vignette.html", "type": [ "Training material" ], "note": null }, { "url": "https://cran.r-project.org/web/packages/haploR/haploR.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.10742.2", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "haploR: An R package for querying web-based annotation tools", "abstract": "© 2017 Zhbannikov IY et al.We developed haploR, an R package for querying web based genome annotation tools HaploReg and RegulomeDB. haploR gathers information in a data frame which is suitable for downstream bioinformatic analyses. This will facilitate post-genome wide association studies streamline analysis for rapid discovery and interpretation of genetic associations.", "date": "2017-01-01T00:00:00Z", "citationCount": 13, "authors": [ { "name": "Zhbannikov I.Y." }, { "name": "Arbeev K." }, { "name": "Ukraintseva S." }, { "name": "Yashin A.I." } ], "journal": "F1000Research" } } ], "credit": [ { "name": "Ilya Y. Zhbannikov", "email": "ilya.zhbannikov@duke.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-21T10:19:59Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ClusterFlow", "description": "Simple and flexible bioinformatics pipeline that automates and standardizes bioinformatics analyses on high-performance cluster environments.", "homepage": "http://clusterflow.io", "biotoolsID": "clusterflow", "biotoolsCURIE": "biotools:clusterflow", "version": [ "0.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_3432", "term": "Clustering" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [], "language": [ "Perl", "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ewels/clusterflow", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.12688/f1000research.10335.2", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Phil Ewels", "email": null, "url": "http://phil.ewels.co.uk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-21T10:30:24Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AR2", "description": "Novel automatic muscle artifact reduction method for ictal EEG interpretation.", "homepage": "https://github.com/shennanw/AR2", "biotoolsID": "ar2", "biotoolsCURIE": "biotools:ar2", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3557", "term": "Imputation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" }, { "uri": "http://edamontology.org/topic_3303", "term": "Medicine" } ], "operatingSystem": [], "language": [ "MATLAB" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.12688/f1000research.10569.2", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "AR2, a novel automatic muscle artifact reduction software method for ictal EEG interpretation: Validation and comparison of performance with commercially available software", "abstract": "© 2017 Weiss SA et al.Objective: To develop a novel software method (AR2) for reducing muscle contamination of ictal scalp electroencephalogram (EEG), and validate this method on the basis of its performance in comparison to a commercially available software method (AR1) to accurately depict seizure-onset location. Methods: A blinded investigation used 23 EEG recordings of seizures from 8 patients. Each recording was uninterpretable with digital filtering because of muscle artifact and processed using AR1 and AR2 and reviewed by 26 EEG specialists. EEG readers assessed seizure-onset time, lateralization, and region, and specified confidence for each determination. The two methods were validated on the basis of the number of readers able to render assignments, confidence, the intra-class correlation (ICC), and agreement with other clinical findings. Results: Among the 23 seizures, two-thirds of the readers were able to delineate seizure-onset time in 10 of 23 using AR1, and 15 of 23 using AR2 (p<0.01). Fewer readers could lateralize seizure-onset (p<0.05). The confidence measures of the assignments were low (probable-unlikely), but increased using AR2 (p<0.05). The ICC for identifying the time of seizure-onset was 0.15 (95% confidence interval (CI), 0.11-0.18) using AR1 and 0.26 (95% CI 0.21-0.30) using AR2. The EEG interpretations were often consistent with behavioral, neurophysiological, and neuro-radiological findings, with left sided assignments correct in 95.9% (CI 85.7-98.9%, n=4) of cases using AR2, and 91.9% (77.0-97.5%) (n=4) of cases using AR1. Conclusions: EEG artifact reduction methods for localizing seizure-onset does not result in high rates of interpretability, reader confidence, and inter-reader agreement. However, the assignments by groups of readers are often congruent with other clinical data. Utilization of the AR2 software method may improve the validity of ictal EEG artifact reduction.", "date": "2017-01-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Weiss S.A." }, { "name": "Asadi-Pooya A.A." }, { "name": "Vangala S." }, { "name": "Moy S." }, { "name": "Wyeth D.H." }, { "name": "Orosz I." }, { "name": "Gibbs M." }, { "name": "Schrader L." }, { "name": "Lerner J." }, { "name": "Cheng C.K." }, { "name": "Chang E." }, { "name": "Rajaraman R." }, { "name": "Keselman I." }, { "name": "Churchman P." }, { "name": "Bower-Baca C." }, { "name": "Numis A.L." }, { "name": "Ho M.G." }, { "name": "Rao L." }, { "name": "Bhat A." }, { "name": "Suski J." }, { "name": "Asadollahi M." }, { "name": "Ambrose T." }, { "name": "Fernandez A." }, { "name": "Nei M." }, { "name": "Skidmore C." }, { "name": "Mintzer S." }, { "name": "Eliashiv D.S." }, { "name": "Mathern G.W." }, { "name": "Nuwer M.R." }, { "name": "Sperling M." }, { "name": "Engel J." }, { "name": "Stern J.M." } ], "journal": "F1000Research" } }, { "doi": "10.12688/f1000research.10569.2", "pmid": null, "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "AR2, a novel automatic muscle artifact reduction software method for ictal EEG interpretation: Validation and comparison of performance with commercially available software", "abstract": "© 2017 Weiss SA et al.Objective: To develop a novel software method (AR2) for reducing muscle contamination of ictal scalp electroencephalogram (EEG), and validate this method on the basis of its performance in comparison to a commercially available software method (AR1) to accurately depict seizure-onset location. Methods: A blinded investigation used 23 EEG recordings of seizures from 8 patients. Each recording was uninterpretable with digital filtering because of muscle artifact and processed using AR1 and AR2 and reviewed by 26 EEG specialists. EEG readers assessed seizure-onset time, lateralization, and region, and specified confidence for each determination. The two methods were validated on the basis of the number of readers able to render assignments, confidence, the intra-class correlation (ICC), and agreement with other clinical findings. Results: Among the 23 seizures, two-thirds of the readers were able to delineate seizure-onset time in 10 of 23 using AR1, and 15 of 23 using AR2 (p<0.01). Fewer readers could lateralize seizure-onset (p<0.05). The confidence measures of the assignments were low (probable-unlikely), but increased using AR2 (p<0.05). The ICC for identifying the time of seizure-onset was 0.15 (95% confidence interval (CI), 0.11-0.18) using AR1 and 0.26 (95% CI 0.21-0.30) using AR2. The EEG interpretations were often consistent with behavioral, neurophysiological, and neuro-radiological findings, with left sided assignments correct in 95.9% (CI 85.7-98.9%, n=4) of cases using AR2, and 91.9% (77.0-97.5%) (n=4) of cases using AR1. Conclusions: EEG artifact reduction methods for localizing seizure-onset does not result in high rates of interpretability, reader confidence, and inter-reader agreement. However, the assignments by groups of readers are often congruent with other clinical data. Utilization of the AR2 software method may improve the validity of ictal EEG artifact reduction.", "date": "2017-01-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Weiss S.A." }, { "name": "Asadi-Pooya A.A." }, { "name": "Vangala S." }, { "name": "Moy S." }, { "name": "Wyeth D.H." }, { "name": "Orosz I." }, { "name": "Gibbs M." }, { "name": "Schrader L." }, { "name": "Lerner J." }, { "name": "Cheng C.K." }, { "name": "Chang E." }, { "name": "Rajaraman R." }, { "name": "Keselman I." }, { "name": "Churchman P." }, { "name": "Bower-Baca C." }, { "name": "Numis A.L." }, { "name": "Ho M.G." }, { "name": "Rao L." }, { "name": "Bhat A." }, { "name": "Suski J." }, { "name": "Asadollahi M." }, { "name": "Ambrose T." }, { "name": "Fernandez A." }, { "name": "Nei M." }, { "name": "Skidmore C." }, { "name": "Mintzer S." }, { "name": "Eliashiv D.S." }, { "name": "Mathern G.W." }, { "name": "Nuwer M.R." }, { "name": "Sperling M." }, { "name": "Engel J." }, { "name": "Stern J.M." } ], "journal": "F1000Research" } } ], "credit": [ { "name": null, "email": null, "url": "https://github.com/shennanw/AR2/issues", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-21T11:00:06Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SurvELM", "description": "A set of six survival analysis models to model high dimensional right-censored survival data by combining kernel ELMs with the Buckley–James estimator, regularized Cox model, random forests and boosting.", "homepage": "https://github.com/whcsu/SurvELM", "biotoolsID": "survelm", "biotoolsCURIE": "biotools:survelm", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3503", "term": "Incident curve plotting" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [ "Linux" ], "language": [ "R", "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/whcsu/SurvELM/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/whcsu/SurvELM/blob/master/SurvELM-Manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.knosys.2018.07.009", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "SurvELM: An R package for high dimensional survival analysis with extreme learning machine", "abstract": "© 2018 Elsevier B.V.Due to its fast learning speed, simplicity of code implementation and effectiveness in prediction, extreme learning machine(ELM) for single hidden layer feedforward neural networks (SLFNs) has received considerable attentions recently. However, few researchers consider its possible applications in high dimensional survival analysis. In this article, we present a set of six survival analysis models to model high dimensional right-censored survival data by combining kernel ELMs with the Buckley–James estimator, regularized Cox model, random forests and boosting. In addition to a traditional R package “SurvELM”, we also provide a simple and interactive web-based version using Shiny. The R Package is available at https://github.com/whcsu/SurvELM and its Shiny version is available at https://whcsu.shinyapps.io/SurvELM/. Experimental results on several real datasets demonstrate that the proposed models are strong competitors to other popular survival prediction models under high or ultra-high dimensional setting.", "date": "2018-11-15T00:00:00Z", "citationCount": 4, "authors": [ { "name": "Wang H." }, { "name": "Zhou L." } ], "journal": "Knowledge-Based Systems" } } ], "credit": [ { "name": "Hong Wang", "email": "wh@csu.edu.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "daniel_stefan", "additionDate": "2018-08-22T10:16:30Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PSSA", "description": "Pathogen Sequence Signature Analysis. Computational analysis of nucleotides sequences of different microorganisms. It uses phylogenetic analysis to identify the Serotype/Clade and Genotype of selected microorganisms. Analyses may be performed on very large data sets. The report of the analysis per sequence contains a brief overview of the nucleotide changes that produce an amino acid change, followed by details of the phylogenetic analysis including a phylogenetic tree.", "homepage": "http://pssa.itiud.org", "biotoolsID": "pssa", "biotoolsCURIE": "biotools:pssa", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0323", "term": "Phylogenetic tree generation" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_0324", "term": "Phylogenetic tree analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0781", "term": "Virology" }, { "uri": "http://edamontology.org/topic_3324", "term": "Infectious disease" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "PHP" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/florezfernandez/pssa", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.12688/F1000RESEARCH.10393.1", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Pathogen Sequence Signature Analysis (PSSA): A software tool for analyzing sequences to identify microorganism genotypes", "abstract": "© 2017 Salvatierra K and Florez H.Introduction The chikungunya virus (CHIKV) is an arbovirus vectored by Aedes mosquitoes that infects humans in tropical and sub-tropical areas of Asia and Africa. Recently, outbreaks have been reported in tropical and sub-tropical areas of countries that were previously unaffected (e.g., Brazil, Colombia). Currently, the following geographical genotypes have been identified through phylogenetic analysis of CHIKV E1 gene sequences: the West African (WAf), East/Central/South African (ECSA), and Asian genotypes. Outbreaks in a geographical area can happen with the same or different genotypes. Determining which genotypes are circulating in an outbreak is important for public health management. Objectives To create a computer-based system available online that is suitable for detecting changes in CHIKV nucleotide and amino acid sequences and identifying their corresponding geographical genotype. Methods We used several computer frameworks, tools, programming languages, algorithms, and infrastructure systems to build a software tool that analyzes changes in nucleotide and amino acid sequences and identifies different geographical genotypes through phylogenetic analysis. Results We have built an online software tool called Pathogen Sequence Signature Analysis (PSSA) that allows researchers to analyze nucleotide and amino acid sequence variations between sample CHIKV sequences taken from infected patients and obtained through conventional Sanger sequencing, to identify their corresponding geographical genotype. Conclusion PSSA is able to analyze sequences in a simple and effective manner, and includes proper documentation (i.e., UML diagrams) and also basic examples that serve to test the algorithm. Furthermore, PSSA provides various ways to visualize the data in order to aid understanding and interpretation of results. Results provided by PSSA will be useful for the identification of circulating CHIKV genotypes and public health surveillance.", "date": "2017-01-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Salvatierra K." }, { "name": "Florez H." } ], "journal": "F1000Research" } } ], "credit": [ { "name": null, "email": "iti@udistrital.edu.co", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-22T10:50:08Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "QALMA", "description": "QALMA (Quality Assurance for Linac with MATLAB), a MALAB toolkit which aims to simplify the quantitative analysis of quality assurance for medical linear accelerator.", "homepage": "https://github.com/ElsevierSoftwareX/SOFTX-D-17-00089", "biotoolsID": "qalma", "biotoolsCURIE": "biotools:qalma", "version": [ "V1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "MATLAB" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/ElsevierSoftwareX/SOFTX-D-17-00089/blob/master/qalma_manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.softx.2018.03.003", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "QALMA: A computational toolkit for the analysis of quality protocols for medical linear accelerators in radiation therapy", "abstract": "© 2018 The AuthorsQuality Assurance (QA) for medical linear accelerator (linac) is one of the primary concerns in external beam radiation Therapy. Continued advancements in clinical accelerators and computer control technology make the QA procedures more complex and time consuming which often, adequate software accompanied with specific phantoms is required. To ameliorate that matter, we introduce QALMA (Quality Assurance for Linac with MATLAB), a MALAB toolkit which aims to simplify the quantitative analysis of QA for linac which includes Star-Shot analysis, Picket Fence test, Winston–Lutz test, Multileaf Collimator (MLC) log file analysis and verification of light & radiation field coincidence test.", "date": "2018-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Rahman M.M." }, { "name": "Lei Y." }, { "name": "Kalantzis G." } ], "journal": "SoftwareX" } } ], "credit": [ { "name": "Georgios Kalantzis", "email": "gkalan@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "daniel_stefan", "additionDate": "2018-08-22T11:02:51Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Phylommand", "description": "Four programs to create, manipulate, and/or analyze phylogenetic trees or pairwise alignments.", "homepage": "https://github.com/mr-y/phylommand", "biotoolsID": "phylommand", "biotoolsCURIE": "biotools:phylommand", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0323", "term": "Phylogenetic tree generation" }, { "uri": "http://edamontology.org/operation_0326", "term": "Phylogenetic tree editing" }, { "uri": "http://edamontology.org/operation_0324", "term": "Phylogenetic tree analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2523", "term": "Phylogenetic data" }, "format": [ { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_1423", "term": "Phylip distance matrix" }, { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2523", "term": "Phylogenetic data" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.12688/F1000RESEARCH.10446.1", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": null, "email": null, "url": "https://github.com/mr-y/phylommand/issues", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-08-22T11:06:44Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FAIMS", "description": "FAIMS is a native Android application that can be used for data capture when doing field work.", "homepage": "https://github.com/ElsevierSoftwareX/SOFTX-D-17-00021", "biotoolsID": "faims_mobile", "biotoolsCURIE": "biotools:faims_mobile", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" } ], "operatingSystem": [ "Linux" ], "language": [ "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://faimsproject.atlassian.net/wiki/spaces/FAIMS/overview", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.softx.2017.12.006", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "FAIMS Mobile: Flexible, open-source software for field research", "abstract": "© 2017 The AuthorsFAIMS Mobile is a native Android application supported by an Ubuntu server facilitating human-mediated field research across disciplines. It consists of ‘core’ Java and Ruby software providing a platform for data capture, which can be deeply customised using ‘definition packets’ consisting of XML documents (data schema and UI) and Beanshell scripts (automation). Definition packets can also be generated using an XML-based domain-specific language, making customisation easier. FAIMS Mobile includes features allowing rich and efficient data capture tailored to the needs of fieldwork. It also promotes synthetic research and improves transparency and reproducibility through the production of comprehensive datasets that can be mapped to vocabularies or ontologies as they are created.", "date": "2018-01-01T00:00:00Z", "citationCount": 4, "authors": [ { "name": "Ballsun-Stanton B." }, { "name": "Ross S.A." }, { "name": "Sobotkova A." }, { "name": "Crook P." } ], "journal": "SoftwareX" } } ], "credit": [ { "name": null, "email": "support@fedarch.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "daniel_stefan", "additionDate": "2018-08-22T11:17:40Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Ergo", "description": "Ergo is a C++ program for all-electron Hartree–Fock and Kohn–Sham density functional theory electronic structure calculations using Gaussian basis sets.", "homepage": "https://github.com/ElsevierSoftwareX/SOFTX-D-18-00001", "biotoolsID": "ergo_structure", "biotoolsCURIE": "biotools:ergo_structure", "version": [ "3.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2476", "term": "Molecular dynamics" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "C++", "C" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ElsevierSoftwareX/SOFTX-D-18-00001/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "http://ergoscf.org/documentation.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.softx.2018.03.005", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Ergo: An open-source program for linear-scaling electronic structure calculations", "abstract": "© 2018 The AuthorsErgo is a C++ program for all-electron Hartree–Fock and Kohn–Sham density functional theory electronic structure calculations using Gaussian basis sets. The program uses algorithms for which the computational cost increases linearly with system size for all parts of the calculation, including computation of the Fock/Kohn–Sham matrix and density matrix construction. Both spin-restricted and unrestricted calculations are supported, and both pure and hybrid density functionals. The program also supports linear-scaling computation of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) vectors. This paper briefly describes how the code is organized and provides examples of how it can be used.", "date": "2018-01-01T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Rudberg E." }, { "name": "Rubensson E.H." }, { "name": "Salek P." }, { "name": "Kruchinina A." } ], "journal": "SoftwareX" } } ], "credit": [ { "name": null, "email": "info@ergoscf.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "daniel_stefan", "additionDate": "2018-08-23T04:36:42Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MLDA", "description": "MLDA is a tool for the exploration and analysis of multi-label datasets with both simple and multiple views. MLDA comprises a GUI and a Java API, providing the user with a wide set of charts, metrics, methods for transforming and preprocessing data, as well as comparison of several datasets.", "homepage": "https://github.com/i02momuj/MLDA/releases/tag/1.2.2", "biotoolsID": "mlda", "biotoolsCURIE": "biotools:mlda", "version": [ "1.2.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3802", "term": "Sorting" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/i02momuj/MLDA/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/i02momuj/MLDA/blob/master/doc/MLDA_Doc.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.knosys.2017.01.018", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MLDA: A tool for analyzing multi-label datasets", "abstract": "© 2017The objective of this paper is to present MLDA, a tool for the exploration and analysis of multi-label datasets with both simple and multiple views. MLDA comprises a GUI and a Java API, providing the user with a wide set of charts, metrics, methods for transforming and preprocessing data, as well as comparison of several datasets. The paper introduces the main features of the framework, and introduces its use toward some illustrative examples.", "date": "2017-04-01T00:00:00Z", "citationCount": 11, "authors": [ { "name": "Moyano J.M." }, { "name": "Gibaja E.L." }, { "name": "Ventura S." } ], "journal": "Knowledge-Based Systems" } } ], "credit": [ { "name": "Sebastian Ventura", "email": "sventura@uco.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "daniel_stefan", "additionDate": "2018-08-23T05:37:12Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ConfocalGN", "description": "ConfocalGN is a user-friendly software that can generate synthetic microscopy stacks from a ground truth (i.e. the observed object) specified as a 3D bitmap or a list of fluorophore coordinates. This software can analyze a real microscope image stack to set the noise parameters and directly generate new images of the object with noise characteristics similar to that of the sample image.", "homepage": "https://github.com/ElsevierSoftwareX/SOFTX-D-17-00018", "biotoolsID": "confocalgn", "biotoolsCURIE": "biotools:confocalgn", "version": [ "v1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3385", "term": "Light microscopy" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "MATLAB" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/SergeDmi/ConfocalGN/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.softx.2017.09.002", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ConfocalGN: A minimalistic confocal image generator", "abstract": "© 2017Validating image analysis pipelines and training machine-learning segmentation algorithms require images with known features. Synthetic images can be used for this purpose, with the advantage that large reference sets can be produced easily. It is however essential to obtain images that are as realistic as possible in terms of noise and resolution, which is challenging in the field of microscopy. We describe ConfocalGN, a user-friendly software that can generate synthetic microscopy stacks from a ground truth (i.e. the observed object) specified as a 3D bitmap or a list of fluorophore coordinates. This software can analyze a real microscope image stack to set the noise parameters and directly generate new images of the object with noise characteristics similar to that of the sample image. With a minimal input from the user and a modular architecture, ConfocalGN is easily integrated with existing image analysis solutions.", "date": "2017-01-01T00:00:00Z", "citationCount": 4, "authors": [ { "name": "Dmitrieff S." }, { "name": "Nedelec F." } ], "journal": "SoftwareX" } } ], "credit": [ { "name": "Serge Dmitrieff", "email": "serge.dmitrieff@embl.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "daniel_stefan", "additionDate": "2018-08-23T05:50:16Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "eRDF Analyser", "description": "eRDF Analyser is an interactive MATLAB GUI for reduced density function (RDF) or pair distribution function (PDF) analysis of amorphous and polycrystalline materials to study their local structure.", "homepage": "https://github.com/ElsevierSoftwareX/SOFTX-D-17-00005", "biotoolsID": "erdf_analyser", "biotoolsCURIE": "biotools:erdf_analyser", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2476", "term": "Molecular dynamics" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Plug-in", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" }, { "uri": "http://edamontology.org/topic_0611", "term": "Electron microscopy" } ], "operatingSystem": [ "Windows" ], "language": [ "MATLAB" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://erdfanalyser.github.io/MATLABv1/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.softx.2017.07.001", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "eRDF Analyser: An interactive GUI for electron reduced density function analysis", "abstract": "© 2017 The AuthorseRDF Analyser is an interactive MATLAB GUI for reduced density function (RDF) or pair distribution function (PDF) analysis of amorphous and polycrystalline materials to study their local structure. It is developed as an integrated tool with an easy-to-use interface that offers a streamlined approach to extract RDF from electron diffraction data without the need for external routines. The software incorporates recent developments in scattering factor parameterisation and an automated fitting routine for the atomic scattering curve. It also features an automated optimisation routine for determination of the position of the centre of diffraction patterns recorded using both central and off-centre locations of the incident beam. It is available in both open source code (MATLAB m-file) and executable form.", "date": "2017-01-01T00:00:00Z", "citationCount": 11, "authors": [ { "name": "Shanmugam J." }, { "name": "Borisenko K.B." }, { "name": "Chou Y.-J." }, { "name": "Kirkland A.I." } ], "journal": "SoftwareX" } } ], "credit": [ { "name": "Janaki Shanmugam", "email": "shanmugamjanaki+eRDF@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "daniel_stefan", "additionDate": "2018-08-23T11:59:06Z", "lastUpdate": "2018-12-10T12:59:01Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }