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Ralph. (2019). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources 19(2), 552–566.", "metadata": { "title": "Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes", "abstract": "", "date": "2019-03-01T00:00:00Z", "citationCount": 123, "authors": [], "journal": "Molecular Ecology Resources" } }, { "doi": "10.1101/2025.08.07.669155", "pmid": "40832315", "pmcid": "PMC12363870", "type": [ "Primary" ], "version": "5.0", "note": "BC Haller, PL Ralph, PW Messer. (2025). SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes. bioRxiv, 2025.08. 07.669155", "metadata": null }, { "doi": "10.1086/723601", "pmid": "37130229", "pmcid": "PMC10793872", "type": [ "Primary" ], "version": "4.0", "note": "B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary modeling. 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"https://pypi.io/packages/source/m/metasbt/metasbt-0.1.4.post1.tar.gz", "type": "Software package", "note": null, "version": "0.1.4" } ], "documentation": [ { "url": "https://github.com/cumbof/MetaSBT/wiki", "type": [ "General" ], "note": "Official MetaSBT Wiki" } ], "publication": [], "credit": [ { "name": "Fabio Cumbo", "email": "fabio.cumbo@gmail.com", "url": "https://cumbof.github.io", "orcidid": "https://orcid.org/0000-0003-2920-5838", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Maintainer", "Support" ], "note": null } ], "owner": "fabiocumbo", "additionDate": "2025-06-17T20:53:54.551980Z", "lastUpdate": "2025-08-29T00:30:28.809173Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ProteinProspector", "description": "A suite of protein identification tools.", "homepage": "http://prospector.ucsf.edu", "biotoolsID": "proteinprospector", "biotoolsCURIE": "biotools:proteinprospector", "version": [], "otherID": [ { "value": "RRID:SCR_014558", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2929", "term": "Protein fragment weight comparison" }, { "uri": "http://edamontology.org/operation_3647", "term": "Blind peptide database search" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3489", "term": "Database management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://prospector.ucsf.edu/prospector/html/instruct/allman.htm", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1074/mcp.d500002-mcp200", "pmid": "15937296", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cells, time-of-flight mass spectrometer: II New developments in protein prospector allow for reliable and comprehensive automatic analysis of large datasets", "abstract": "A thorough analysis of the protein interaction partners of the yeast GTPase Gsp1p was carried out by a multidimensional chromatography strategy of strong cation exchange fractionation of peptides followed by reverse phase LC-ESI-MSMS using a QSTAR instrument. This dataset was then analyzed using the latest developmental version of Protein Prospector. The Prospector search results were also compared with results from the search engine \"Mascot\" using a new results comparison program within Prospector named \"SearchCompare.\" The results from this study demonstrate that the high quality data produced on a quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry instrument allows for confident assignment of the vast majority of interpretable spectra by current search engines. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.", "date": "2005-08-01T00:00:00Z", "citationCount": 165, "authors": [ { "name": "Chalkley R.J." }, { "name": "Baker P.R." }, { "name": "Huang L." }, { "name": "Hansen K.C." }, { "name": "Allen N.P." }, { "name": "Rexach M." }, { "name": "Burlingame A.L." } ], "journal": "Molecular and Cellular Proteomics" } } ], "credit": [ { "name": "Admin", "email": "ppadmin@cgl.ucsf.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": null, "email": "webmaster@ms-utils.org", "url": "http://ms-utils.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null } ], "owner": "msutils_import", "additionDate": "2017-01-17T14:51:18Z", "lastUpdate": "2025-08-28T15:15:11.245617Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "n.m.palmblad@lumc.nl" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "VAPOR", "description": "VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.", "homepage": "https://github.com/wm75/vaporup", "biotoolsID": "vapor", "biotoolsCURIE": "biotools:vapor", "version": [ "1.0.3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" }, { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/connor-lab/vapor", "type": [ "Other" ], "note": "Original VAPOR repository from which versions prior to 1.0.3 were released" } ], "download": [ { "url": "https://pypi.org/project/vaporup/#files", "type": "Software package", "note": null, "version": null }, { "url": "https://doi.org/10.5281/zenodo.15364147", "type": "Biological data", "note": "A curated collection of reference sequences for each influenza A genome segment that can be used with the tool for classification of sequences from this virus", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/btz814", "pmid": "31693070", "pmcid": "PMC7703727", "type": [], "version": null, "note": null, "metadata": { "title": "Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications", "abstract": "Motivation: Influenza viruses represent a global public health burden due to annual epidemics and pandemic potential. Due to a rapidly evolving RNA genome, inter-species transmission, intra-host variation, and noise in short-read data, reads can be lost during mapping, and de novo assembly can be time consuming and result in misassembly. We assessed read loss during mapping and designed a graph-based classifier, VAPOR, for selecting mapping references, assembly validation and detection of strains of non-human origin. Results: Standard human reference viruses were insufficient for mapping diverse influenza samples in simulation. VAPOR retrieved references for 257 real whole-genome sequencing samples with a mean of > 99:8% identity to assemblies, and increased the proportion of mapped reads by up to 13.3% compared to standard references. VAPOR has the potential to improve the robustness of bioinformatics pipelines for surveillance and could be adapted to other RNA viruses.", "date": "2020-01-01T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Southgate J.A." }, { "name": "Bull M.J." }, { "name": "Brown C.M." }, { "name": "Watkins J." }, { "name": "Corden S." }, { "name": "Southgate B." }, { "name": "Moore C." }, { "name": "Connor T.R." } ], "journal": "Bioinformatics" } } ], "credit": [], "owner": "Kigaard", "additionDate": "2020-01-14T09:34:01Z", "lastUpdate": "2025-08-28T14:32:58.093703Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "wm75" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Make2D-DB II", "description": "Make2D-DB II is an environment to create, convert, publish, interconnect and keep up-to-date 2D-PAGE databases. The tool offers the possibility to automatically update data related to numerous external data resources. It is also possible to dynamically interconnect several remote databases or projects to form a virtual global database accessible from one single entry point. This tool can also be used to build up 2D-PAGE repositories, accessible by any one from the Web.", "homepage": "https://world-2dpage.expasy.org/make2ddb/", "biotoolsID": "make2d-db_ii", "biotoolsCURIE": "biotools:make2d-db_ii", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" }, { "uri": "http://edamontology.org/operation_3630", "term": "Protein quantification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://world-2dpage.expasy.org/make2ddb/1.Readme_main.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/pmic.200300483", "pmid": "12923769", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The Make 2D-DB II package: Conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases", "abstract": "The Make 2D-DB tool has been previously developed to help build federated two-dimensional gel electrophoresis (2-DE) databases on one's own web site. The purpose of our work is to extend the strength of the first package and to build a more efficient environment. Such an environment should be able to fulfill the different needs and requirements arising from both the growing use of 2-DE techniques and the increasing amount of distributed experimental data.", "date": "2003-08-01T00:00:00Z", "citationCount": 27, "authors": [ { "name": "Mostaguir K." }, { "name": "Hoogland C." }, { "name": "Binz P.-A." }, { "name": "Appel R.D." } ], "journal": "Proteomics" } } ], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:40Z", "lastUpdate": "2025-08-28T13:43:51.088758Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Swiss Mass Abacus", "description": "Calculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations.", "homepage": "https://glycoproteome.expasy.org/swiss-mass-abacus/", "biotoolsID": "swiss_mass_abacus", "biotoolsCURIE": "biotools:swiss_mass_abacus", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0417", "term": "Protein post-translation modification site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0122", "term": "Structural genomics" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://glycoproteome.expasy.org/swiss-mass-abacus/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:54Z", "lastUpdate": "2025-08-28T13:43:28.119620Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Glydin", "description": "Glydin' compiles and maps information relative to glycoepitopes (glycan determinants) as published in the literature or reported in databases. The output is an interactive network of strucutrally related glycan sub-structures.", "homepage": "https://glycoproteome.expasy.org/epitopes/", "biotoolsID": "glydin", "biotoolsCURIE": "biotools:glydin", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0417", "term": "Protein post-translation modification site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://glycoproteome.expasy.org/epitopes/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:30Z", "lastUpdate": "2025-08-28T13:41:40.603256Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "IScan", "description": "A package to identify insertion sequences and similar transposable elements, their inverted repeats, and the direct target repeats they generate in entire genomes.", "homepage": "https://www.expasy.org/resources/iscan", "biotoolsID": "iscan", "biotoolsCURIE": "biotools:iscan", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0226", "term": "Annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Linux" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ieu.uzh.ch/wagner/software/IScan/index.html", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:10Z", "lastUpdate": "2025-08-28T13:33:36.585259Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }
