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{ "count": 986, "next": "?page=2", "previous": null, "list": [ { "name": "fermo-core", "description": "fermo-core is the backend of the metabolomics dashboard FERMO. It can be used for large-scale processing of metabolomics data and integration of phenotypic and other orthogonal data.", "homepage": "https://github.com/fermo-metabolomics/fermo_core", "biotoolsID": "fermo-core", "biotoolsCURIE": "biotools:fermo-core", "version": [ "0.6.3" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [ "FERMO" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/fermo-metabolomics/fermo_core", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/fermo-metabolomics", "type": [ "Repository" ], "note": "GitHub Community managing FERMO-related repositories" }, { "url": "https://github.com/orgs/fermo-metabolomics/discussions", "type": [ "Discussion forum" ], "note": null } ], "download": [ { "url": "https://github.com/fermo-metabolomics/fermo_core/releases/tag/0.6.3", "type": "Source code", "note": null, "version": "0.6.3" }, { "url": "https://pypi.org/project/fermo-core/0.6.3/", "type": "Source code", "note": "PyPI-deposited wheel and source code", "version": "0.6.3" } ], "documentation": [ { "url": "https://fermo-metabolomics.github.io/fermo_docs/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/2022.12.21.521422", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "Preprint released on bioRxiv", "metadata": null } ], "credit": [ { "name": "Mitja M. Zdouc", "email": "zdoucmm@gmail.com", "url": "https://github.com/mmzdouc", "orcidid": "https://orcid.org/0000-0001-6534-6609", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Lead Developer and Initiator" }, { "name": "Fermo Metabolomics", "email": null, "url": "https://github.com/fermo-metabolomics", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Maintainer" ], "note": "GitHub Community overseeing development of the project" } ], "owner": "mmzdouc", "additionDate": "2025-05-09T18:13:37.471507Z", "lastUpdate": "2025-05-09T18:46:02.403653Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fermo", "description": "FERMO is a metabolomics dashboard designed to facilitate hypothesis-driven prioritization of molecules and samples, and integrates LC-MS metabolomics data with phenotype information, sample grouping, and genomic data. FERMO is applicable in a variety of biological sciences, including natural product drug discovery, microbiology, or agriculture.", "homepage": "https://github.com/fermo-metabolomics/fermo", "biotoolsID": "fermo", "biotoolsCURIE": "biotools:fermo", "version": [ "1.1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [ "FERMO" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/fermo-metabolomics/fermo", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/fermo-metabolomics", "type": [ "Repository" ], "note": "GitHub Organization page organizing repositories related to FERMO" }, { "url": "https://github.com/orgs/fermo-metabolomics/discussions", "type": [ "Discussion forum" ], "note": null } ], "download": [ { "url": "https://github.com/fermo-metabolomics/FERMO/releases/tag/1.1.0", "type": "Source code", "note": null, "version": "1.1.0" } ], "documentation": [ { "url": "https://fermo-metabolomics.github.io/fermo_docs/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/2022.12.21.521422", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": "Preprint released on bioRxiv", "metadata": null } ], "credit": [ { "name": "Mitja M. Zdouc", "email": "zdoucmm@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0001-6534-6609", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Initiator and lead developer" }, { "name": "Fermo Metabolomics", "email": null, "url": "https://github.com/fermo-metabolomics", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Maintainer" ], "note": "Governing body overseeing development" } ], "owner": "mmzdouc", "additionDate": "2025-05-09T18:02:39.924632Z", "lastUpdate": "2025-05-09T18:14:33.071182Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AMICI", "description": "AMICI provides a multi-language (Python, C++, Matlab) interface for the SUNDIALS solvers CVODES (for ordinary differential equations) and IDAS (for algebraic differential equations). AMICI allows the user to read differential equation models specified as SBML or PySB and automatically compiles such models into .mex simulation files (Matlab), C++ executables or Python modules.\n\nBeyond forward integration, the compiled simulation file also allows for forward sensitivity analysis, steady state sensitivity analysis and adjoint sensitivity analysis for likelihood-based output functions.\n\nThe interface was designed to provide routines for efficient gradient computation in parameter estimation of biochemical reaction models but it is also applicable to a wider range of differential equation constrained optimization problems.", "homepage": "https://github.com/AMICI-dev/AMICI", "biotoolsID": "AMICI", "biotoolsCURIE": "biotools:AMICI", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3562", "term": "Network simulation" }, { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_2585", "term": "SBML" }, { "uri": "http://edamontology.org/format_4015", "term": "PEtab" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3870", "term": "Trajectory data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "MATLAB", "C++", "Python" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/AMICI-dev/AMICI/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "https://amici.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btab227", "pmid": "33821950", "pmcid": "PMC8545331", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "AMICI: high-performance sensitivity analysis for large ordinary differential equation models", "abstract": "Ordinary differential equation models facilitate the understanding of cellular signal transduction and other biological processes. However, for large and comprehensive models, the computational cost of simulating or calibrating can be limiting. AMICI is a modular toolbox implemented in C++/Python/MATLAB that provides efficient simulation and sensitivity analysis routines tailored for scalable, gradient-based parameter estimation and uncertainty quantification.", "date": "2021-10-15T00:00:00Z", "citationCount": 37, "authors": [ { "name": "Frohlich F." }, { "name": "Weindl D." }, { "name": "Schalte Y." }, { "name": "Pathirana D." }, { "name": "Paszkowski L." }, { "name": "Lines G.T." }, { "name": "Stapor P." }, { "name": "Hasenauer J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Fabian Fröhlich", "email": "fabian_froehlich@hms.harvard.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Maintainer", "Developer" ], "note": null }, { "name": "Jan Hasenauer", "email": "jan.hasenauer@uni-bonn.de", "url": null, "orcidid": "https://orcid.org/0000-0002-4935-3312", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Daniel Weindl", "email": "daniel.weindl@uni-bonn.de", "url": null, "orcidid": "https://orcid.org/0000-0001-9963-6057", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Maintainer", "Developer" ], "note": null } ], "owner": "dweindl", "additionDate": "2019-09-28T12:06:10Z", "lastUpdate": "2025-05-08T07:28:52.817175Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PIA - Protein Inference Algorithms", "description": "The main focus lays on the integrated inference algorithms, concluding the proteins from a set of identified spectra. But it also allows you to integrate results of various search engines, inspect your peptide spectrum matches, calculate FDR values across different results and visualize the correspondence between PSMs, peptides and proteins.", "homepage": "https://github.com/medbioinf/pia", "biotoolsID": "pia", "biotoolsCURIE": "biotools:pia", "version": [ "1.5" ], "otherID": [], "relation": [ { "biotoolsID": "knime", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_3649", "term": "Target-Decoy" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrometry spectra" }, "format": [ { "uri": "http://edamontology.org/format_3713", "term": "Mascot .dat file" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3684", "term": "PRIDE XML" }, { "uri": "http://edamontology.org/format_3711", "term": "X!Tandem XML" }, { "uri": "http://edamontology.org/format_3702", "term": "MSF" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" }, { "uri": "http://edamontology.org/format_3765", "term": "KNIME datatable format" }, { "uri": "http://edamontology.org/format_3764", "term": "idXML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" } ] }, { "data": { "uri": "http://edamontology.org/data_0989", "term": "Protein identifier" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" }, { "uri": "http://edamontology.org/format_3765", "term": "KNIME datatable format" }, { "uri": "http://edamontology.org/format_3764", "term": "idXML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" } ] } ], "note": "PIA allows you to inspect the results of common proteomics spectrum identification search engines, combine them seamlessly and conduct statistical analyses. The main focus of PIA lays on the integrated inference algorithms, i.e. concluding the proteins from a set of identified spectra. But it also allows you to inspect your peptide spectrum matches, calculate FDR values across different search engine results and visualize the correspondence between PSMs, peptides and proteins. Search engine results in several formats peptide spectrum matches (PSMs) and peptides Inferred Proteins", "cmd": null } ], "toolType": [ "Command-line tool", "Library", "Desktop application", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3120", "term": "Protein variants" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "BSD-3-Clause", "collectionID": [ "KNIME", "de.NBI", "Proteomics", "BioInfra.Prot", "CUBiMed.RUB" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "Proteomics" ], "link": [ { "url": "https://github.com/medbioinf/pia", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/mpc-bioinformatics/pia", "type": "Source code", "note": null, "version": null }, { "url": "http://bioconda.github.io/recipes/pia/README.html", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/mpc-bioinformatics/pia/releases", "type": "Binaries", "note": null, "version": null }, { "url": "https://hub.docker.com/r/julianusz/pia", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/medbioinf/pia/wiki", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jproteome.5b00121", "pmid": "25938255", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface", "abstract": "Protein inference connects the peptide spectrum matches (PSMs) obtained from database search engines back to proteins, which are typically at the heart of most proteomics studies. Different search engines yield different PSMs and thus different protein lists. Analysis of results from one or multiple search engines is often hampered by different data exchange formats and lack of convenient and intuitive user interfaces. We present PIA, a flexible software suite for combining PSMs from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data analysis workflows in several ways. A user-friendly graphical user interface can be run either locally or (e.g., for larger core facilities) from a central server. For automated data processing, stand-alone tools are available. PIA implements several established protein inference algorithms and can combine results from different search engines seamlessly. On several benchmark data sets, we show that PIA can identify a larger number of proteins at the same protein FDR when compared to that using inference based on a single search engine. PIA supports the majority of established search engines and data in the mzIdentML standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia.", "date": "2015-07-02T00:00:00Z", "citationCount": 57, "authors": [ { "name": "Uszkoreit J." }, { "name": "Maerkens A." }, { "name": "Perez-Riverol Y." }, { "name": "Meyer H.E." }, { "name": "Marcus K." }, { "name": "Stephan C." }, { "name": "Kohlbacher O." }, { "name": "Eisenacher M." } ], "journal": "Journal of Proteome Research" } }, { "doi": "10.1021/acs.jproteome.8b00723", "pmid": "30474983", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Protein Inference Using PIA Workflows and PSI Standard File Formats", "abstract": "Proteomics using LC-MS/MS has become one of the main methods to analyze the proteins in biological samples in high-throughput. But the existing mass-spectrometry instruments are still limited with respect to resolution and measurable mass ranges, which is one of the main reasons why shotgun proteomics is the major approach. Here proteins are digested, which leads to the identification and quantification of peptides instead. While often neglected, the important step of protein inference needs to be conducted to infer from the identified peptides to the actual proteins in the original sample. In this work, we highlight some of the previously published and newly added features of the tool PIA - Protein Inference Algorithms, which helps the user with the protein inference of measured samples. We also highlight the importance of the usage of PSI standard file formats, as PIA is the only current software supporting all available standards used for spectrum identification and protein inference. Additionally, we briefly describe the benefits of working with workflow environments for proteomics analyses and show the new features of the PIA nodes for the KNIME Analytics Platform. Finally, we benchmark PIA against a recently published data set for isoform detection. PIA is open source and available for download on GitHub (https://github.com/mpc-bioinformatics/pia) or directly via the community extensions inside the KNIME analytics platform.", "date": "2019-02-01T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Uszkoreit J." }, { "name": "Perez-Riverol Y." }, { "name": "Eggers B." }, { "name": "Marcus K." }, { "name": "Eisenacher M." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "Julian Uszkoreit", "email": "julian.uszkoreit@rub.de", "url": null, "orcidid": "http://orcid.org/0000-0001-7522-4007", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "CUBiMed.RUB", "email": "cubimed@rub.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "julianu", "additionDate": "2016-07-12T10:54:05Z", "lastUpdate": "2025-05-02T13:15:26.717477Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "epimutacions", "description": "The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.", "homepage": "https://www.bioconductor.org/packages/release/bioc/html/epimutacions.html", "biotoolsID": "epimutacions", "biotoolsCURIE": "biotools:epimutacions", "version": [ "1.2.0" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3295", "term": "Epigenetics" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.bioconductor.org/packages/epimutacions", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://www.bioconductor.org/packages/release/bioc/src/contrib/epimutacions_1.2.0.tar.gz", "type": "Source code", "note": null, "version": "1.2.0" } ], "documentation": [ { "url": "https://www.bioconductor.org/packages/release/bioc/manuals/epimutacions/man/epimutacions.pdf", "type": [ "API documentation" ], "note": null }, { "url": "https://www.bioconductor.org/packages/release/bioc/vignettes/epimutacions/inst/doc/epimutacions.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1080/15592294.2023.2230670", "pmid": "37409354", "pmcid": "PMC10327521", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Epimutation detection in the clinical context: guidelines and a use case from a new Bioconductor package", "abstract": "Epimutations are rare alterations of the normal DNA methylation pattern at specific loci, which can lead to rare diseases. Methylation microarrays enable genome-wide epimutation detection, but technical limitations prevent their use in clinical settings: methods applied to rare diseases’ data cannot be easily incorporated to standard analyses pipelines, while epimutation methods implemented in R packages (ramr) have not been validated for rare diseases. We have developed epimutacions, a Bioconductor package (https://bioconductor.org/packages/release/bioc/html/epimutacions.html). epimutacions implements two previously reported methods and four new statistical approaches to detect epimutations, along with functions to annotate and visualize epimutations. Additionally, we have developed an user-friendly Shiny app to facilitate epimutations detection (https://github.com/isglobal-brge/epimutacionsShiny) to non-bioinformatician users. We first compared the performance of epimutacions and ramr packages using three public datasets with experimentally validated epimutations. Methods in epimutacions had a high performance at low sample sizes and outperformed methods in ramr. Second, we used two general population children cohorts (INMA and HELIX) to determine the technical and biological factors that affect epimutations detection, providing guidelines on how designing the experiments or preprocessing the data. In these cohorts, most epimutations did not correlate with detectable regional gene expression changes. Finally, we exemplified how epimutacions can be used in a clinical context. We run epimutacions in a cohort of children with autism disorder and identified novel recurrent epimutations in candidate genes for autism. Overall, we present epimutacions a new Bioconductor package for incorporating epimutations detection to rare disease diagnosis and provide guidelines for the design and data analyses.", "date": "2023-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Ruiz-Arenas C." }, { "name": "Abarrategui L." }, { "name": "Hernandez-Ferrer C." }, { "name": "Escriba-Montagut X." }, { "name": "Pelegri-Siso D." }, { "name": "Ryser-Welch P." }, { "name": "Vrijheid M." }, { "name": "Bustamante M." }, { "name": "Grazuleviciene R." }, { "name": "Lepeule J." }, { "name": "Mathai M." }, { "name": "Vafeiadi M." }, { "name": "Beltran S." }, { "name": "Perez-Jurado L.A." }, { "name": "Gonzalez J.R." } ], "journal": "Epigenetics" } } ], "credit": [ { "name": "Carlos Ruiz-Arenas", "email": "carlos.ruiz@isglobal.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Leire Abarrategui", "email": "leire.abarrategui@isglobal.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Carles Hernandez-Ferrer", "email": "carles.hernandez@isglobal.org", "url": "http://www.carleshf.com", "orcidid": "https://orcid.org/0000-0002-8029-7160", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Dolors Pelegri-Siso", "email": "dolors.pelegri@isglobal.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Juan R. Gonzalez", "email": "juanr.gonzalez@isglobal.org", "url": "https://brge.isglobal.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "chernan3", "additionDate": "2023-02-07T14:25:10.924789Z", "lastUpdate": "2025-05-01T22:27:05.714967Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "compareMS2", "description": "compareMS2 is a tool for comparing sets of (tandem) mass spectra for clustering samples, molecular phylogenetics, identification of biological species or tissues, and quality control. compareMS2 currently consumes Mascot Generic Format, or MGF, and produces output in a variety of common image and distance matrix formats.", "homepage": "https://github.com/524D/compareMS2", "biotoolsID": "comparems2", "biotoolsCURIE": "biotools:comparems2", "version": [ "1.0", "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2424", "term": "Comparison" }, { "uri": "http://edamontology.org/operation_0567", "term": "Phylogenetic tree visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3651", "term": "MGF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3272", "term": "Species tree" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_2855", "term": "Distance matrix" }, "format": [ { "uri": "http://edamontology.org/format_1991", "term": "mega" }, { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C", "JavaScript" ], "license": "MIT", "collectionID": [ "ms-utils", "Proteomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Netherlands" ], "elixirCommunity": [ "Proteomics" ], "link": [ { "url": "https://github.com/524D/compareMS2", "type": [ "Repository" ], "note": null }, { "url": "https://www.ms-utils.org/compareMS2.html", "type": [ "Software catalogue" ], "note": null }, { "url": "https://research-software-directory.org/software/comparems2", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://www.ms-utils.org/compareMS2.c", "type": "Source code", "note": null, "version": "1.0" }, { "url": "http://www.ms-utils.org/compareMS2.html", "type": "Binaries", "note": null, "version": "1.0" }, { "url": "http://www.ms-utils.org/compareMS2.c", "type": "Source code", "note": null, "version": "1.0" }, { "url": "https://github.com/524D/compareMS2/tree/main/src", "type": "Source code", "note": null, "version": "2.0" }, { "url": "https://github.com/524D/compareMS2/tree/main", "type": "Binaries", "note": null, "version": "2.0" } ], "documentation": [ { "url": "http://www.ms-utils.org/compareMS2.html", "type": [ "General", "Command-line options" ], "note": null }, { "url": "https://github.com/524D/compareMS2", "type": [ "General", "User manual", "Command-line options", "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1002/rcm.6162", "pmid": "22368051", "pmcid": null, "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "Molecular phylogenetics by direct comparison of tandem mass spectra", "abstract": "Rationale: Molecular phylogenetics is the study of evolution and relatedness of organisms or genes. Mass spectrometry is used routinely for bacterial identification and has also been used for phylogenetic analysis, for instance from bone material. Unfortunately, only a small fraction of the acquired tandem mass spectra allow direct interpretation. Methods: We describe a new algorithm and software for molecular phylogenetics using pairwise comparisons of tandem mass spectra from enzymatically digested proteins. The spectra need not be annotated and all acquired data is used in the analysis. To demonstrate the method, we analyzed tryptic digests of sera from four great apes and two other primates. Results: The distribution of spectra dot products for thousands of tandem mass spectra collected from two samples provides a measure on the fraction of shared peptides between the two samples. When inverted, this becomes a distance metric. By pairwise comparison between species and averaging over four individuals per species, it was possible to reconstruct the unique correct phylogenetic tree for the great apes and other primates. Conclusions: The new method described here has several attractive features compared with existing methods, among them simplicity, the unbiased use of all acquired data rather than a small subset of spectra, and the potential use of heavily degraded proteins or proteins with a priori unknown modifications. © 2012 John Wiley & Sons, Ltd.", "date": "2012-04-15T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Palmblad M." }, { "name": "Deelder A.M." } ], "journal": "Rapid Communications in Mass Spectrometry" } }, { "doi": "10.1021/acs.jproteome.2c00457", "pmid": "36173614", "pmcid": "PMC9903320", "type": [ "Primary" ], "version": "2.0", "note": null, "metadata": { "title": "compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets", "abstract": "It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as routinely collected in proteomics. This method has seen use in species identification and mixture characterization in food and feed products, as well as other applications. Here, we present the first major update of this software, including a new metric, a graphical user interface and additional functionality. The data have been deposited to ProteomeXchange with dataset identifier PXD034932.", "date": "2023-02-03T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Marissen R." }, { "name": "Varunjikar M.S." }, { "name": "Laros J.F.J." }, { "name": "Rasinger J.D." }, { "name": "Neely B.A." }, { "name": "Palmblad M." } ], "journal": "Journal of Proteome Research" } }, { "doi": "10.1021/acs.jproteome.1c00528", "pmid": "34523928", "pmcid": "PMC8491155", "type": [ "Review" ], "version": "2.0", "note": null, "metadata": { "title": "Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics", "abstract": "Science is full of overlooked and undervalued research waiting to be rediscovered. Proteomics is no exception. In this perspective, we follow the ripples from a 1960 study of Zuckerkandl, Jones, and Pauling comparing tryptic peptides across animal species. This pioneering work directly led to the molecular clock hypothesis and the ensuing explosion in molecular phylogenetics. In the decades following, proteins continued to provide essential clues on evolutionary history. While technology has continued to improve, contemporary proteomics has strayed from this larger biological context, rarely comparing species or asking how protein structure, function, and interactions have evolved. Here we recombine proteomics with molecular phylogenetics, highlighting the value of framing proteomic results in a larger biological context and how almost forgotten research, though technologically surpassed, can still generate new ideas and illuminate our work from a different perspective. Though it is infeasible to read all research published on a large topic, looking up older papers can be surprisingly rewarding when rediscovering a \"gem\"at the end of a long citation chain, aided by digital collections and perpetually helpful librarians. Proper literature study reduces unnecessary repetition and allows research to be more insightful and impactful by truly standing on the shoulders of giants. All data was uploaded to MassIVE (https://massive.ucsd.edu/) as dataset MSV000087993.", "date": "2021-10-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Neely B.A." }, { "name": "Palmblad M." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "lumc.nl", "email": null, "url": "https://www.lumc.nl", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Support" ], "note": null }, { "name": "Magnus Palmblad", "email": "magnus.palmblad@gmail.com", "url": "https://github.com/magnuspalmblad", "orcidid": "http://orcid.org/0000-0002-5865-8994", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact", "Documentor" ], "note": null }, { "name": "Rob Marissen", "email": null, "url": "https://github.com/524D", "orcidid": "https://orcid.org/0000-0002-1220-9173", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "n.m.palmblad@lumc.nl", "additionDate": "2016-04-15T11:52:42Z", "lastUpdate": "2025-04-16T14:22:04.957317Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Exposome Maps", "description": "The Exposome Maps contain geospatially resolved data on environmental exposures (Exposome Surfaces), categorized into the following Exposome dimensions:\nBuilt Environment28 exposures related to:\n•\tGreen space\n•\tBlue space\n•\tGrey space\nFood Environment4 exposures related to:\n•\tFood landscape / healthy food index\nPhysico-Chemical Environment99 exposures related to:\n•\tAir pollution\n•\tBiodiversity\n•\tWeather conditions\n•\tLight intensity at night\n•\tNoise\n•\tPesticides\n•\tElectromagnetic fields\nSocial Environment70 exposures related to:\n•\tNeighbourhood socio-economic position\n•\tNeighbourhood Demographic surfaces and population characteristics\n•\tSocial capital\n•\tSecurity\n•\tMental health\n•\tProximity to facilities\n•\tEnergy use\n•\tLabour market", "homepage": "https://exposome.dataplatform.nl/", "biotoolsID": "exposome_maps", "biotoolsCURIE": "biotools:exposome_maps", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" }, { "uri": "http://edamontology.org/topic_3855", "term": "Environmental sciences" } ], "operatingSystem": [], "language": [], "license": "Other", "collectionID": [ "EXPANSE", "EHEN" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://expanseproject.eu/", "type": [ "Other" ], "note": "Project information page" } ], "download": [], "documentation": [ { "url": "https://surfdrive.surf.nl/files/index.php/s/uqUORDrd428H2F9", "type": [ "User manual" ], "note": "Description of Environmental variables available through Exposome Maps" }, { "url": "https://surfdrive.surf.nl/files/index.php/s/fI0Gmuu5O1MJAI9", "type": [ "Terms of use" ], "note": "Exposome-NL data platform Data Access and Publication Policy" } ], "publication": [ { "doi": "10.1126/science.aay3164", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "The exposome and health: Where chemistry meets biology", "abstract": "Despite extensive evidence showing that exposure to specific chemicals can lead to disease, current research approaches and regulatory policies fail to address the chemical complexity of our world. To safeguard current and future generations from the increasing number of chemicals polluting our environment, a systematic and agnostic approach is needed. The “exposome” concept strives to capture the diversity and range of exposures to synthetic chemicals, dietary constituents, psychosocial stressors, and physical factors, as well as their corresponding biological responses. Technological advances such as high-resolution mass spectrometry and network science have allowed us to take the first steps toward a comprehensive assessment of the exposome. Given the increased recognition of the dominant role that nongenetic factors play in disease, an effort to characterize the exposome at a scale comparable to that of the human genome is warranted.", "date": "2020-01-24T00:00:00Z", "citationCount": 597, "authors": [ { "name": "Vermeulen R." }, { "name": "Schymanski E.L." }, { "name": "Barabasi A.-L." }, { "name": "Miller G.W." } ], "journal": "Science" } }, { "doi": "10.1097/EE9.0000000000000162", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Developing the building blocks to elucidate the impact of the urban exposome on cardiometabolic-pulmonary disease: The EU EXPANSE project", "abstract": "By 2030, more than 80% of Europe's population will live in an urban environment. The urban exposome, consisting of factors such as where we live and work, where and what we eat, our social network, and what chemical and physical hazards we are exposed to, provides important targets to improve population health. The EXPANSE (EXposome Powered tools for healthy living in urbAN SEttings) project will study the impact of the urban exposome on the major contributors to Europe's burden of disease: Cardio-Metabolic and Pulmonary Disease. EXPANSE will address one of the most pertinent questions for urban planners, policy makers, and European citizens: \"How to maximize one's health in a modern urban environment?\" EXPANSE will take the next step in exposome research by (1) bringing together exposome and health data of more than 55 million adult Europeans and OMICS information for more than 2 million Europeans; (2) perform personalized exposome assessment for 5,000 individuals in five urban regions; (3) applying ultra-high-resolution mass-spectrometry to screen for chemicals in 10,000 blood samples; (4) evaluating the evolution of the exposome and health through the life course; and (5) evaluating the impact of changes in the urban exposome on the burden of cardiometabolic and pulmonary disease. EXPANSE will translate its insights and innovations into research and dissemination tools that will be openly accessible via the EXPANSE toolbox. By applying innovative ethics-by-design throughout the project, the social and ethical acceptability of these tools will be safeguarded. EXPANSE is part of the European Human Exposome Network.", "date": "2021-08-01T00:00:00Z", "citationCount": 38, "authors": [ { "name": "Vlaanderen J." }, { "name": "De Hoogh K." }, { "name": "Hoek G." }, { "name": "Peters A." }, { "name": "Probst-Hensch N." }, { "name": "Scalbert A." }, { "name": "Melen E." }, { "name": "Tonne C." }, { "name": "De Wit G.A." }, { "name": "Chadeau-Hyam M." }, { "name": "Katsouyanni K." }, { "name": "Esko T." }, { "name": "Jongsma K.R." }, { "name": "Vermeulen R." } ], "journal": "Environmental Epidemiology" } } ], "credit": [ { "name": "Roel Vermeulen", "email": "R.C.H.Vermeulen@uu.nl", "url": null, "orcidid": "https://orcid.org/0000-0003-4082-8163", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "Zimbo Boudewijns", "email": "z.s.r.m.boudewijns@uu.nl", "url": null, "orcidid": "https://orcid.org/0000-0002-9383-9571", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Maintainer" ], "note": null }, { "name": "Lloyd Roga", "email": "l.q.roga@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null } ], "owner": "Channel2291", "additionDate": "2025-03-17T14:01:59.601345Z", "lastUpdate": "2025-04-15T08:35:02.159681Z", "editPermission": { "type": "group", "authors": [ "hkucukali" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Cloud-based Workflow Manager (CloWM)", "description": "Data analysis in the life sciences often suffers from reproducibility, standardization and accessibility issues and these problems become even more severe with the escalating volume and complexity of data. While best-practice data analysis workflows try to tackle these challenges, many existing workflows still grapple with scalability issues, limited portability due to tight coupling with the execution environment and accessibility constraints arising from the absence of user-friendly interfaces. To overcome these issues, we created CloWM, a comprehensive cloud-based workflow management platform that allows the generic transformation of command-line driven workflows into user-friendly web-based services. CloWM offers the seamless integration of (1) scientific workflows written in the Nextflow DSL, (2) robust data storage, (3) a highly scalable compute layer for data-intensive analysis tasks and (4) a user-friendly interface.", "homepage": "https://clowm.bi.denbi.de", "biotoolsID": "clowm", "biotoolsCURIE": "biotools:clowm", "version": [], "otherID": [], "relation": [ { "biotoolsID": "sans", "type": "includes" } ], "function": [], "toolType": [ "Web API", "Web service", "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [], "language": [ "Python", "JavaScript" ], "license": "Apache-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://gitlab.ub.uni-bielefeld.de/cmg/clowm", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://clowm.bi.denbi.de/api/v1/openapi.json", "type": "API specification", "note": null, "version": null }, { "url": "https://gitlab.ub.uni-bielefeld.de/cmg/clowm", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://clowm.bi.denbi.de/api/v1/docs", "type": [ "API documentation" ], "note": null }, { "url": "https://clowm.bi.denbi.de/terms", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.5281/zenodo.14039069", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Göbel", "email": "dgoebel@techfak.uni-bielefeld.de", "url": "https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=223066601", "orcidid": "https://orcid.org/0009-0009-9985-3823", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer", "Developer", "Primary contact" ], "note": null }, { "name": "Michael Beckstette", "email": "mbeckste@cebitec.uni-bielefeld.de", "url": null, "orcidid": "https://orcid.org/0000-0002-3707-1692", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Documentor" ], "note": null }, { "name": "Bielefeld University", "email": null, "url": "https://www.uni-bielefeld.de", "orcidid": null, "gridid": null, "rorid": "02hpadn98", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Genome Informatics", "email": null, "url": "https://gi.cebitec.uni-bielefeld.de", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "NFDI4Microbiota", "email": null, "url": "https://nfdi4microbiota.de", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null } ], "owner": "dgoebel", "additionDate": "2025-04-09T13:19:17.715967Z", "lastUpdate": "2025-04-09T14:21:50.981521Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ChemFH", "description": "An integrated online platform developed for the screening and prediction of potential frequent drug hitters, thus improving the efficiency of drug R&D in colloidal aggregate, firefly luciferase reporter enzyme inhibition, fluorescence, chemical reactivity, and promiscuity. ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery.", "homepage": "https://chemfh.scbdd.com/", "biotoolsID": "chemfh", "biotoolsCURIE": "biotools:chemfh", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3938", "term": "Virtual screening" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2301", "term": "SMILES string" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1696", "term": "Drug report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1712", "term": "Chemical structure image" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Script", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0209", "term": "Medicinal chemistry" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "JavaScript" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/antwiser/ChemFH", "type": [ "Repository" ], "note": null }, { "url": "https://chemfh.scbdd.com/", "type": [ "Other" ], "note": "Webpage of the tool" } ], "download": [ { "url": "https://github.com/antwiser/ChemFH/releases/tag/ChemFH-1.0.0", "type": "Source code", "note": null, "version": "1.0.0" } ], "documentation": [ { "url": "https://github.com/antwiser/ChemFH/blob/main/README.md", "type": [ "General" ], "note": null }, { "url": "https://chemfh.scbdd.com/documentation/#/", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkae424", "pmid": "38783035", "pmcid": "PMC11223804", "type": [ "Method" ], "version": "1.0.0", "note": "High-throughput screening rapidly tests an extensive array of chemical compounds to identify hit compounds for specific biological targets in drug discovery. However, false-positive results disrupt hit compound screening, leading to wastage of time and resources. To address this, we propose ChemFH, an integrated online platform facilitating rapid virtual evaluation of potential false positives, including colloidal aggregators, spectroscopic interference compounds, firefly luciferase inhibitors, chemical reactive compounds, promiscuous compounds, and other assay interferences. ChemFH is freely available via https://chemfh.scbdd.com/.", "metadata": { "title": "ChemFH: An integrated tool for screening frequent false positives in chemical biology and drug discovery", "abstract": "High-throughput screening rapidly tests an extensive array of chemical compounds to identify hit compounds for specific biological targets in drug discovery. However, false-positive results disrupt hit compound screening, leading to wastage of time and resources. To address this, we propose ChemFH, an integrated online platform facilitating rapid virtual evaluation of potential false positives, including colloidal aggregators, spectroscopic interference compounds, firefly luciferase inhibitors, chemical reactive compounds, promiscuous compounds, and other assay interferences. By leveraging a dataset containing 823 391 compounds, we constructed high-quality prediction models using multi-task directed message-passing network (DMPNN) architectures combining uncertainty estimation, yielding an average AUC value of 0.91. Furthermore, ChemFH incorporated 1441 representative alert substructures derived from the collected data and ten commonly used frequent hitter screening rules. ChemFH was validated with an external set of 75 compounds. Subsequently, the virtual screening capability of ChemFH was successfully confirmed through its application to five virtual screening libraries. Furthermore, ChemFH underwent additional validation on two natural products and FDA-approved drugs, yielding reliable and accurate results. ChemFH is a comprehensive, reliable, and computationally efficient screening pipeline that facilitates the identification of true positive results in assays, contributing to enhanced efficiency and success rates in drug discovery. ChemFH is freely available via https://chemfh.scbdd.com/.", "date": "2024-07-05T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Shi S." }, { "name": "Fu L." }, { "name": "Yi J." }, { "name": "Yang Z." }, { "name": "Zhang X." }, { "name": "Deng Y." }, { "name": "Wang W." }, { "name": "Wu C." }, { "name": "Zhao W." }, { "name": "Hou T." }, { "name": "Zeng X." }, { "name": "Lyu A." }, { "name": "Cao D." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Jiacai Yi", "email": "yjc@nudt.edu.cn", "url": "https://github.com/antwiser", "orcidid": "https://orcid.org/0000-0001-6823-1882", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "National University of Defense Technology, Changsha, Hunan" } ], "owner": "etepf22", "additionDate": "2025-03-28T11:01:52.929561Z", "lastUpdate": "2025-03-28T12:04:07.529430Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WorkflowHub", "description": "WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows.\n\nThe registry supports any workflow in its native repository.\n\nWorkflowHub aims to facilitate discovery and re-use of workflows in an accessible and interoperable way. 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"note": "Prediction of the impact of non-synonymous polymorphisms on protein stability from sequence.", "cmd": null }, { "operation": [], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1008", "term": "Polypeptide chain ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [] } ], "note": "Prediction of the impact of non-synonymous polymorphisms on protein stability from structure.", "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "https://inpsmd.biocomp.unibo.it/help", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btv291", "pmid": "25957347", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "INPS: Predicting the impact of non-synonymous variations on protein stability from sequence", "abstract": "Motivation: A tool for reliably predicting the impact of variations on protein stability is extremely important for both protein engineering and for understanding the effects of Mendelian and somatic mutations in the genome. Next Generation Sequencing studies are constantly increasing the number of protein sequences. Given the huge disproportion between protein sequences and structures, there is a need for tools suited to annotate the effect of mutations starting from protein sequence without relying on the structure. Here, we describe INPS, a novel approach for annotating the effect of non-synonymous mutations on the protein stability from its sequence. INPS is based on SVM regression and it is trained to predict the thermodynamic free energy change upon single-point variations in protein sequences. Results: We show that INPS performs similarly to the state-of-the-art methods based on protein structure when tested in cross-validation on a non-redundant dataset. INPS performs very well also on a newly generated dataset consisting of a number of variations occurring in the tumor suppressor protein p53. Our results suggest that INPS is a tool suited for computing the effect of non-synonymous polymorphisms on protein stability when the protein structure is not available. We also show that INPS predictions are complementary to those of the state-of-the-art, structure-based method mCSM. When the two methods are combined, the overall prediction on the p53 set scores significantly higher than those of the single methods.", "date": "2015-02-06T00:00:00Z", "citationCount": 111, "authors": [ { "name": "Fariselli P." }, { "name": "Martelli P.L." }, { "name": "Savojardo C." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/bioinformatics/btw192", "pmid": "27153629", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "INPS-MD: A web server to predict stability of protein variants from sequence and structure", "abstract": "Motivation: Protein function depends on its structural stability. The effects of single point variations on protein stability can elucidate the molecular mechanisms of human diseases and help in developing new drugs. Recently, we introduced INPS, a method suited to predict the effect of variations on protein stability from protein sequence and whose performance is competitive with the available state-of-the-art tools. Results: In this article, we describe INPS-MD (Impact of Non synonymous variations on Protein Stability-Multi-Dimension), a web server for the prediction of protein stability changes upon single point variation from protein sequence and/or structure. Here, we complement INPS with a new predictor (INPS3D) that exploits features derived from protein 3D structure. INPS3D scores with Pearson's correlation to experimental ΔΔG values of 0.58 in cross validation and of 0.72 on a blind test set. The sequence-based INPS scores slightly lower than the structure-based INPS3D and both on the same blind test sets well compare with the state-of-the-art methods.", "date": "2016-08-15T00:00:00Z", "citationCount": 189, "authors": [ { "name": "Savojardo C." }, { "name": "Fariselli P." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "https://www.biocomp.unibo.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Piero Fariselli", "email": "piero.fariselli@unito.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Castrense Savojardo", "email": "savojard@biocomp.unibo.it", "url": "http://biocomp.unibo.it/savojard/", "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2016-05-04T15:36:53Z", "lastUpdate": "2025-03-19T15:01:04.207003Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-BOLOGNA", "savo", "Pub2Tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DDGemb", "description": "Predicting the impact of mutations on protein stability from sequence using protein language models", "homepage": "https://ddgemb.biocomp.unibo.it", "biotoolsID": "ddgemb", "biotoolsCURIE": "biotools:ddgemb", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [ "Rare Diseases", "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "https://ddgemb.biocomp.unibo.it/help/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btaf019", "pmid": "39799516", "pmcid": "PMC11783275", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning", "abstract": "Motivation: The knowledge of protein stability upon residue variation is an important step for functional protein design and for understanding how protein variants can promote disease onset. Computational methods are important to complement experimental approaches and allow a fast screening of large datasets of variations. Results: In this work, we present DDGemb, a novel method combining protein language model embeddings and transformer architectures to predict protein ΔΔG upon both single- and multi-point variations. DDGemb has been trained on a high-quality dataset derived from literature and tested on available benchmark datasets of single- and multi-point variations. DDGemb performs at the state of the art in both single- and multi-point variations.", "date": "2025-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Savojardo C." }, { "name": "Manfredi M." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "https://www.biocomp.unibo.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer", "Developer", "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2025-03-17T14:56:35.753220Z", "lastUpdate": "2025-03-17T15:08:51.796427Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "INPS", "description": "Predicting the impact of mutations on protein stability from sequence", "homepage": "https://inpsmd.biocomp.unibo.it", "biotoolsID": "inps", "biotoolsCURIE": "biotools:inps", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [] } ], "note": "Prediction of the impact of non-synonymous polymorphisms on protein stability", "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://inpsmd.biocomp.unibo.it/help", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btv291", "pmid": "25957347", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "INPS: Predicting the impact of non-synonymous variations on protein stability from sequence", "abstract": "Motivation: A tool for reliably predicting the impact of variations on protein stability is extremely important for both protein engineering and for understanding the effects of Mendelian and somatic mutations in the genome. Next Generation Sequencing studies are constantly increasing the number of protein sequences. Given the huge disproportion between protein sequences and structures, there is a need for tools suited to annotate the effect of mutations starting from protein sequence without relying on the structure. Here, we describe INPS, a novel approach for annotating the effect of non-synonymous mutations on the protein stability from its sequence. INPS is based on SVM regression and it is trained to predict the thermodynamic free energy change upon single-point variations in protein sequences. Results: We show that INPS performs similarly to the state-of-the-art methods based on protein structure when tested in cross-validation on a non-redundant dataset. INPS performs very well also on a newly generated dataset consisting of a number of variations occurring in the tumor suppressor protein p53. Our results suggest that INPS is a tool suited for computing the effect of non-synonymous polymorphisms on protein stability when the protein structure is not available. We also show that INPS predictions are complementary to those of the state-of-the-art, structure-based method mCSM. When the two methods are combined, the overall prediction on the p53 set scores significantly higher than those of the single methods.", "date": "2015-02-06T00:00:00Z", "citationCount": 111, "authors": [ { "name": "Fariselli P." }, { "name": "Martelli P.L." }, { "name": "Savojardo C." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/bioinformatics/btw192", "pmid": "27153629", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "INPS-MD: A web server to predict stability of protein variants from sequence and structure", "abstract": "Motivation: Protein function depends on its structural stability. The effects of single point variations on protein stability can elucidate the molecular mechanisms of human diseases and help in developing new drugs. Recently, we introduced INPS, a method suited to predict the effect of variations on protein stability from protein sequence and whose performance is competitive with the available state-of-the-art tools. Results: In this article, we describe INPS-MD (Impact of Non synonymous variations on Protein Stability-Multi-Dimension), a web server for the prediction of protein stability changes upon single point variation from protein sequence and/or structure. Here, we complement INPS with a new predictor (INPS3D) that exploits features derived from protein 3D structure. INPS3D scores with Pearson's correlation to experimental ΔΔG values of 0.58 in cross validation and of 0.72 on a blind test set. The sequence-based INPS scores slightly lower than the structure-based INPS3D and both on the same blind test sets well compare with the state-of-the-art methods.", "date": "2016-08-15T00:00:00Z", "citationCount": 189, "authors": [ { "name": "Savojardo C." }, { "name": "Fariselli P." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "http://www.biocomp.unibo.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": null }, { "name": "Piero Fariselli", "email": "piero.fariselli@unito.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2016-05-04T15:36:53Z", "lastUpdate": "2025-03-17T14:54:19.762674Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-BOLOGNA", "savo" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Raster extraction", "description": "This Python script provides functions to process raster files in chunks and extract values at specified coordinates using multiprocessing. 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Unlike many machine-learning approaches (e.g., AlphaFold2, TrRosetta, RaptorX), it integrates the Debye-Hückel formalism for charged side-chain interactions with a Mie potential for intramolecular forces. Based on a coarse-grained representation, PEP-FOLD4 performs competitively on well-structured peptides and shows significant improvements for poly-charged peptides, making it particularly useful for studying pH- and salt-dependent conformations.", "homepage": "https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4", "biotoolsID": "pep-fold4", "biotoolsCURIE": "biotools:pep-fold4", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" }, { "uri": "http://edamontology.org/operation_0476", "term": "Ab initio structure prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_1475", "term": "PDB database entry format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" }, { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" } ], "operatingSystem": [], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "https://mobyle2.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD4", "type": [ "Service" ], "note": "Link to the PEP-FOLD4 web page service" } ], "download": [ { "url": "https://owncloud.rpbs.univ-paris-diderot.fr/owncloud/index.php/s/7NHDSJXiQA0V2zy", "type": "Source code", "note": "Source code and recipe for docker images allowing to run PEP-FOLD4 locally. All repository content is covered by a non-commercial license agreement and may be used for non-commercial and internal research purposes only.", "version": null } ], "documentation": [ { "url": "https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkad376", "pmid": "37166962", "pmcid": "PMC10320157", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PEP-FOLD4: A pH-dependent force field for peptide structure prediction in aqueous solution", "abstract": "Accurate and fast structure prediction of peptides of less 40 amino acids in aqueous solution has many biological applications, but their conformations are pH-and salt concentration-dependent. In this work, we present PEP-FOLD4 which goes one step beyond many machine-learning approaches, such as AlphaFold2, TrRosetta and RaptorX. Adding the Debye-Hueckel formalism for charged-charged side chain interactions to a Mie formalism for all intramolecular (backbone and side chain) interactions, PEP-FOLD4, based on a coarse-grained representation of the peptides, performs as well as machine-learning methods on well-structured peptides, but displays significant improvements for poly-charged peptides. PEP-FOLD4 is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4. This server is free and there is no login requirement.", "date": "2023-07-05T00:00:00Z", "citationCount": 39, "authors": [ { "name": "Rey J." }, { "name": "Murail S." }, { "name": "De Vries S." }, { "name": "Derreumaux P." }, { "name": "Tuffery P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Julien Rey", "email": "julien.rey@u-paris.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-3050-511X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support", "Developer", "Primary contact" ], "note": null }, { "name": "Samuel Murail", "email": "samuel.muriail@u-paris.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-3842-5333", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Sjoerd de Vries", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-7701-3454", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Philippe Derreumaux", "email": "philippe.derreumaux@ibpc.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Pierre Tufféry", "email": "pierre.tuffery@inserm.fr", "url": null, "orcidid": "https://orcid.org/0000-0003-1033-9895", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "nchevrollier", "additionDate": "2025-03-04T16:25:28.372680Z", "lastUpdate": "2025-03-05T16:21:19.399517Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Coxmos", "description": "The Coxmos (Cox MultiBlock Survival) R package is an end-to-end pipeline designed for the study of survival analysis for high dimensional data. 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Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes. Metano is a standalone, open-source toolbox for the analysis and refinement of metabolic models. While flux distributions in metabolic networks are predominantly analyzed from a reaction-centric point of view, the Metano methods of split-ratio analysis and metabolite flux minimization also allow a metabolite-centric view on flux distributions. In addition, we present MMTB (mmtb.brendaenzymes.org), a web-based toolbox for metabolic modeling including a user-friendly interface to Metano methods. MMTB assists during bottom-up construction of metabolic models by integrating reaction and enzymatic annotation data from different databases. Furthermore, MMTB is especially designed for non-experienced users by providing an intuitive interface to the most commonly used modeling methods and offering novel visualizations. Additionally, MMTB allows users to upload their models, which can in turn be explored and analyzed by the community. We introduce MMTB by two use cases, involving a published model of Corynebacterium glutamicum and a newly created model of Phaeobacter inhibens.", "date": "2021-02-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Koblitz J." }, { "name": "Will S.E." }, { "name": "Riemer S.A." }, { "name": "Ulas T." }, { "name": "Neumann-Schaal M." }, { "name": "Schomburg D." } ], "journal": "Metabolites" } } ], "credit": [ { "name": "Julia Koblitz", "email": "julia.koblitz@dsmz.de", "url": "https://research.dsmz.de/person/651cecd8b3c97f11cc28cfc2", "orcidid": "https://orcid.org/0000-0002-7260-2129", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH", "email": "hub@dsmz.de", "url": "https://dsmz.de", "orcidid": null, "gridid": null, "rorid": "02tyer376", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "JKoblitz", "additionDate": "2025-01-22T10:00:56.561701Z", "lastUpdate": "2025-01-22T10:09:15.144513Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MediaDive", "description": "Comprehensive database on cultivation media and growth conditions for all domains of life. 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MediaDive is designed to enable broad range applications from every-day-use in research and diagnostic laboratories to knowledge-driven support of new media design and artificial intelligence-driven data mining. It offers a number of intuitive search functions and comparison tools, for example to identify media for related taxonomic groups and to integrate strain-specific modifications. Besides classical PDF archiving and printing, the state-of-the-art website allows paperless use of media recipes on mobile devices for convenient wet-lab use. In addition, data can be retrieved using a RESTful web service for large-scale data analyses. An internal editor interface ensures continuous extension and curation of media by cultivation experts from the Leibniz Institute DSMZ, which is interlinked with the growing microbial collections at DSMZ. External user engagement is covered by a dedicated media builder tool. The standardized and programmatically accessible data will foster new approaches for the design of cultivation media to target the vast majority of uncultured microorganisms.", "date": "2023-01-06T00:00:00Z", "citationCount": 22, "authors": [ { "name": "Koblitz J." }, { "name": "Halama P." }, { "name": "Spring S." }, { "name": "Thiel V." }, { "name": "Baschien C." }, { "name": "Hahnke R.L." }, { "name": "Pester M." }, { "name": "Overmann J." }, { "name": "Reimer L.C." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Julia Koblitz", "email": "julia.koblitz@dsmz.de", "url": "https://research.dsmz.de/person/651cecd8b3c97f11cc28cfc2", "orcidid": "https://orcid.org/0000-0002-7260-2129", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer", "Primary contact", "Developer" ], "note": null }, { "name": "Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH", "email": "hub@dsmz.de", "url": "https://dsmz.de", "orcidid": null, "gridid": null, "rorid": "02tyer376", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "JKoblitz", "additionDate": "2022-11-09T17:22:40.898557Z", "lastUpdate": "2025-01-22T09:37:58.121773Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MediaDive SPARQL", "description": "SPARQL endpoint for the MediaDive cultivation media database.", "homepage": "https://sparql.dsmz.de/mediadive", "biotoolsID": "mediadive-sparql", "biotoolsCURIE": "biotools:mediadive-sparql", "version": [], "otherID": [], "relation": [ { "biotoolsID": "mediadive", "type": "includes" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3786", "term": "Query script" }, "format": [ { "uri": "http://edamontology.org/format_3790", "term": "SPARQL" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_2376", "term": "RDF format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "SPARQL endpoint" ], "topic": [ { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" }, { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" } ], "operatingSystem": [], "language": [], "license": "CC-BY-4.0", "collectionID": [ "DSMZ Digital Diversity" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Julia Koblitz", "email": "julia.koblitz@dsmz.de", "url": "https://research.dsmz.de/person/651cecd8b3c97f11cc28cfc2", "orcidid": "https://orcid.org/0000-0002-7260-2129", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact", "Maintainer" ], "note": null }, { "name": "Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH", "email": "hub@dsmz.de", "url": "https://dsmz.de", "orcidid": null, "gridid": null, "rorid": "02tyer376", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "JKoblitz", "additionDate": "2025-01-22T09:29:34.165303Z", "lastUpdate": "2025-01-22T09:36:15.642971Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Marine Metagenomics Portal", "description": "The Marine Metagenomics Portal (MMP) hosts the marine databases MarRef, MarDB, MarFun, and SalDB. These databases provide the marine scientific community with openly accessible, comprehensive microbial genomics and metagenomics resources, including high-quality, manually curated sequences. 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These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/.", "date": "2018-01-01T00:00:00Z", "citationCount": 79, "authors": [ { "name": "Klemetsen T." }, { "name": "Raknes I.A." }, { "name": "Fu J." }, { "name": "Agafonov A." }, { "name": "Balasundaram S.V." }, { "name": "Tartari G." }, { "name": "Robertsen E." }, { "name": "Willassen N.P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "MMP team", "email": "mmp@uit.no", "url": "https://mmp2.sfb.uit.no/contact/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact", "Developer", "Maintainer", "Support" ], "note": null }, { "name": "Terje Klemetsen", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-2024-1798", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk", "email": "support@elixir.no", "url": "https://elixir.no/helpdesk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Support" ], "note": null }, { "name": "Nils Peder Willassen", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-4397-8020", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "nwi000", "additionDate": "2018-01-16T22:02:06Z", "lastUpdate": "2025-01-17T09:29:45.738020Z", "editPermission": { "type": "group", "authors": [ "eca008", "terjek014", "ElixirServicePro" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MARome", "description": "MARome is a resource for annotation of Scaffold and Matrix Attachment Regions (S/MARs) in Human Genome such as associated genes, genomic region, associated S/MAR binding proteins, associated Retroviral Integration sites for HIV and HTLV (Source: RID) etc. MARome is interlinked to other genomic resources such as, UCSC Genome Browser (For visualization of S/MAR genomic location), ensemble, NCBI-Gene.", "homepage": "https://marome.bionivid.in/", "biotoolsID": "marome", "biotoolsCURIE": "biotools:marome", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0077", "term": "Nucleic acids" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://marome.bionivid.in/download", "type": "Biological data", "note": null, "version": null } ], "documentation": [ { "url": "https://marome.bionivid.in/help", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkz562", "pmid": "31265077", "pmcid": "PMC6698742", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Mapping of scaffold/matrix attachment regions in human genome: a data mining exercise", "abstract": "Scaffold/matrix attachment regions (S/MARs) are DNA elements that serve to compartmentalize the chromatin into structural and functional domains. These elements are involved in control of gene expression which governs the phenotype and also plays role in disease biology. Therefore, genome-wide understanding of these elements holds great therapeutic promise. Several attempts have been made toward identification of S/MARs in genomes of various organisms including human. However, a comprehensive genome-wide map of human S/MARs is yet not available. Toward this objective, ChIP-Seq data of 14 S/MAR binding proteins were analyzed and the binding site coordinates of these proteins were used to prepare a non-redundant S/MAR dataset of human genome. Along with co-ordinate (location) details of S/MARs, the dataset also revealed details of S/MAR features, namely, length, inter-SMAR length (the chromatin loop size), nucleotide repeats, motif abundance, chromosomal distribution and genomic context. S/MARs identified in present study and their subsequent analysis also suggests that these elements act as hotspots for integration of retroviruses. Therefore, these data will help toward better understanding of genome functioning and designing effective anti-viral therapeutics. In order to facilitate user friendly browsing and retrieval of the data obtained in present study, a web interface, MARome (http://bioinfo.net.in/MARome), has been developed.", "date": "2019-08-22T00:00:00Z", "citationCount": 28, "authors": [ { "name": "Narwade N." }, { "name": "Patel S." }, { "name": "Alam A." }, { "name": "Chattopadhyay S." }, { "name": "Mittal S." }, { "name": "Kulkarni A." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Nitin Narwade", "email": "nitinnarwade1504@gmail.com", "url": "http://bioinfo.net.in/", "orcidid": "https://orcid.org/0000-0002-1368-307X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Developer" ], "note": null } ], "owner": "nitinnarwade1504", "additionDate": "2020-03-19T13:08:18Z", "lastUpdate": "2025-01-14T13:36:01.792295Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PHIStruct", "description": "PHIStruct is a phage-host interaction prediction tool that uses structure-aware protein embeddings to represent the receptor-binding proteins (RBPs) of phages. \n\nBy incorporating structure information, it presents improvements over using sequence-only protein embeddings and feature-engineered sequence properties — especially for phages with RBPs that have low sequence similarity to those of known phages.", "homepage": "https://github.com/bioinfodlsu/PHIStruct", "biotoolsID": "phistruct", "biotoolsCURIE": "biotools:phistruct", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "Predicts the host genus of a phage given its receptor-binding protein sequences", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0781", "term": "Virology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bioinfodlsu/PHIStruct", "type": [ "Repository" ], "note": null }, { "url": "http://phistruct.bioinfodlsu.com/", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://github.com/bioinfodlsu/PHIStruct", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/bioinfodlsu/PHIStruct", "type": [ "Installation instructions", "Quick start guide", "Citation instructions", "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btaf016", "pmid": "39804673", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Mark Edward M. Gonzales", "email": "gonzales.markedward@gmail.com", "url": "https://github.com/memgonzales", "orcidid": "https://orcid.org/0000-0001-5050-3157", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Research Assistant, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines" }, { "name": "Jennifer C. Ureta", "email": "jennifer.ureta@gmail.com", "url": "https://scholar.google.com/citations?user=v0Tf_u4AAAAJ&hl=en", "orcidid": "https://orcid.org/0000-0003-0427-5311", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Faculty, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines" }, { "name": "Anish M.S. Shrestha", "email": "anish.shrestha@dlsu.edu.ph", "url": "https://a-transposable-element.com/", "orcidid": "https://orcid.org/0000-0002-9192-9709", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Head, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines" } ], "owner": "memgonzales", "additionDate": "2025-01-14T09:14:56.273060Z", "lastUpdate": "2025-01-14T09:14:56.275331Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PHIEmbed", "description": "PHIEmbed is a phage-host interaction prediction tool that uses protein language models to represent the receptor-binding proteins of phages. It presents improvements over using handcrafted (manually feature-engineered) sequence properties and eliminates the need to manually extract and select features from phage sequences.", "homepage": "https://github.com/bioinfodlsu/phage-host-prediction", "biotoolsID": "phiembed", "biotoolsCURIE": "biotools:phiembed", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "Predicts the host genus of a phage given its receptor-binding protein sequences", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0781", "term": "Virology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bioinfodlsu/phage-host-prediction", "type": [ "Repository" ], "note": null }, { "url": "http://phiembed.bioinfodlsu.com/", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://github.com/bioinfodlsu/phage-host-prediction", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/bioinfodlsu/phage-host-prediction", "type": [ "Installation instructions", "Quick start guide", "Citation instructions", "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0289030", "pmid": "37486915", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Protein embeddings improve phage-host interaction prediction", "abstract": "With the growing interest in using phages to combat antimicrobial resistance, computational methods for predicting phage-host interactions have been explored to help shortlist candidate phages. Most existing models consider entire proteomes and rely on manual feature engineering, which poses difficulty in selecting the most informative sequence properties to serve as input to the model. In this paper, we framed phage-host interaction prediction as a multiclass classification problem that takes as input the embeddings of a phage’s receptor-binding proteins, which are known to be the key machinery for host recognition, and predicts the host genus. We explored different protein language models to automatically encode these protein sequences into dense embeddings without the need for additional alignment or structural information. We show that the use of embeddings of receptor-binding proteins presents improvements over handcrafted genomic and protein sequence features. The highest performance was obtained using the transformer-based protein language model ProtT5, resulting in a 3% to 4% increase in weighted F1 and recall scores across different prediction confidence thresholds, compared to using selected handcrafted sequence features.", "date": "2023-07-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Gonzales M.E.M." }, { "name": "Ureta J.C." }, { "name": "Shrestha A.M.S." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "Mark Edward M. Gonzales", "email": "gonzales.markedward@gmail.com", "url": "https://github.com/memgonzales", "orcidid": "https://orcid.org/0000-0001-5050-3157", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Research Assistant, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines" }, { "name": "Jennifer C. Ureta", "email": "jennifer.ureta@gmail.com", "url": "https://scholar.google.com/citations?user=v0Tf_u4AAAAJ&hl=en", "orcidid": "https://orcid.org/0000-0003-0427-5311", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Faculty, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines" }, { "name": "Anish M.S. Shrestha", "email": "anish.shrestha@dlsu.edu.ph", "url": "https://a-transposable-element.com/", "orcidid": "https://orcid.org/0000-0002-9192-9709", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Head, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines" } ], "owner": "memgonzales", "additionDate": "2024-05-05T10:53:14.688391Z", "lastUpdate": "2025-01-14T09:13:55.932761Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SDM", "description": "A server for predicting effects of mutations on protein stability", "homepage": "https://compbio.medschl.cam.ac.uk/sdm2/", "biotoolsID": "sdm2", "biotoolsCURIE": "biotools:sdm2", "version": [ "2.0" ], "otherID": [], "relation": [ { "biotoolsID": "sdm", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [], "operatingSystem": [ "Linux" ], "language": [], "license": null, "collectionID": [ "3D-BioInfo" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "UK" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "https://compbio.medschl.cam.ac.uk/sdm2/help", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkx439", "pmid": "28525590", "pmcid": "PMC5793720", "type": [ "Method" ], "version": "2.0", "note": "SDM: a server for predicting effects of mutations on protein stability", "metadata": { "title": "SDM: A server for predicting effects of mutations on protein stability", "abstract": "Here, we report a webserver for the improved SDM, used for predicting the effects of mutations on protein stability. As a pioneering knowledge-based approach, SDM has been highlighted as the most appropriate method to use in combination with many other approaches. We have updated the environment-specific amino-acid substitution tables based on the current expanded PDB (a 5-fold increase in information), and introduced new residue-conformation and interaction parameters, including packing density and residue depth. The updated server has been extensively tested using a benchmark containing 2690 point mutations from 132 different protein structures. The revised method correlates well against the hypothetical reverse mutations, better than comparable methods built using machine-learning approaches, highlighting the strength of our knowledge-based approach for identifying stabilising mutations. Given a PDB file (a Protein Data Bank file format containing the 3D coordinates of the protein atoms), and a point mutation, the server calculates the stability difference score between the wildtype and mutant protein.", "date": "2017-07-03T00:00:00Z", "citationCount": 374, "authors": [ { "name": "Pandurangan A.P." }, { "name": "Ochoa-Montano B." }, { "name": "Ascher D.B." }, { "name": "Blundell T.L." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "ARUN PRASAD PANDURANGAN", "email": "app41@cam.ac.uk", "url": "https://www.infectiousdisease.cam.ac.uk/directory/apandura%40mrc-lmb.cam.ac.uk", "orcidid": "https://orcid.org/0000-0001-7168-7143", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact", "Maintainer" ], "note": "Computational Biologist at the University of Cambridge" } ], "owner": "apandura", "additionDate": "2023-08-29T21:12:45.977710Z", "lastUpdate": "2025-01-08T14:32:09.070558Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bakta", "description": "Rapid & standardized annotation of bacterial genomes, MAGs & plasmids", "homepage": "https://github.com/oschwengers/bakta", "biotoolsID": "bakta", "biotoolsCURIE": "biotools:bakta", "version": [ "v1.10.3" ], "otherID": [], "relation": [ { "biotoolsID": "diamond", "type": "uses" }, { "biotoolsID": "hmmer3", "type": "uses" }, { "biotoolsID": "infernal", "type": "uses" }, { "biotoolsID": "trnascan-se", "type": "uses" }, { "biotoolsID": "blast", "type": "uses" }, { "biotoolsID": "aragorn", "type": "uses" }, { "biotoolsID": "pilercr", "type": "uses" }, { "biotoolsID": "deepsig", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0925", "term": "Sequence assembly" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2914", "term": "Sequence features metadata" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [ { "uri": "http://edamontology.org/format_1975", "term": "GFF3" } ] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1364", "term": "Hidden Markov model" }, "format": [ { "uri": "http://edamontology.org/format_3329", "term": "HMMER3" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" }, { "uri": 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"note": null, "cmd": "bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fasta" } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/oschwengers/bakta", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://bioconda.github.io/recipes/bakta/README.html", "type": [ "Other" ], "note": null }, { "url": "https://bakta.computational.bio", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://zenodo.org/records/7669534", "type": "Other", "note": "Mandatory annotation database", "version": "v5.1" } ], "documentation": [ { "url": "https://github.com/oschwengers/bakta/blob/main/README.md", "type": [ "General" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.md", "type": [ "Contributions policy" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.md", "type": [ "Code of conduct" ], "note": null }, { "url": "https://bakta.readthedocs.io/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1099/mgen.0.000685", "pmid": "34739369", "pmcid": "PMC8743544", "type": [ "Primary" ], "version": "1.1", "note": null, "metadata": { "title": "Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free sequence identification", "abstract": "Command-line annotation software tools have continuously gained popularity compared to centralized online services due to the worldwide increase of sequenced bacterial genomes. However, results of existing command-line software pipelines heavily depend on taxon-specific databases or sufficiently well annotated reference genomes. Here, we introduce Bakta, a new command-line software tool for the robust, taxon-independent, thorough and, nonetheless, fast annotation of bacterial genomes. Bakta conducts a comprehensive annotation workflow including the detection of small proteins taking into account replicon metadata. The annotation of coding sequences is accelerated via an alignment-free sequence identification approach that in addition facilitates the precise assignment of public database cross-references. Annotation results are exported in GFF3 and International Nucleotide Sequence Database Collaboration (INSDC)-compliant flat files, as well as comprehensive JSON files, facilitating automated downstream analysis. We compared Bakta to other rapid contemporary command-line annotation software tools in both targeted and taxonomically broad benchmarks including isolates and metagenomic-assembled genomes. We demonstrated that Bakta outperforms other tools in terms of functional annotations, the assignment of functional categories and database cross-references, whilst providing comparable wall-clock runtimes. Bakta is implemented in Python 3 and runs on MacOS and Linux systems. It is freely available under a GPLv3 license at https://github.com/oschwengers/bakta. An accompanying web version is available at https://bakta.computational.bio.", "date": "2021-01-01T00:00:00Z", "citationCount": 323, "authors": [ { "name": "Schwengers O." }, { "name": "Jelonek L." }, { "name": "Dieckmann M.A." }, { "name": "Beyvers S." }, { "name": "Blom J." }, { "name": "Goesmann A." } ], "journal": "Microbial Genomics" } } ], "credit": [ { "name": "Oliver Schwengers", "email": "oliver.schwengers@cb.jlug.de", "url": "https://github.com/oschwengers", "orcidid": "https://orcid.org/0000-0003-4216-2721", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Justus Liebig University Giessen", "email": null, "url": "https://www.uni-giessen.de", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "oschwengers", "additionDate": "2021-05-08T17:25:21Z", "lastUpdate": "2024-12-23T21:48:50.049892Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "bebatut" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "EURISCO", "description": "Search catalogue providing information about plant genetic resources collections maintained in Europe. It is based on a European network of ex situ and in situ National Inventories (NIs). Currently, it comprises information about 2.1 million germplasm accessions from more than 400 holding institutions from 43 countries. It contains both passport data and phenotypic data.", "homepage": "http://eurisco.ecpgr.org", "biotoolsID": "eurisco", "biotoolsCURIE": "biotools:eurisco", "version": [ "2.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "Based on the Multi Crop Passport Descriptors (MCPD) format", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux" ], "language": [ "SQL" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "Plant Sciences" ], "link": [ { "url": "http://eurisco.ecpgr.org/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "http://eurisco.ecpgr.org/", "type": [ "Terms of use", "Citation instructions", "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkw755", "pmid": "27580718", "pmcid": "PMC5210606", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "EURISCO: The European search catalogue for plant genetic resources", "abstract": "The European Search Catalogue for Plant Genetic Resources, EURISCO, provides information about 1.8 million crop plant accessions preserved by almost 400 institutes in Europe and beyond. EURISCO is being maintained on behalf of the European Cooperative Programme for Plant Genetic Resources. It is based on a network of National Inventories of 43 member countries and represents an important effort for the preservation of world's agrobiological diversity by providing information about the large genetic diversity kept by the collaborating collections. Moreover, EURISCO also assists its member countries in fulfilling legal obligations and commitments, e.g. with respect to the International Treaty on Plant Genetic Resources, the Second Global Plan of Action for Plant Genetic Resources for Food and Agriculture of the United Nation's Food and Agriculture Organization, or the Convention on Biological Diversity. EURISCO is accessible at http://eurisco.ecpgr.org.", "date": "2017-01-01T00:00:00Z", "citationCount": 47, "authors": [ { "name": "Weise S." }, { "name": "Oppermann M." }, { "name": "Maggioni L." }, { "name": "Van Hintum T." }, { "name": "Knupffer H." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkac852", "pmid": "36189883", "pmcid": "PMC9825528", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "EURISCO update 2023: the European Search Catalogue for Plant Genetic Resources, a pillar for documentation of genebank material", "abstract": "The European Search Catalogue for Plant Genetic Resources (EURISCO) is a central entry point for information on crop plant germplasm accessions from institutions in Europe and beyond. In total, it provides data on more than two million accessions, making an important contribution to unlocking the vast genetic diversity that lies deposited in >400 germplasm collections in 43 countries. EURISCO serves as the reference system for the Plant Genetic Resources Strategy for Europe and represents a significant approach for documenting and making available the world's agrobiological diversity. EURISCO is well established as a resource in this field and forms the basis for a wide range of research projects. In this paper, we present current developments of EURISCO, which is accessible at http://eurisco.ecpgr.org.", "date": "2023-01-06T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Kotni P." }, { "name": "Van Hintum T." }, { "name": "Maggioni L." }, { "name": "Oppermann M." }, { "name": "Weise S." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "European Cooperative Programme for Plant Genetic Resources (ECPGR)", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Stephan Weise", "email": "weise@ipk-gatersleben.de", "url": null, "orcidid": "http://orcid.org/0000-0003-4031-9131", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Stephan Weise", "email": "weise@ipk-gatersleben.de", "url": null, "orcidid": "http://orcid.org/0000-0003-4031-9131", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ipk", "additionDate": "2016-10-05T07:15:57Z", "lastUpdate": "2024-12-18T16:46:20.716446Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MALDIquant", "description": "MALDIquant is a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. 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A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. The original motivation came from our efforts to perform parameter estimation and forward simulation of the dynamics of a differential equations model of a small GRN with 21 nodes and 31 edges. We wanted a quick and easy way to visualize the weight parameters from the model which represent the direction and magnitude of the influence of a transcription factor on its target gene, so we created GRNsight. GRNsight automatically lays out either an unweighted or weighted network graph based on an Excel spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows, a Simple Interaction Format (SIF) text file, or a GraphML XML file. When a user uploads an input file specifying an unweighted network, GRNsight automatically lays out the graph using black lines and pointed arrowheads. For a weighted network, GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (positive for activation or negative for repression) and magnitude of the weight parameter. GRNsight is written in JavaScript, with diagrams facilitated by D3.js, a data visualization library. Node.js and the Express framework handle server-side functions. GRNsight's diagrams are based on D3.js's force graph layout algorithm, which was then extensively customized to support the specific needs of GRNs. Nodes are rectangular and support gene labels of up to 12 characters. The edges are arcs, which become straight lines when the nodes are close together. Self-regulatory edges are indicated by a loop.When a user mouses over an edge, the numerical value of the weight parameter is displayed. Visualizations can be modified by sliders that adjust the force graph layout parameters and through manual node dragging. GRNsight is best-suited for visualizing networks of fewer than 35 nodes and 70 edges, although it accepts networks of up to 75 nodes or 150 edges. GRNsight has general applicability for displaying any small, unweighted or weighted network with directed edges for systems biology or other application domains. GRNsight serves as an example of following and teaching best practices for scientific computing and complying with FAIR principles, using an open and test-driven development model with rigorous documentation of requirements and issues on GitHub. An exhaustive unit testing framework using Mocha and the Chai assertion library consists of around 160 automated unit tests that examine nearly 530 test files to ensure that the program is running as expected. 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