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Bergmann", "email": "frank.bergmann@bioquant.uni-heidelberg.de", "url": null, "orcidid": "https://orcid.org/0000-0001-5553-4702", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null } ], "owner": "frankbergmann", "additionDate": "2025-02-26T14:07:27.855714Z", "lastUpdate": "2025-07-07T11:16:29.397538Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MirGeneDB", "description": "MirGeneDB is a database of manually curated microRNA genes that have been validated and annotated as initially described in Fromm et al. 2015 , Fromm et al. 2020 and Fromm et al 2022. MirGeneDB 3.0 (Clarke and Hoye et al. 2024 ) includes more than 21,000 microRNA gene entries representing more than 1,700 microRNA families from 114 metazoan species. All microRNAs can be browsed, searched and downloaded.", "homepage": "http://mirgenedb.org/", "biotoolsID": "mirgen", "biotoolsCURIE": "biotools:mirgen", "version": [ "3.0" ], "otherID": [ { "value": "doi:10.25504/FAIRsharing.QXSgvF", "type": "doi", "version": "2.0" } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1097", "term": "Sequence accession (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1869", "term": "Organism identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3134", "term": "Gene transcript report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_0880", "term": "RNA secondary structure" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "Data retrieval: curated miRNA. Organism identifier: a specific miRNA identifier or a species for all miRNAs for that species. Gene transcript report: with metadata and visualization. RNA secondary structure: the hairpin loop of the miRNA with bases.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1097", "term": "Sequence accession (nucleic acid)" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [ { "uri": "http://edamontology.org/format_2305", "term": "GFF" }, { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] }, { "data": { "uri": "http://edamontology.org/data_3917", "term": "Count matrix" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_0204", "term": "Gene regulation" }, { "uri": "http://edamontology.org/topic_3299", "term": "Evolutionary biology" }, { "uri": "http://edamontology.org/topic_3500", "term": "Zoology" }, { "uri": "http://edamontology.org/topic_2815", "term": "Human biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC0-1.0", "collectionID": [ "UiO tools", "ELIXIR-NO", "ELIXIR-Norway" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Norway" ], "elixirCommunity": [], "link": [ { "url": "https://elixir.no/helpdesk", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "https://www.mirgenedb.org/download", "type": "Biological data", "note": "Sequence downloads for 75 species", "version": "3.0" } ], "documentation": [ { "url": "https://www.mirgenedb.org/information", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkab1101", "pmid": "34850127", "pmcid": "PMC8728216", "type": [ "Primary" ], "version": "2.1", "note": null, "metadata": { "title": "MirGeneDB 2.1: Toward a complete sampling of all major animal phyla", "abstract": "We describe an update of MirGeneDB, the manually curated microRNA gene database. Adhering to uniform and consistent criteria for microRNA annotation and nomenclature, we substantially expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning over ∼800 million years of animal evolution, and contains a total number of 16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new phylogenetically important species, especially those relevant for the study of whole genome duplication events, and through updating evolutionary nodes of origin for many families and genes, we were able to substantially refine our nomenclature system. All changes are traceable in the specifically developed MirGeneDB version tracker. The performance of read-pages is improved and microRNA expression matrices for all tissues and species are now also downloadable. Altogether, this update represents a significant step toward a complete sampling of all major metazoan phyla, and a widely needed foundation for comparative microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.", "date": "2022-01-07T00:00:00Z", "citationCount": 95, "authors": [ { "name": "Fromm B." }, { "name": "Hoye E." }, { "name": "Domanska D." }, { "name": "Zhong X." }, { "name": "Aparicio-Puerta E." }, { "name": "Ovchinnikov V." }, { "name": "Umu S.U." }, { "name": "Chabot P.J." }, { "name": "Kang W." }, { "name": "Aslanzadeh M." }, { "name": "Tarbier M." }, { "name": "Marmol-Sanchez E." }, { "name": "Urgese G." }, { "name": "Johansen M." }, { "name": "Hovig E." }, { "name": "Hackenberg M." }, { "name": "Friedlander M.R." }, { "name": "Peterson K.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkz885", "pmid": "31598695", "pmcid": "PMC6943042", "type": [ "Primary" ], "version": "2.0", "note": null, "metadata": { "title": "MirGeneDB 2.0: The metazoan microRNA complement", "abstract": "Small non-coding RNAs have gained substantial attention due to their roles in animal development and human disorders. Among them, microRNAs are special because individual gene sequences are conserved across the animal kingdom. In addition, unique and mechanistically well understood features can clearly distinguish bona fide miRNAs from the myriad other small RNAs generated by cells. However, making this distinction is not a common practice and, thus, not surprisingly, the heterogeneous quality of available miRNA complements has become a major concern in microRNA research. We addressed this by extensively expanding our curated microRNA gene database-MirGeneDB-to 45 organisms, encompassing a wide phylogenetic swath of animal evolution. By consistently annotating and naming 10,899 microRNA genes in these organisms, we show that previous microRNA annotations contained not only many false positives, but surprisingly lacked >2000 bona fide microRNAs. Indeed, curated microRNA complements of closely related organisms are very similar and can be used to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust platform for microRNA-based research, providing deeper and more significant insights into the biology and evolution of miRNAs as well as biomedical and biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.", "date": "2020-01-01T00:00:00Z", "citationCount": 178, "authors": [ { "name": "Fromm B." }, { "name": "Domanska D." }, { "name": "Hoye E." }, { "name": "Ovchinnikov V." }, { "name": "Kang W." }, { "name": "Aparicio-Puerta E." }, { "name": "Johansen M." }, { "name": "Flatmark K." }, { "name": "Mathelier A." }, { "name": "Hovig E." }, { "name": "Hackenberg M." }, { "name": "Friedlander M.R." }, { "name": "Peterson K.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1146/annurev-genet-120213-092023", "pmid": "26473382", "pmcid": "PMC4743252", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome", "abstract": "Although microRNAs (miRNAs) are among the most intensively studied molecules of the past 20 years, determining what is and what is not a miRNA has not been straightforward. Here, we present a uniform system for the annotation and nomenclature of miRNA genes. We show that less than a third of the 1,881 human miRBase entries, and only approximately 16% of the 7,095 metazoan miRBase entries, are robustly supported as miRNA genes. Furthermore, we show that the human repertoire of miRNAs has been shaped by periods of intense miRNA innovation and that mature gene products show a very different tempo and mode of sequence evolution than star products. We establish a new open access database-MirGeneDB (http://mirgenedb.org)-to catalog this set of miRNAs, which complements the efforts of miRBase but differs from it by annotating the mature versus star products and by imposing an evolutionary hierarchy upon this curated and consistently named repertoire.", "date": "2015-11-23T00:00:00Z", "citationCount": 435, "authors": [ { "name": "Fromm B." }, { "name": "Billipp T." }, { "name": "Peck L.E." }, { "name": "Johansen M." }, { "name": "Tarver J.E." }, { "name": "King B.L." }, { "name": "Newcomb J.M." }, { "name": "Sempere L.F." }, { "name": "Flatmark K." }, { "name": "Hovig E." }, { "name": "Peterson K.J." } ], "journal": "Annual Review of Genetics" } }, { "doi": "10.1093/nar/gkae1094", "pmid": "39673268", "pmcid": "PMC11701709", "type": [ "Primary" ], "version": "3.0", "note": null, "metadata": { "title": "MirGeneDB 3.0: Improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models", "abstract": "We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to a new server and the creation of a computational mirror, we have expanded the database with the addition of 33 invertebrate species, including representatives of 5 previously unsampled phyla, and 6 mammal species. MirGeneDB now contains entries for 21 822 microRNA genes (5160 of these from the new species) belonging to 1743 microRNA families. The inclusion of these new species allowed us to refine both the evolutionary node of appearance of a number of microRNA genes/families, as well as MirGeneDB's phylogenetically informed nomenclature system. Updated covariance models of all microRNA families, along with all smallRNA read data are now downloadable. These enhanced annotations will allow researchers to analyze microRNA properties such as secondary structure and features of their biogenesis within a robust phylogenetic context and without the database plagued with numerous false positives and false negatives. In light of these improvements, MirGeneDB 3.0 will assume the responsibility for naming conserved novel metazoan microRNAs. MirGeneDB is part of RNAcentral and Elixir Norway and is publicly and freely available at mirgenedb.org.", "date": "2025-01-06T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Clarke A.W." }, { "name": "Hoye E." }, { "name": "Hembrom A.A." }, { "name": "Paynter V.M." }, { "name": "Vinther J." }, { "name": "Wyrozemski L." }, { "name": "Biryukova I." }, { "name": "Formaggioni A." }, { "name": "Ovchinnikov V." }, { "name": "Herlyn H." }, { "name": "Pierce A." }, { "name": "Wu C." }, { "name": "Aslanzadeh M." }, { "name": "Cheneby J." }, { "name": "Martinez P." }, { "name": "Friedlander M.R." }, { "name": "Hovig E." }, { "name": "Hackenberg M." }, { "name": "Umu S.U." }, { "name": "Johansen M." }, { "name": "Peterson K.J." }, { "name": "Fromm B." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Bastian Fromm", "email": "BastianFromm@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-0352-3037", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer", "Support" ], "note": null }, { "name": "Kevin J. Peterson", "email": "kevin.j.peterson@dartmouth.edu", "url": null, "orcidid": null, "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": "University of Oslo", "email": null, "url": "https://www.uio.no/english/index.html", "orcidid": null, "gridid": "grid.5510.1", "rorid": "01xtthb56", "fundrefid": "10.13039/501100005366", "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "UiO", "additionDate": "2016-02-09T13:19:44Z", "lastUpdate": "2025-07-05T22:33:30.082420Z", "editPermission": { "type": "group", "authors": [ "eca008" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "purge_dups", "description": "Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences", "homepage": "https://github.com/dfguan/purge_dups", "biotoolsID": "purge_dups", "biotoolsCURIE": "biotools:purge_dups", "version": [ "v.1.2.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_3798", "term": "Read binning" }, { "uri": "http://edamontology.org/operation_3216", "term": "Scaffolding" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python", "C" ], "license": "MIT", "collectionID": [ "ONTeater" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/dfguan/purge_dups", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/dfguan/purge_dups/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/729962", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Dengfeng Guan", "email": null, "url": "https://www.chatlink.com.cn", "orcidid": "https://orcid.org/0000-0002-6376-3940", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "Pub2Tools", "additionDate": "2019-11-14T18:08:10Z", "lastUpdate": "2025-06-30T15:34:51.626796Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Compleasm", "description": "Compleasm: a faster and more accurate reimplementation of BUSCO.\nIt provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.", "homepage": "https://github.com/huangnengCSU/compleasm", "biotoolsID": "compleasm", "biotoolsCURIE": "biotools:compleasm", "version": [ "v.0.2.5" ], "otherID": [], "relation": [ { "biotoolsID": "busco", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [] } ], "note": "Runs compleasm using the BUSCO set corresponding to the lineage given.", "cmd": "compleasm run -l \"$lineage\" -a assembly.fa -o output_prefix" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "ONTeater" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/huangnengCSU/compleasm", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/huangnengCSU/compleasm/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://busco.ezlab.org/list_of_lineages.html", "type": [ "Other" ], "note": "List of accepted lineages (taxonomic groups with curated BUSCO sets)" } ], "download": [], "documentation": [ { "url": "https://github.com/huangnengCSU/compleasm/blob/0.2.6/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btad595", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "compleasm: a faster and more accurate reimplementation of BUSCO", "abstract": "Motivation: Evaluating the gene completeness is critical to measuring the quality of a genome assembly. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses. Benchmarking Universal Single-Copy Orthologs (BUSCO) is a widely used tool for assessing the completeness of genome assembly by testing the presence of a set of single-copy orthologs conserved across a wide range of taxa. However, BUSCO is slow particularly for large genome assemblies. It is cumbersome to apply BUSCO to a large number of assemblies. Results: Here, we present compleasm, an efficient tool for assessing the completeness of genome assemblies. Compleasm utilizes the miniprot protein-to-genome aligner and the conserved orthologous genes from BUSCO. It is 14 times faster than BUSCO for human assemblies and reports a more accurate completeness of 99.6% than BUSCO's 95.7%, which is in close agreement with the annotation completeness of 99.5% for T2T-CHM13.", "date": "2023-10-01T00:00:00Z", "citationCount": 95, "authors": [ { "name": "Huang N." }, { "name": "Li H." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Neng Huang", "email": "neng@ds.dfci.harvard.edu", "url": null, "orcidid": "https://orcid.org/0000-0001-7187-0749", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "rlibouban", "additionDate": "2024-03-18T14:51:49.667412Z", "lastUpdate": "2025-06-30T15:30:41.266812Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FANTASIAV2", "description": "FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) is a pipeline for protein annotating via GO term transference using the embedding space. FANTASIA’s latest developments include additional protein language models and provide enhanced functionalities.", "homepage": "https://github.com/CBBIO/FANTASIA", "biotoolsID": "fantasiav2", "biotoolsCURIE": "biotools:fantasiav2", "version": [ "2.8.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3945", "term": "Molecular evolution" }, { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" }, { "uri": "http://edamontology.org/topic_4010", "term": "Open science" } ], "operatingSystem": [ "Linux" ], "language": [ "Python", "SQL" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Spain" ], "elixirCommunity": [ "3D-BioInfo", "Proteomics" ], "link": [ { "url": "https://github.com/CBBIO/FANTASIA", "type": [ "Repository" ], "note": "Main repository contains documentation from latest version" }, { "url": "https://github.com/MetazoaPhylogenomicsLab/FANTASIA", "type": [ "Repository" ], "note": "Main repository contains documentation from linitial version based on Bioembeddings implementation." }, { "url": "https://www.earthbiogenome.org/report-on-annotation-recommended-tools", "type": [ "Software catalogue" ], "note": "Recommended tool for the Earth Biogenome Project" } ], "download": [], "documentation": [ { "url": "https://fantasia.readthedocs.io/en/latest/", "type": [ "General" ], "note": "Full documetnation with user cases, benchmarking, and cluster implementations" } ], "publication": [ { "doi": "10.1093/nargab/lqae078", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Decoding functional proteome information in model organisms using protein language models", "abstract": "Protein language models have been tested and proved to be reliable when used on curated datasets but have not yet been applied to full proteomes. Accordingly, we tested how two different machine learning-based methods performed when decoding functional information from the proteomes of selected model organisms. We found that protein language models are more precise and informative than deep learning methods for all the species tested and across the three gene ontologies studied, and that they better recover functional information from transcriptomic experiments. The results obtained indicate that these language models are likely to be suitable for large-scale annotation and downstream analyses, and we recommend a guide for their use.", "date": "2024-09-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Barrios-Nunez I." }, { "name": "Martinez-Redondo G.I." }, { "name": "Medina-Burgos P." }, { "name": "Cases I." }, { "name": "Fernandez R." }, { "name": "Rojas A.M." } ], "journal": "NAR Genomics and Bioinformatics" } }, { "doi": "10.1101/2024.02.28.582465", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Francisco Miguel Pérez Canales", "email": "fmpercan@upo.es", "url": "http://www.bioinfocb.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer", "Support", "Provider" ], "note": "Programmer" }, { "name": "Ana M Rojas Mendoza", "email": "a.rojas.m@csic.es", "url": "http://www.bioinfocb.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Contributor", "Documentor", "Support" ], "note": "Scientific concept and functionalities" }, { "name": "Rosa Fernandez", "email": "rosa.fernandez@ibe.upf-csic.es", "url": "https://www.metazomics.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Documentor" ], "note": "Scientific concept and functionalities" }, { "name": "Francisco J. Ruiz Mota", "email": "fraruimot@alum.us.es", "url": "http://www.bioinfocb.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Junior developer" }, { "name": "Gemma Martinez Redondo", "email": "gemma.martinez@ibe.upf-csic.es", "url": "https://www.metazomics.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Developer" ], "note": "Contributed as developer of the first version of FANTASIA V1" } ], "owner": "arojas", "additionDate": "2025-06-25T13:31:29.384393Z", "lastUpdate": "2025-06-25T14:34:50.629045Z", "editPermission": { "type": "group", "authors": [ "frapercan" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "DeepSig", "description": "Prediction of secretory signal peptides in protein sequences", "homepage": "https://busca.biocomp.unibo.it/deepsig/", "biotoolsID": "deepsig", "biotoolsCURIE": "biotools:deepsig", "version": [ "1.2.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0418", "term": "Protein signal peptide detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python", "C++" ], "license": "GPL-3.0", "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/BolognaBiocomp/deepsig", "type": "Source code", "note": null, "version": "1.2.5" }, { "url": "https://hub.docker.com/r/bolognabiocomp/deepsig", "type": "Container file", "note": null, "version": "1.2.5" } ], "documentation": [ { "url": "https://github.com/BolognaBiocomp/deepsig", "type": [ "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btx818", "pmid": "29280997", "pmcid": "PMC5946842", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "DeepSig: Deep learning improves signal peptide detection in proteins", "abstract": "Motivation The identification of signal peptides in protein sequences is an important step toward protein localization and function characterization. Results Here, we present DeepSig, an improved approach for signal peptide detection and cleavage-site prediction based on deep learning methods. Comparative benchmarks performed on an updated independent dataset of proteins show that DeepSig is the current best performing method, scoring better than other available state-of-the-art approaches on both signal peptide detection and precise cleavage-site identification. Availability and implementation DeepSig is available as both standalone program and web server at https://deepsig.biocomp.unibo.it. All datasets used in this study can be obtained from the same website.", "date": "2018-05-15T00:00:00Z", "citationCount": 96, "authors": [ { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Fariselli P." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "http://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", "Primary contact" ], "note": null }, { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": "http://biocomp.unibo.it", "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2018-05-28T14:50:09Z", "lastUpdate": "2025-06-19T11:55:09.017105Z", "editPermission": { "type": "group", "authors": [ "savo", "ELIXIR-ITA-BOLOGNA" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "NanoPlot", "description": "NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences", "homepage": "https://github.com/wdecoster/NanoPlot", "biotoolsID": "nanoplot", "biotoolsCURIE": "biotools:nanoplot", "version": [ "v.1.42.0" ], "otherID": [], "relation": [ { "biotoolsID": "nanopack", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2940", "term": "Scatter plot plotting" }, { "uri": "http://edamontology.org/operation_2943", "term": "Box-Whisker plot plotting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" }, { "uri": "http://edamontology.org/format_1207", "term": "nucleotide" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "ONTeater" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/wdecoster/NanoPlot", "type": [ "Repository" ], "note": "Issue tracker and most up to date software version" }, { "url": "http://nanoplot.bioinf.be/", "type": [ "Service" ], "note": "Web service with more limited options compared to the command line tool" } ], "download": [ { "url": "https://anaconda.org/bioconda/nanoplot", "type": "Command-line specification", "note": null, "version": null }, { "url": "https://pypi.org/project/NanoPlot/", "type": "Command-line specification", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/wdecoster/NanoPlot", "type": [ "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bty149", "pmid": "29547981", "pmcid": "PMC6061794", "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "NanoPack: Visualizing and processing long-read sequencing data", "abstract": "Summary: Here we describe NanoPack, a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Availability and implementation: The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.", "date": "2018-08-01T00:00:00Z", "citationCount": 1840, "authors": [ { "name": "De Coster W." }, { "name": "D'Hert S." }, { "name": "Schultz D.T." }, { "name": "Cruts M." }, { "name": "Van Broeckhoven C." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Wouter De Coster", "email": null, "url": "https://gigabaseorgigabyte.wordpress.com/", "orcidid": "https://orcid.org/0000-0002-5248-8197", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "wdecoster", "additionDate": "2021-07-06T20:27:27Z", "lastUpdate": "2025-06-18T12:31:48.762608Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SKM", "description": "Stress Knowledge Map: A compilation of knowledge on mechanisms underlying responses of plants to stress, the so called stress signalling network.", "homepage": "https://skm.nib.si/", "biotoolsID": "skm", "biotoolsCURIE": "biotools:skm", "version": [], "otherID": [], "relation": [ { "biotoolsID": "gomapman", "type": "uses" }, { "biotoolsID": "newt-ve", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2299", "term": "Gene name" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3619", "term": "sif" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_0950", "term": "Mathematical model" }, "format": [ { "uri": "http://edamontology.org/format_2585", "term": "SBML" }, { "uri": "http://edamontology.org/format_3692", "term": "SBGN-ML" }, { "uri": "http://edamontology.org/format_3619", "term": "sif" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "ELIXIR-SI", "Plant Systems Biology" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Slovenia" ], "elixirCommunity": [ "Plant Sciences" ], "link": [ { "url": "https://skm.nib.si/contact", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "https://skm.nib.si/documentation", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.xplc.2024.100920", "pmid": "38616489", "pmcid": null, "type": [ "Primary" ], "version": null, "note": "Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses", "metadata": { "title": "Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses", "abstract": "Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.", "date": "2024-06-10T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Bleker C." }, { "name": "Ramsak" }, { "name": "Bittner A." }, { "name": "Podpecan V." }, { "name": "Zagorscak M." }, { "name": "Wurzinger B." }, { "name": "Baebler" }, { "name": "Petek M." }, { "name": "Kriznik M." }, { "name": "van Dieren A." }, { "name": "Gruber J." }, { "name": "Afjehi-Sadat L." }, { "name": "Weckwerth W." }, { "name": "Zupanic A." }, { "name": "Teige M." }, { "name": "Vothknecht U.C." }, { "name": "Gruden K." } ], "journal": "Plant Communications" } } ], "credit": [ { "name": "National Institute of Biology, Department of Biotechnology and Systems Biology", "email": null, "url": "http://www.nib.si/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Carissa Bleker", "email": "carissarobyn.bleker@nib.si", "url": null, "orcidid": "https://orcid.org/0000-0003-1617-7145", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Kristina Gruden", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Živa Ramšak", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Vid Podpečan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null } ], "owner": "carissa", "additionDate": "2022-05-16T13:26:15.720803Z", "lastUpdate": "2025-06-18T12:10:26.465410Z", "editPermission": { "type": "group", "authors": [ "zagor" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Flye", "description": "Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.", "homepage": "https://github.com/fenderglass/Flye", "biotoolsID": "Flye", "biotoolsCURIE": "biotools:Flye", "version": [ "2.9.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" }, { "uri": "http://edamontology.org/operation_0523", "term": "Mapping assembly" }, { "uri": "http://edamontology.org/operation_3730", "term": "Cross-assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "C++", "Python", "C" ], "license": "BSD-3-Clause", "collectionID": [ "ONTeater" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/fenderglass/Flye/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/mikolmogorov/Flye", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1099/mgen.0.000294", "pmid": "31483244", "pmcid": "PMC6807382", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes", "abstract": "Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods affect hybrid assembly accuracy. Relative automation of the assembly process is also crucial to facilitating high-throughput complete bacterial genome reconstruction, avoiding multiple bespoke filtering and data manipulation steps. In this study, we compared hybrid assemblies for 20 bacterial isolates, including two reference strains, using Illumina sequencing and long reads from either Oxford Nanopore Technologies (ONT) or SMRT Pacific Biosciences (PacBio) sequencing platforms. We chose isolates from the family Enterobacteriaceae, as these frequently have highly plastic, repetitive genetic structures, and complete genome reconstruction for these species is relevant for a precise understanding of the epidemiology of antimicrobial resistance. We de novo assembled genomes using the hybrid assembler Unicycler and compared different read processing strategies, as well as comparing to long-read-only assembly with Flye followed by short-read polishing with Pilon. Hybrid assembly with either PacBio or ONT reads facilitated high-quality genome reconstruction, and was superior to the longread assembly and polishing approach evaluated with respect to accuracy and completeness. Combining ONT and Illumina reads fully resolved most genomes without additional manual steps, and at a lower consumables cost per isolate in our setting. Automated hybrid assembly is a powerful tool for complete and accurate bacterial genome assembly.", "date": "2019-01-01T00:00:00Z", "citationCount": 166, "authors": [ { "name": "De Maio N." }, { "name": "Shaw L.P." }, { "name": "Hubbard A." }, { "name": "George S." }, { "name": "Sanderson N.D." }, { "name": "Swann J." }, { "name": "Wick R." }, { "name": "Oun M.A." }, { "name": "Stubberfield E." }, { "name": "Hoosdally S.J." }, { "name": "Crook D.W." }, { "name": "Peto T.E.A." }, { "name": "Sheppard A.E." }, { "name": "Bailey M.J." }, { "name": "Read D.S." }, { "name": "Anjum M.F." }, { "name": "Sarah Walker A." }, { "name": "Stoesser N." } ], "journal": "Microbial Genomics" } }, { "doi": "10.1038/s41587-019-0072-8", "pmid": "30936562", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Assembly of long, error-prone reads using repeat graphs", "abstract": "Accurate genome assembly is hampered by repetitive regions. Although long single molecule sequencing reads are better able to resolve genomic repeats than short-read data, most long-read assembly algorithms do not provide the repeat characterization necessary for producing optimal assemblies. Here, we present Flye, a long-read assembly algorithm that generates arbitrary paths in an unknown repeat graph, called disjointigs, and constructs an accurate repeat graph from these error-riddled disjointigs. We benchmark Flye against five state-of-the-art assemblers and show that it generates better or comparable assemblies, while being an order of magnitude faster. Flye nearly doubled the contiguity of the human genome assembly (as measured by the NGA50 assembly quality metric) compared with existing assemblers.", "date": "2019-05-01T00:00:00Z", "citationCount": 3077, "authors": [ { "name": "Kolmogorov M." }, { "name": "Yuan J." }, { "name": "Lin Y." }, { "name": "Pevzner P.A." } ], "journal": "Nature Biotechnology" } }, { "doi": "10.1038/s41592-020-00971-x", "pmid": "33020656", "pmcid": "PMC10699202", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "metaFlye: scalable long-read metagenome assembly using repeat graphs", "abstract": "Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products.", "date": "2020-11-01T00:00:00Z", "citationCount": 511, "authors": [ { "name": "Kolmogorov M." }, { "name": "Bickhart D.M." }, { "name": "Behsaz B." }, { "name": "Gurevich A." }, { "name": "Rayko M." }, { "name": "Shin S.B." }, { "name": "Kuhn K." }, { "name": "Yuan J." }, { "name": "Polevikov E." }, { "name": "Smith T.P.L." }, { "name": "Pevzner P.A." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Mikhail Kolmogorov", "email": "fenderglass@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Support" ], "note": null }, { "name": "Yu Lin", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jeffrey Yuan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "Pub2Tools", "additionDate": "2019-11-14T20:08:20Z", "lastUpdate": "2025-06-18T10:20:03.775603Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "BioSimulations", "description": "BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. 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Packages", "abstract": "Summary: Genomics has dramatically improved our understanding of the molecular origins of certain human diseases. Nonetheless, our health is also influenced by the cumulative impact of exposures experienced across the life course (termed 'exposome'). The study of the high-dimensional exposome offers a new paradigm for investigating environmental contributions to disease etiology. However, there is a lack of bioinformatics tools for managing, visualizing and analyzing the exposome. The analysis data should include both association with health outcomes and integration with omic layers. We provide a generic framework called rexposome project, developed in the R/Bioconductor architecture that includes object-oriented classes and methods to leverage high-dimensional exposome data in disease association studies including its integration with a variety of high-throughput data types. The usefulness of the package is illustrated by analyzing a real dataset including exposome data, three health outcomes related to respiratory diseases and its integration with the transcriptome and methylome.", "date": "2019-12-15T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Hernandez-Ferrer C." }, { "name": "Wellenius G.A." }, { "name": "Tamayo I." }, { "name": "Basagana X." }, { "name": "Sunyer J." }, { "name": "Vrijheid M." }, { "name": "Gonzalez J.R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1038/s41467-022-34422-2", "pmid": "36411288", "pmcid": "PMC9678903", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Multi-omics signatures of the human early life exposome", "abstract": "Environmental exposures during early life play a critical role in life-course health, yet the molecular phenotypes underlying environmental effects on health are poorly understood. In the Human Early Life Exposome (HELIX) project, a multi-centre cohort of 1301 mother-child pairs, we associate individual exposomes consisting of >100 chemical, outdoor, social and lifestyle exposures assessed in pregnancy and childhood, with multi-omics profiles (methylome, transcriptome, proteins and metabolites) in childhood. We identify 1170 associations, 249 in pregnancy and 921 in childhood, which reveal potential biological responses and sources of exposure. Pregnancy exposures, including maternal smoking, cadmium and molybdenum, are predominantly associated with child DNA methylation changes. In contrast, childhood exposures are associated with features across all omics layers, most frequently the serum metabolome, revealing signatures for diet, toxic chemical compounds, essential trace elements, and weather conditions, among others. Our comprehensive and unique resource of all associations (https://helixomics.isglobal.org/) will serve to guide future investigation into the biological imprints of the early life exposome.", "date": "2022-12-01T00:00:00Z", "citationCount": 81, "authors": [ { "name": "Maitre L." }, { "name": "Bustamante M." }, { "name": "Hernandez-Ferrer C." }, { "name": "Thiel D." }, { "name": "Lau C.-H.E." }, { "name": "Siskos A.P." }, { "name": "Vives-Usano M." }, { "name": "Ruiz-Arenas C." }, { "name": "Pelegri-Siso D." }, { "name": "Robinson O." }, { "name": "Mason D." }, { "name": "Wright J." }, { "name": "Cadiou S." }, { "name": "Slama R." }, { "name": "Heude B." }, { "name": "Casas M." }, { "name": "Sunyer J." }, { "name": "Papadopoulou E.Z." }, { "name": "Gutzkow K.B." }, { "name": "Andrusaityte S." }, { "name": "Grazuleviciene R." }, { "name": "Vafeiadi M." }, { "name": "Chatzi L." }, { "name": "Sakhi A.K." }, { "name": "Thomsen C." }, { "name": "Tamayo I." }, { "name": "Nieuwenhuijsen M." }, { "name": "Urquiza J." }, { "name": "Borras E." }, { "name": "Sabido E." }, { "name": "Quintela I." }, { "name": "Carracedo A." }, { "name": "Estivill X." }, { "name": "Coen M." }, { "name": "Gonzalez J.R." }, { "name": "Keun H.C." }, { "name": "Vrijheid M." } ], "journal": "Nature Communications" } } ], "credit": [ { "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": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Xavier Escribà Montagut", "email": "xavier.escriba@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": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "chernan3", "additionDate": "2018-07-25T15:26:58Z", "lastUpdate": "2025-05-29T11:42:05.422761Z", "editPermission": { "type": "group", "authors": [ "brgelab", "sergitobara", "chernan3" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "VIPER", "description": "VIPER is a framework and tool for the automated design of inhibitory decoy peptides based on structural binding data of two proteins.", "homepage": "https://github.com/A-Klingenberg/VIPER/tree/main", "biotoolsID": "viper-decoypep", "biotoolsCURIE": "biotools:viper-decoypep", "version": [ "1.0.1" ], "otherID": [ { "value": "doi:10.5281/zenodo.10897888", "type": "doi", "version": "1.0.1" } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_4008", "term": "Protein design" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0781", "term": "Virology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/A-Klingenberg/VIPER/tree/main", "type": [ "Repository" ], "note": "Source code" } ], "download": [ { "url": "https://github.com/A-Klingenberg/VIPER/releases/tag/1.0.1", "type": "Downloads page", "note": "Source code", "version": "1.0.1" } ], "documentation": [ { "url": "https://github.com/A-Klingenberg/VIPER/blob/main/VIPER_Manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1089/cmb.2024.0866", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "VIPER: Virus Inhibition Via Peptide Engineering and Receptor Mimicry", "abstract": "A key step in most viral infections is the binding of a viral protein to a host receptor, leading to the virus entering the host cell. Disrupting this protein-protein interaction is an effective strategy for preventing infection and subsequent disease. Building on recent advances in computational tools for structural biology, we introduce Virus Inhibition via Peptide Engineering and Receptor Mimicry (VIPER), a novel approach for the automatic derivation and optimization of biomimetic decoy peptides that mimic binding sites of human proteins. VIPER leverages structural data from human-pathogen protein complexes, yielding peptides that can competitively inhibit viral entry by mimicking the natural receptor. We computationally validated VIPER using molecular dynamics simulations and showcased its applicability on three clinically relevant viruses, highlighting its potential to accelerate therapeutic development. With a focus on reproducibility and extensibility, VIPER can facilitate the rapid development of antiviral inhibitors by automating the design and optimization of biomimetic compounds.", "date": "2025-04-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Klingenberg A.S." }, { "name": "Ghersi D." } ], "journal": "Journal of computational biology : a journal of computational molecular cell biology" } }, { "doi": "10.5281/zenodo.10897858", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Anna Sophie Klingenberg", "email": "aklingenberg@unomaha.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Dario Ghersi", "email": "dghersi@unomaha.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-0630-0843", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "aklingenberg", "additionDate": "2024-03-30T14:51:09.814337Z", "lastUpdate": "2025-05-16T12:04:59.507285Z", "editPermission": { "type": "group", "authors": [ "aklingenberg" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "KVFinder-web", "description": "KVFinder-web is an open-source web-based application of an updated version of parKVFinder software (v1.2.0) for cavity detection and characterization of any type of biomolecular structure, including but not limited to proteins and nucleic acids. \n\nKVFinder-web employs a geometric grid-and-sphere-based method with a dual-probe system for efficient cavity detection. The web-based application provides comprehensive characterizations, including shape, volume, area, depth, constitutional, and hydropathy information.", "homepage": "https://kvfinder-web.cnpem.br/", "biotoolsID": "kvfinder-web", "biotoolsCURIE": "biotools:kvfinder-web", "version": [ "v1.1.1" ], "otherID": [], "relation": [ { "biotoolsID": "parKVFinder", "type": "uses" }, { "biotoolsID": "KVFinder", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2575", "term": "Binding site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2878", "term": "Protein structural motif" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web service", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R", "C", "Other" ], "license": "Apache-2.0", "collectionID": [ "COVID-19", "Rare Disease", "KVFinder suite" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/LBC-LNBio/KVFinder-web", "type": [ "Other" ], "note": null }, { "url": "https://github.com/LBC-LNBio/KVFinder-web-service", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/LBC-LNBio/KVFinder-web-portal", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/LBC-LNBio/PyMOL-KVFinder-web-Tools", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://lbc-lnbio.github.io/KVFinder-web/", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkad324", "pmid": "37140050", "pmcid": "PMC10320092", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "KVFinder-web: A web-based application for detecting and characterizing biomolecular cavities", "abstract": "Molecular interactions that modulate catalytic processes occur mainly in cavities throughout the molecular surface. Such interactions occur with specific small molecules due to geometric and physicochemical complementarity with the receptor. In this scenario, we present KVFinder-web, an open-source web-based application of parKVFinder software for cavity detection and characterization of biomolecular structures. The KVFinder-web has two independent components: A RESTful web service and a web graphical portal. Our web service, KVFinder-web service, handles client requests, manages accepted jobs, and performs cavity detection and characterization on accepted jobs. Our graphical web portal, KVFinder-web portal, provides a simple and straightforward page for cavity analysis, which customizes detection parameters, submits jobs to the web service component, and displays cavities and characterizations. We provide a publicly available KVFinder-web at https://kvfinder-web.cnpem.br, running in a cloud environment as docker containers. Further, this deployment type allows KVFinder-web components to be configured locally and customized according to user demand. Hence, users may run jobs on a locally configured service or our public KVFinder-web.", "date": "2023-07-05T00:00:00Z", "citationCount": 13, "authors": [ { "name": "Guerra J.V.S." }, { "name": "Ribeiro-Filho H.V." }, { "name": "Pereira J.G.C." }, { "name": "Lopes-De-Oliveira P.S." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1021/acs.jcim.3c00328", "pmid": "37129917", "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Cavity Characterization in Supramolecular Cages", "abstract": "Confining molecular guests within artificial hosts has provided a major driving force in the rational design of supramolecular cages with tailored properties. Over the last 30 years, a set of design strategies have been developed that enabled the controlled synthesis of a myriad of cages. Recently, there has been a growing interest in involving in silico methods in this toolbox. Cavity shape and size are important parameters that can be easily accessed by inexpensive geometric algorithms. Although these algorithms are well developed for the detection of nonartificial cavities (e.g., enzymes), they are not routinely used for the rational design of supramolecular cages. In order to test the capabilities of this tool, we have evaluated the performance and characteristics of seven different cavity characterization software in the context of 22 analogues of well-known supramolecular cages. Among the tested software, KVFinder project and Fpocket proved to be the most software to characterize supramolecular cavities. With the results of this work, we aim to popularize this underused technique within the supramolecular community.", "date": "2023-06-26T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Guerra J.V.S." }, { "name": "Alves L.F.G." }, { "name": "Bourissou D." }, { "name": "Lopes-De-Oliveira P.S." }, { "name": "Szaloki G." } ], "journal": "Journal of Chemical Information and Modeling" } } ], "credit": [ { "name": "João V. S. Guerra", "email": "joao.guerra@lnbio.cnpem.br", "url": "https://github.com/jvsguerra", "orcidid": "https://orcid.org/0000-0002-6800-4425", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Primary contact" ], "note": null }, { "name": "Helder V. Ribeiro-Filho", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "José G. C. 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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. 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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. 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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. 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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. The script is designed to handle large raster datasets efficiently by dividing the workload across multiple CPU cores.", "homepage": "https://github.com/UtrechtUniversity/raster_extraction", "biotoolsID": "raster_extraction", "biotoolsCURIE": "biotools:raster_extraction", "version": [], "otherID": [], "relation": [ { "biotoolsID": "exposome_maps", "type": "uses" } ], "function": [ { "operation": [], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3855", "term": "Environmental sciences" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [], "language": [], "license": "Not licensed", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Lloyd Roga", "email": "l.q.roga@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "Channel2291", "additionDate": "2025-03-17T14:11:03.252329Z", "lastUpdate": "2025-03-17T14:13:20.238876Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }