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{ "count": 30395, "next": "?page=2", "previous": null, "list": [ { "name": "EUCAIM ETL toolset", "description": "Modular toolchain for an extensible and customizable ETL pipeline that extracts, transforms, and loads clinical data and medical imaging metadata, applying dataset-specific mappings to generate outputs compatible with the EUCAIM Common Data Model (CDM). Its design aims to minimize manual data preparation efforts and facilitate customization and integration with other components, such as data quality assurance tools.\nContainerized, currently supports input datasets in CSV, JSON, XLSX.", "homepage": "https://bahiasoftware.es/home", "biotoolsID": "eetl_toolset", "biotoolsCURIE": "biotools:eetl_toolset", "version": [ "0.9.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Data formatting" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Data deposition" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3345", "term": "Data identity and mapping" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Linux", "Windows" ], "language": [ "Java", "Python" ], "license": null, "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "victorsp", "additionDate": "2025-04-24T13:00:12.867477Z", "lastUpdate": "2025-04-24T13:50:30.032187Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EUCAIM DICOM Anonymizer", "description": "The EUCAIM DICOM Anonymizer anonymizes a set of DICOM files. It supports both anonymization on a case-by-case scenario, meaning one DICOM Study at a time (single-mode) or on multiple cases concurrently (batch mode). Additionally it hashes and links clinical data.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/eucaim-anonymizer/", "biotoolsID": "eucaim_dicom_anonymizer", "biotoolsCURIE": "biotools:eucaim_dicom_anonymizer", "version": [ "0.12.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3283", "term": "Anonymisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "C++" ], "license": null, "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "vkalokyri", "additionDate": "2025-04-14T16:46:40.806977Z", "lastUpdate": "2025-04-24T13:06:17.802389Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "sylph", "description": "fast and precise species-level metagenomic profiling with ANIs", "homepage": "https://github.com/bluenote-1577/sylph", "biotoolsID": "sylph", "biotoolsCURIE": "biotools:sylph", "version": [ "v0.4.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "pauffret", "additionDate": "2023-12-06T15:45:20.587393Z", "lastUpdate": "2025-04-24T09:31:08.371089Z", "editPermission": { "type": "group", "authors": [ "vashokan" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Longitools Exposome Toolbox", "description": "The LongITools toolbox is an open-source platform developed to support exposome research analysis. This cloud-based computational environment enables researchers to construct customized analytical platforms suited to their specific research requirements. The system provides a web-based interface that integrates various analytical resources, including statistical tools, computational pipelines, connections to external data repositories, and data visualization capabilities.", "homepage": "https://longitools.bsc.es/vre/", "biotoolsID": "longitools_exposome_toolbox", "biotoolsCURIE": "biotools:longitools_exposome_toolbox", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application", "Command-line tool", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3376", "term": "Medicines research and development" } ], "operatingSystem": [], "language": [ "R", "Python", "PHP" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://longitools.bsc.es/vre/", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/inab/openVRE/tree/longitools", "type": [ "Quick start guide" ], "note": null } ], "publication": [], "credit": [ { "name": "Karim Lekadir", "email": "karim.lekadir@ub.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-9456-1612", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null } ], "owner": "noussair", "additionDate": "2025-04-23T10:31:12.521148Z", "lastUpdate": "2025-04-23T10:31:21.719823Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Gemma", "description": "Gemma provides data, experimental design annotations, and differential expression analysis results for thousands of microarray and RNA-seq experiments. We re-analyze raw data from public sources (primarily NCBI GEO), annotate experimental conditions, conduct quality control and compute differential expression using standardized procedures. We have especially good coverage of experiments relevant to the nervous system.", "homepage": "https://gemma.msl.ubc.ca/", "biotoolsID": "gemma", "biotoolsCURIE": "biotools:gemma", "version": [ "1.31.13" ], "otherID": [], "relation": [ { "biotoolsID": "rsem", "type": "uses" }, { "biotoolsID": "multiqc", "type": "uses" }, { "biotoolsID": "cutadapt", "type": "uses" }, { "biotoolsID": "star", "type": "uses" }, { "biotoolsID": "ncbi_geo", "type": "uses" }, { "biotoolsID": "sradb", "type": "uses" }, { "biotoolsID": "ncbi_gene", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3110", "term": "Raw microarray data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1636", "term": "Heat map" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3914", "term": "Quality control report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" }, { "uri": "http://edamontology.org/topic_3518", "term": "Microarray experiment" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data curation and archival" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java", "JavaScript" ], "license": "CC-BY-NC-4.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/PavlidisLab/Gemma", "type": [ "Repository", "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/PavlidisLab/Gemma/releases", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://pavlidislab.github.io/Gemma/", "type": [ "General" ], "note": null }, { "url": "https://gemma.msl.ubc.ca/resources/restapidocs/", "type": [ "API documentation" ], "note": "Documentation for the Gemma REST API." } ], "publication": [ { "doi": "10.1093/bioinformatics/btp259", "pmid": "19376825", "pmcid": "PMC2687992", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Application and evaluation of automated semantic annotation of gene expression experiments", "abstract": "Motivation: Many microarray datasets are available online with formalized standards describing the probe sequences and expression values. Unfortunately, the description, conditions and parameters of the experiments are less commonly formalized and often occur as natural language text. This hinders searching, high-throughput analysis, organization and integration of the datasets. Results: We use the lexical resources and software tools from the Unified Medical Language System (UMLS) to extract concepts from text. We then link the UMLS concepts to classes in open biomedical ontologies. The result is accessible and clear semantic annotations of gene expression experiments. We applied the method to 595 expression experiments from Gemma, a resource for re-use and meta-analysis of gene expression profiling data. We evaluated and corrected all stages of the annotation process. The majority of missed annotations were due to a lack of cross-references. The most error-prone stage was the extraction of concepts from phrases. Final review of the annotations in context of the experiments revealed 89% precision. A naive system, lacking the phrase to concept corrections is 68% precise. We have integrated this annotation pipeline into Gemma. © 2009 The Author(s).", "date": "2009-06-09T00:00:00Z", "citationCount": 9, "authors": [ { "name": "French L." }, { "name": "Lane S." }, { "name": "Law T." }, { "name": "Xu L." }, { "name": "Pavlidis P." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/database/baab006", "pmid": "33599246", "pmcid": "PMC7904053", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Curation of over 10 000 transcriptomic studies to enable data reuse", "abstract": "Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe-gene mappings across microarray technologies. Thus, extensive curation and data reprocessing are necessary prior to any reuse. The Gemma bioinformatics system was created to help address these issues. Gemma consists of a database of curated transcriptomic datasets, analytical software, a web interface and web services. Here we present an update on Gemma's holdings, data processing and analysis pipelines, our curation guidelines, and software features. As of June 2020, Gemma contains 10 811 manually curated datasets (primarily human, mouse and rat), over 395 000 samples and hundreds of curated transcriptomic platforms (both microarray and RNA sequencing). Dataset topics were represented with 10 215 distinct terms from 12 ontologies, for a total of 54 316 topic annotations (mean topics/dataset = 5.2). While Gemma has broad coverage of conditions and tissues, it captures a large majority of available brain-related datasets, accounting for 34% of its holdings. Users can access the curated data and differential expression analyses through the Gemma website, RESTful service and an R package. Database URL: https://gemma.msl.ubc.ca/home.html", "date": "2021-01-01T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Lim N." }, { "name": "Tesar S." }, { "name": "Belmadani M." }, { "name": "Poirier-Morency G." }, { "name": "Mancarci B.O." }, { "name": "Sicherman J." }, { "name": "Jacobson M." }, { "name": "Leong J." }, { "name": "Tan P." }, { "name": "Pavlidis P." } ], "journal": "Database" } } ], "credit": [ { "name": "Pavlidis Lab Support", "email": "pavlab-support@msl.ubc.ca", "url": "https://pavlab.msl.ubc.ca/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null } ], "owner": "artrymix", "additionDate": "2017-04-22T17:35:18Z", "lastUpdate": "2025-04-22T22:09:03.811075Z", "editPermission": { "type": "group", "authors": [ "artrymix", "paulpavlidis" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MetaPhlAn", "description": "Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.", "homepage": "http://segatalab.cibio.unitn.it/tools/metaphlan/index.html", "biotoolsID": "metaphlan", "biotoolsCURIE": "biotools:metaphlan", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "note": null, "cmd": "metaphlan <fastq_input> --input_type fastq -o <output>" }, { "operation": [ { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "note": "Convert SGB-based profile to GTDB taxonomy", "cmd": "sgb_to_gtdb_profile.py -i <metaphlan_output> -o <gtdb_metaphlan_output>" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_0194", "term": "Phylogenomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "MIT", "collectionID": [ "Animal and Crop Genomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/biobakery/MetaPhlAn", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/nmeth.2066", "pmid": "22688413", "pmcid": "PMC3443552", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Metagenomic microbial community profiling using unique clade-specific marker genes", "abstract": "Metagenomic shotgun sequencing data can identify microbes populating a microbial community and their proportions, but existing taxonomic profiling methods are inefficient for increasingly large data sets. We present an approach that uses clade-specific marker genes to unambiguously assign reads to microbial clades more accurately and >50Ã-faster than current approaches. We validated our metagenomic phylogenetic analysis tool, MetaPhlAn, on terabases of short reads and provide the largest metagenomic profiling to date of the human gut. It can be accessed at http://huttenhower.sph.harvard.edu/ metaphlan/. © 2012 Nature America, Inc. All rights reserved.", "date": "2012-08-01T00:00:00Z", "citationCount": 1300, "authors": [ { "name": "Segata N." }, { "name": "Waldron L." }, { "name": "Ballarini A." }, { "name": "Narasimhan V." }, { "name": "Jousson O." }, { "name": "Huttenhower C." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": null, "email": null, "url": "https://groups.google.com/forum/#!forum/metaphlan-users", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-08-20T15:57:59Z", "lastUpdate": "2025-04-22T12:44:24.859435Z", "editPermission": { "type": "group", "authors": [ "animalandcropgenomics", "ELIXIR-CZ", "bebatut", "vashokan" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "samclip", "description": "Filter SAM file for soft and hard clipped alignments", "homepage": "https://github.com/tseemann/samclip", "biotoolsID": "samclip", "biotoolsCURIE": "biotools:samclip", "version": [ "0.4.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/tseemann/samclip", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://anaconda.org/bioconda/samclip", "type": "Software package", "note": null, "version": "0.4.0" } ], "documentation": [ { "url": "https://github.com/tseemann/samclip", "type": [ "General" ], "note": null } ], "publication": [], "credit": [], "owner": "emmcauley", "additionDate": "2025-04-21T21:06:51.624399Z", "lastUpdate": "2025-04-21T21:06:51.626575Z", "editPermission": { "type": "group", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NetPicoRNA", "description": "Neural network predictions of cleavage sites of picornaviral proteases.", "homepage": "http://cbs.dtu.dk/services/NetPicoRNA/", "biotoolsID": "netpicorna", "biotoolsCURIE": "biotools:netpicorna", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0422", "term": "Protein cleavage site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "note": "produces neural network predictions of cleavage sites of picornaviral proteases", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "Other", "collectionID": [], "maturity": "Legacy", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://cbs.dtu.dk/services", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.cbs.dtu.dk/services/NetPicoRNA/instructions.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/pro.5560051107", "pmid": "8931139", "pmcid": "PMC2143287", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Cleavage site analysis in picornaviral polyproteins: Discovering cellular targets by neural networks", "abstract": "Picornaviral proteinases are responsible for maturation cleavages of the viral polyprotein, but also catalyze the degradation of cellular targets. Using graphical visualization techniques and neural network algorithms, we have investigated the sequence specificity of the two proteinases 2A(pro) and 3C(pro). The cleavage of VP0 (giving rise to VP2 and VP4), which is carried out by a so-far unknown proteinase, was also examined. In combination with a novel surface exposure prediction algorithm, our neural network approach successfully distinguishes known cleavage sites from noncleavage sites and yields a more consistent definition of features common to these sites. The method is able to predict experimentally determined cleavage sites in cellular proteins. We present a list of mammalian and other proteins that are predicted to be possible targets for the vital proteinases. Whether these proteins are indeed cleaved awaits experimental verification. Additionally, we report several errors detected in the protein databases.", "date": "1996-01-01T00:00:00Z", "citationCount": 204, "authors": [ { "name": "Blom N." }, { "name": "Hansen J." }, { "name": "Blaas D." }, { "name": "Brunak S." } ], "journal": "Protein Science" } } ], "credit": [ { "name": "CBS", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Nikolaj Sorgenfrei Blom", "email": "nikob@cbs.dtu.dk", "url": null, "orcidid": "https://orcid.org/0000-0001-7787-7853", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "CBS", "additionDate": "2015-06-29T10:14:28Z", "lastUpdate": "2025-04-18T18:42:39.901910Z", "editPermission": { "type": "group", "authors": [ "powehi" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SLiM", "description": "Evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Includes a graphical modeling environment.", "homepage": "https://messerlab.org/slim/", "biotoolsID": "SLiM_software", "biotoolsCURIE": "biotools:SLiM_software", "version": [ "5.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0550", "term": "DNA substitution modelling" }, { "uri": "http://edamontology.org/operation_0230", "term": "Sequence generation" }, { "uri": "http://edamontology.org/operation_3946", "term": "Ecological modelling" } ], "input": [], "output": [], "note": "Run individual-based eco-evolutionary simulations with explicit genetics", "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0610", "term": "Ecology" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3299", "term": "Evolutionary biology" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://messerlab.org/slim/", "type": [ "Software catalogue" ], "note": "SLiM home page in the Messer Lab website" }, { "url": "https://github.com/MesserLab/SLiM", "type": [ "Repository" ], "note": "GitHub repository for SLiM" }, { "url": "https://groups.google.com/g/slim-discuss", "type": [ "Discussion forum" ], "note": "Discussion forum for SLiM questions" }, { "url": "https://groups.google.com/g/slim-announce", "type": [ "Mailing list" ], "note": "Announcements mailing list" } ], "download": [ { "url": "http://benhaller.com/slim/SLiM.zip", "type": "Source code", "note": "A source archive for the command-line `slim` tool only. Complete source code is on GitHub, but most platforms have an installer anyway; see the manual, chapter 2, for installation instructions.", "version": null }, { "url": "https://github.com/MesserLab/SLiM/releases/latest", "type": "Downloads page", "note": "The GitHub page for the current release version, to obtain full source code.", "version": null } ], "documentation": [ { "url": "http://benhaller.com/slim/SLiM_Manual.pdf", "type": [ "User manual" ], "note": "The manual for SLiM itself" }, { "url": "http://benhaller.com/slim/Eidos_Manual.pdf", "type": [ "User manual" ], "note": "The manual for Eidos, the scripting language used by SLiM" }, { "url": "http://benhaller.com/slim/SLiMEidosRefSheets.zip", "type": [ "Quick start guide" ], "note": "Quick reference sheets for SLiM and Eidos" } ], "publication": [ { "doi": "10.1093/molbev/msy228", "pmid": "30517680", "pmcid": "PMC6389312", "type": [ "Other" ], "version": null, "note": "B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond the Wright–Fisher Model. Molecular Biology and Evolution 36(3), 632–637.", "metadata": { "title": "SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model", "abstract": "With the desire to model population genetic processes under increasingly realistic scenarios, forward genetic simulations have become a critical part of the toolbox of modern evolutionary biology. The SLiM forward genetic simulation framework is one of the most powerful and widely used tools in this area. However, its foundation in the Wright-Fisher model has been found to pose an obstacle to implementing many types of models; it is difficult to adapt the Wright-Fisher model, with its many assumptions, to modeling ecologically realistic scenarios such as explicit space, overlapping generations, individual variation in reproduction, density-dependent population regulation, individual variation in dispersal or migration, local extinction and recolonization, mating between subpopulations, age structure, fitness-based survival and hard selection, emergent sex ratios, and so forth. In response to this need, we here introduce SLiM 3, which contains two key advancements aimed at abolishing these limitations. First, the new non-Wright-Fisher or \"nonWF\" model type provides a much more flexible foundation that allows the easy implementation of all of the above scenarios and many more. Second, SLiM 3 adds support for continuous space, including spatial interactions and spatial maps of environmental variables. We provide a conceptual overview of these new features, and present several example models to illustrate their use.", "date": "2019-03-01T00:00:00Z", "citationCount": 504, "authors": [ { "name": "Haller B.C." }, { "name": "Messer P.W." } ], "journal": "Molecular Biology and Evolution" } }, { "doi": "10.1093/molbev/msy237", "pmid": "30590560", "pmcid": "PMC6501880", "type": [ "Usage" ], "version": null, "note": "B.C. Haller, P.W. Messer. (2019). Evolutionary modeling in SLiM 3 for beginners. Molecular Biology and Evolution 36(5), 1101–1109.", "metadata": { "title": "Evolutionary Modeling in SLiM 3 for Beginners", "abstract": "The SLiM forward genetic simulation framework has proved to be a powerful and flexible tool for population genetic modeling. However, as a complex piece of software with many features that allow simulating a diverse assortment of evolutionary models, its initial learning curve can be difficult. Here we provide a step-by-step demonstration of how to build a simple evolutionary model in SLiM 3, to help new users get started. We will begin with a panmictic neutral model, and build up to a model of the evolution of a polygenic quantitative trait under selection for an environmental phenotypic optimum.", "date": "2019-05-01T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Haller B.C." }, { "name": "Messer P.W." } ], "journal": "Molecular Biology and Evolution" } }, { "doi": "10.1111/1755-0998.12968", "pmid": "30565882", "pmcid": "PMC6393187", "type": [ "Method" ], "version": null, "note": "B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources 19(2), 552–566.", "metadata": { "title": "Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes", "abstract": "There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual-based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. The recently developed tree-sequence recording method (Kelleher, Thornton, Ashander, & Ralph, 2018), which stores the genealogical history of all genomes in the simulated population, could provide such an advance. This method has several benefits: (1) it allows neutral mutations to be omitted entirely from forward-time simulations and added later, thereby dramatically improving computational efficiency; (2) it allows neutral burn-in to be constructed extremely efficiently after the fact, using “recapitation”; (3) it allows direct examination and analysis of the genealogical trees along the genome; and (4) it provides a compact representation of a population's genealogy that can be analysed in Python using the msprime package. We have implemented the tree-sequence recording method in SLiM 3 (a free, open-source evolutionary simulation software package) and extended it to allow the recording of non-neutral mutations, greatly broadening the utility of this method. To demonstrate the versatility and performance of this approach, we showcase several practical applications that would have been beyond the reach of previously existing methods, opening up new horizons for the modelling and exploration of evolutionary processes.", "date": "2019-03-01T00:00:00Z", "citationCount": 109, "authors": [ { "name": "Haller B.C." }, { "name": "Galloway J." }, { "name": "Kelleher J." }, { "name": "Messer P.W." }, { "name": "Ralph P.L." } ], "journal": "Molecular Ecology Resources" } }, { "doi": "10.1086/723601", "pmid": "37130229", "pmcid": "PMC10793872", "type": [ "Primary" ], "version": null, "note": "B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary modeling. The American Naturalist 201(5), E127–E139.", "metadata": { "title": "SLiM 4: Multispecies Eco-Evolutionary Modeling", "abstract": "The SLiM software framework for genetically explicit forward simulation has been widely used in population genetics. However, it has been largely restricted to modeling only a single species, which has limited its broader utility in evolutionary biology. Indeed, to our knowledge no general-purpose, flexible modeling framework exists that provides support for simulating multiple species while also providing other key features, such as explicit genetics and continuous space. The lack of such software has limited our ability to model higher biological levels such as communities, eco-systems, coevolutionary and eco-evolutionary processes, and bio-diversity, which is crucial for many purposes, from extending our basic understanding of evolutionary ecology to informing conservation and management decisions. We here announce the release of SLiM 4, which fills this important gap by adding support for multiple species, including ecological interactions between species such as predation, parasitism, and mutualism, and illustrate its new features with examples.", "date": "2023-05-01T00:00:00Z", "citationCount": 79, "authors": [ { "name": "Haller B.C." }, { "name": "Messer P.W." } ], "journal": "American Naturalist" } } ], "credit": [ { "name": "Philipp Messer", "email": "messer@cornell.edu", "url": "https://messerlab.org", "orcidid": "https://orcid.org/0000-0001-8453-9377", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Benjamin C. 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Two execution modes are available : manual execution and command line execution.\nFor the tool to scan data successfully, it is important that : 1/ the extension “.dcm” is visible, as the tool only scans those files, and discard any other; 2/ each DICOM series has its own folder, as the tool gets a single .dcm file from each folder and extracts the tags.", "homepage": "https://www.bcplatforms.com/", "biotoolsID": "dicom_tags_extractor", "biotoolsCURIE": "biotools:dicom_tags_extractor", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Data formatting" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [], "language": [], "license": "Not licensed", 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"biotoolsID": "data_ingestion_tool_upv_reference_node", "biotoolsCURIE": "biotools:data_ingestion_tool_upv_reference_node", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_3372", "term": "Software engineering" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" } ], "operatingSystem": [ "Windows" ], "language": [ "Python" ], "license": null, "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "casopon", "additionDate": "2025-04-17T13:07:06.039592Z", "lastUpdate": "2025-04-17T13:07:06.055307Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE", "casopon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "eNRSA", "description": "eNRSA is an enhanced version of NRSA for analyzing nascent transcription profiles generated by PRO-seq, GRO-seq, (m)NET-seq, and Butt-seq data.", "homepage": "https://bioinfo.vanderbilt.edu/eNRSA/", "biotoolsID": "enrsa", "biotoolsCURIE": "biotools:enrsa", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/chc-code/eNRSA", "type": [ "Software catalogue" ], "note": "link to github repo" } ], "download": [ { "url": 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HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "pedromiguel_martinez_HULAFE", "additionDate": "2025-04-15T17:42:40.968987Z", "lastUpdate": "2025-04-16T17:01:17.400957Z", "editPermission": { "type": "private", "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": "Radiomic features extraction", "description": "Implemented by GIBI230, this tool is a Docker-based software designed for extracting radiomic features from 3D medical images in NIfTI format using the PyRadiomics library (if DICOM images, the DICOM to NIFTI converter must be run before using this tool). It streamlines the radiomics calculation process by generating a structured CSV file containing all extracted variables from medical images.\nThe dockerized software enables users to configure parameters like filters, bin width, resampling spacing, and normalization settings can be specified. The output radiomic variables provide quantitative information for further analysis in medical imaging research and machine learning applications. \nSpecially important the parameter selection of the band width. For robust and reproducible results, a bin width of 5 is commonly recommended, but it should be adjusted based on image resolution, modality, and noise levels.", "homepage": "https://www.acim.lafe.san.gva.es/acim/?page_id=675&lang=es", "biotoolsID": "gibi230_radiomic_features_extraction", "biotoolsCURIE": "biotools:gibi230_radiomic_features_extraction", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [ "Python" ], "license": null, "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "pedromiguel_martinez_HULAFE", "additionDate": "2024-12-23T12:44:47.964606Z", "lastUpdate": "2025-04-16T12:17:50.036263Z", "editPermission": { "type": "group", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "openVRE", "description": "The Open Virtual Research Environment is a general purpose analysis platform that can be tailored for domain specific analyses.", "homepage": "https://github.com/inab/openVRE/wiki", "biotoolsID": "openvre", "biotoolsCURIE": "biotools:openvre", "version": [ "1.0" ], "otherID": [], "relation": [ { "biotoolsID": "mugvre", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3760", "term": "Service management" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal", "Workbench" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux" ], "language": [ "PHP", "Python", "JavaScript" ], "license": "Apache-2.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Spain" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/inab/openVRE", "type": "Source code", "note": null, "version": "1.0" } ], "documentation": [ { "url": "http://vre.multiscalegenomics.eu/help/starting.php", "type": [ "Quick start guide" ], "note": "Getting Started Guide" } ], "publication": [], "credit": [ { "name": "Laia Codó", "email": "laia.codo@bsc.es", "url": "https://www.bsc.es/codo-laia", "orcidid": "https://orcid.org/0000-0002-6797-8746", "gridid": "grid.10097.3f", "rorid": "05sd8tv96", "fundrefid": "10.13039/501100006433", "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Senior Researcher at Barcelona Supercomputing Center. Lead of Trusted Research Environments and Cloud Computing at INB Lab." }, { "name": "Josep Lluís Gelpí", "email": "gelpi@ub.edu", "url": "https://webgrec.ub.edu/webpages/000011/ang/gelpi.ub.edu.html", "orcidid": "http://orcid.org/0000-0002-0566-7723", "gridid": "grid.5841.8", "rorid": "021018s57", "fundrefid": "10.13039/501100005774", "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Professor at University of Barcelona and Team Leader at BSC's INB Laboratory" } ], "owner": "gelpi@ub.edu", "additionDate": "2025-04-16T08:53:57.270825Z", "lastUpdate": "2025-04-16T08:53:57.280528Z", "editPermission": { "type": "group", "authors": [ "gelpi@ub.edu" ] }, "validated": 0, "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": "hictkpy", "description": "Python bindings for hictk: read and write .cool and .hic files directly from Python", "homepage": "https://github.com/paulsengroup/hictkpy", "biotoolsID": "hictkpy", "biotoolsCURIE": "biotools:hictkpy", "version": [ "0.0.1", "0.0.2", "0.0.3", "0.0.4", "0.0.5", "1.0.0", "1.1.0", "1.2.0" ], "otherID": [], "relation": [ { "biotoolsID": "hictk", "type": "uses" } ], "function": [], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/paulsengroup/hictkpy", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/paulsengroup/hictkpy/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/paulsengroup/hictkpy/discussions", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "https://github.com/paulsengroup/hictkpy/releases", "type": "Downloads page", "note": null, "version": null }, { "url": "https://pypi.org/project/hictkpy/", "type": "Binaries", "note": null, "version": null }, { "url": "https://anaconda.org/bioconda/hictkpy", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://hictkpy.readthedocs.io/en/stable/", "type": [ "General" ], "note": null }, { "url": "https://hictkpy.readthedocs.io/en/stable/installation.html", "type": [ "Installation instructions" ], "note": null }, { "url": "https://hictkpy.readthedocs.io/en/stable/quickstart.html", "type": [ "Quick start guide" ], "note": null }, { "url": "https://hictkpy.readthedocs.io/en/stable/api/index.html", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btae408", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "hictk: blazing fast toolkit to work with. hic and. cool files", "abstract": "Motivation: Hi-C is gaining prominence as a method for mapping genome organization. With declining sequencing costs and a growing demand for higher-resolution data, efficient tools for processing Hi-C datasets at different resolutions are crucial. Over the past decade, the. hic and Cooler file formats have become the de-facto standard to store interaction matrices produced by Hi-C experiments in binary format. Interoperability issues make it unnecessarily difficult to convert between the two formats and to develop applications that can process each format natively. Results: We developed hictk, a toolkit that can transparently operate on. hic and. cool files with excellent performance. The toolkit is written in C++ and consists of a C++ library with Python and R bindings as well as CLI tools to perform common operations directly from the shell, including converting between. hic and. mcool formats. We benchmark the performance of hictk and compare it with other popular tools and libraries. We conclude that hictk significantly outperforms existing tools while providing the flexibility of natively working with both file formats without code duplication.", "date": "2024-07-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Rossini R." }, { "name": "Paulsen J." } ], "journal": "Bioinformatics" } } ], "credit": [], "owner": "robomics", "additionDate": "2024-04-18T08:31:46.459964Z", "lastUpdate": "2025-04-14T22:54:26.266145Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "hictk", "description": "Blazing fast toolkit to work with .hic and .cool files", "homepage": "https://github.com/paulsengroup/hictk", "biotoolsID": "hictk", "biotoolsCURIE": "biotools:hictk", "version": [ "0.0.1", "0.0.2", "0.0.3", "0.0.4", "0.0.5", "0.0.6", "0.0.7", "0.0.8", "0.0.9", "0.0.10", "0.0.11", "0.0.12", "1.0.0", "2.0.0", "2.0.1", "2.0.2", "2.1.0", "2.1.1" ], "otherID": [], "relation": [ { "biotoolsID": "hictkpy", "type": "usedBy" }, { "biotoolsID": "hictkr", "type": "usedBy" } ], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/paulsengroup/hictk", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/paulsengroup/hictk/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/paulsengroup/hictk/discussions", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "https://github.com/paulsengroup/hictk/releases", "type": "Downloads page", "note": null, "version": null }, { "url": "https://anaconda.org/bioconda/hictk", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/paulsengroup/hictk/pkgs/container/hictk", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "https://hictk.readthedocs.io/en/stable/index.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btae408", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "hictk: blazing fast toolkit to work with. hic and. cool files", "abstract": "Motivation: Hi-C is gaining prominence as a method for mapping genome organization. With declining sequencing costs and a growing demand for higher-resolution data, efficient tools for processing Hi-C datasets at different resolutions are crucial. Over the past decade, the. hic and Cooler file formats have become the de-facto standard to store interaction matrices produced by Hi-C experiments in binary format. Interoperability issues make it unnecessarily difficult to convert between the two formats and to develop applications that can process each format natively. Results: We developed hictk, a toolkit that can transparently operate on. hic and. cool files with excellent performance. The toolkit is written in C++ and consists of a C++ library with Python and R bindings as well as CLI tools to perform common operations directly from the shell, including converting between. hic and. mcool formats. We benchmark the performance of hictk and compare it with other popular tools and libraries. We conclude that hictk significantly outperforms existing tools while providing the flexibility of natively working with both file formats without code duplication.", "date": "2024-07-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Rossini R." }, { "name": "Paulsen J." } ], "journal": "Bioinformatics" } } ], "credit": [], "owner": "robomics", "additionDate": "2024-02-02T14:42:46.030561Z", "lastUpdate": "2025-04-14T22:54:16.319235Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PR2", "description": "an 18S rRNA primer database for protists.\n\nAn interactive database of eukaryotic rRNA primers and primer sets for metabarcoding studies compiled from the literature.\n\nA database of eukaryotic rRNA primers and primer sets for metabarcoding studies compiled from the literature.", "homepage": "https://app.pr2-primers.org", "biotoolsID": "pr2", "biotoolsCURIE": "biotools:pr2", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0308", "term": "PCR primer design" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_3237", "term": "Primer removal" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0632", "term": "Probes and primers" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_3068", "term": "Literature and language" } ], "operatingSystem": [], "language": [ "R" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/pr2database/pr2-primers", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://hub.docker.com/repository/docker/vaulot/pr2-primers", "type": "Container file", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1101/2021.01.04.425170", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Vaulot", "email": "vaulot@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "vaulot", "additionDate": "2021-03-19T08:44:58Z", "lastUpdate": "2025-04-14T13:56:12.948169Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "The MINERVA Platform", "description": "The MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format, including files produced using CellDesigner or SBGN editors. Visualization of uploaded networks generated by the platform is accessible via a web browser to all viewers with the weblink to the resource.\n\nThe MINERVA Platform is a webservice using the Java Server Faces 2 technology. The server side, including data parsing, integration, annotation and verification, is implemented in Java. The platform uses the Postgres SQL database for data storage and the Hibernate framework as a middle layer between web server and database. The user web-interface is generated using React.js. The displayed content is visualized by OpenLayers API, dedicated JavaScript and CSS.", "homepage": "https://minerva.uni.lu", "biotoolsID": "MINERVA_Platform", "biotoolsCURIE": "biotools:MINERVA_Platform", "version": [ "13.1.3", "13.2.0", "14.0.13", "15.0.3", "16.4.0", "17.1.3", "18.1.1" ], "otherID": [], "relation": [ { "biotoolsID": "pathvisio", "type": "uses" }, { "biotoolsID": "sbgn", "type": "uses" }, { "biotoolsID": "libsbml", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3926", "term": "Pathway visualisation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0571", "term": "Expression data visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_3342", "term": "Translational medicine" } ], "operatingSystem": [], "language": [], "license": "AGPL-3.0", "collectionID": [ "ELIXIR-LU", "LCSB" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Luxembourg" ], "elixirCommunity": [], "link": [ { "url": "https://gitlab.lcsb.uni.lu/minerva/core/", "type": [ "Repository" ], "note": "GiLab repository for core functionalities (data and format handling, service stability, API access)" }, { "url": "https://gitlab.lcsb.uni.lu/minerva/core/-/issues", "type": [ "Issue tracker" ], "note": "Issue tracker for core functionalities (data and format handling, service stability, API access)" }, { "url": "https://gitlab.lcsb.uni.lu/minerva/frontend", "type": [ "Repository" ], "note": "GiLab repository for frontend functionalities" }, { "url": "https://gitlab.lcsb.uni.lu/minerva/frontend/-/issues", "type": [ "Issue tracker" ], "note": "Issue tracker for frontend functionalities" } ], "download": [ { "url": "https://minerva.pages.uni.lu/doc/install/", "type": "Other", "note": "Installation instructions, including debian package, virtual machine images and docker containers.", "version": "13.1.3 - 18.1.1" } ], "documentation": [ { "url": "https://minerva.uni.lu", "type": [ "Quick start guide", "Release notes", "User manual", "API documentation", "Citation instructions", "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1038/npjsba.2016.20", "pmid": "28725475", "pmcid": "PMC5516855", "type": [ "Primary" ], "version": "10.0", "note": null, "metadata": { "title": "MINERVA—A platform for visualization and curation of molecular interaction networks", "abstract": "Our growing knowledge about various molecular mechanisms is becoming increasingly more structured and accessible. Different repositories of molecular interactions and available literature enable construction of focused and high-quality molecular interaction networks. Novel tools for curation and exploration of such networks are needed, in order to foster the development of a systems biology environment. In particular, solutions for visualization, annotation and data cross-linking will facilitate usage of network-encoded knowledge in biomedical research. To this end we developed the MINERVA (Molecular Interaction NEtwoRks VisuAlization) platform, a standalone webservice supporting curation, annotation and visualization of molecular interaction networks in Systems Biology Graphical Notation (SBGN)-compliant format. MINERVA provides automated content annotation and verification for improved quality control. The end users can explore and interact with hosted networks, and provide direct feedback to content curators. MINERVA enables mapping drug targets or overlaying experimental data on the visualized networks. Extensive export functions enable downloading areas of the visualized networks as SBGN-compliant models for efficient reuse of hosted networks. The software is available under Affero GPL 3.0 as a Virtual Machine snapshot, Debian package and Docker instance at http://r3lab.uni.lu/web/minerva-website/. We believe that MINERVA is an important contribution to systems biology community, as its architecture enables set-up of locally or globally accessible SBGN-oriented repositories of molecular interaction networks. Its functionalities allow overlay of multiple information layers, facilitating exploration of content and interpretation of data. Moreover, annotation and verification workflows of MINERVA improve the efficiency of curation of networks, allowing life-science researchers to better engage in development and use of biomedical knowledge repositories.", "date": "2016-01-01T00:00:00Z", "citationCount": 60, "authors": [ { "name": "Gawron P." }, { "name": "Ostaszewski M." }, { "name": "Satagopam V." }, { "name": "Gebel S." }, { "name": "Mazein A." }, { "name": "Kuzma M." }, { "name": "Zorzan S." }, { "name": "McGee F." }, { "name": "Otjacques B." }, { "name": "Balling R." }, { "name": "Schneider R." } ], "journal": "npj Systems Biology and Applications" } }, { "doi": "10.1093/bioinformatics/btz286", "pmid": "31074494", "pmcid": "PMC6821317", "type": [ "Primary" ], "version": "12.2.3", "note": null, "metadata": { "title": "MINERVA API and plugins: Opening molecular network analysis and visualization to the community", "abstract": "Summary: The complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and management of molecular networks. Here, we introduce an extension to MINERVA architecture that greatly facilitates the access and use of the stored molecular network data. It allows to incorporate such data in analytical pipelines via a programmatic access interface, and to extend the platform's visual exploration and analytics functionality via plugin architecture. This is possible for any molecular network hosted by the MINERVA platform encoded in well-recognized systems biology formats. To showcase the possibilities of the plugin architecture, we have developed several plugins extending the MINERVA core functionalities. In the article, we demonstrate the plugins for interactive tree traversal of molecular networks, for enrichment analysis and for mapping and visualization of known disease variants or known adverse drug reactions to molecules in the network. Availability and implementation: Plugins developed and maintained by the MINERVA team are available under the AGPL v3 license at https://git-r3lab.uni.lu/minerva/plugins/. The MINERVA API and plugin documentation is available at https://minerva-web.lcsb.uni.lu.", "date": "2019-11-01T00:00:00Z", "citationCount": 24, "authors": [ { "name": "Hoksza D." }, { "name": "Gawron P." }, { "name": "Ostaszewski M." }, { "name": "Smula E." }, { "name": "Schneider R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/bib/bbz067", "pmid": "31273380", "pmcid": "PMC7373180", "type": [ "Primary" ], "version": "13.1.1", "note": null, "metadata": { "title": "Closing the gap between formats for storing layout information in systems biology", "abstract": "The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology.", "date": "2019-07-10T00:00:00Z", "citationCount": 15, "authors": [ { "name": "Hoksza D." }, { "name": "Gawron P." }, { "name": "Ostaszewski M." }, { "name": "Hasenauer J." }, { "name": "Schneider R." } ], "journal": "Briefings in Bioinformatics" } }, { "doi": "10.1089/big.2015.0057", "pmid": "27441714", "pmcid": "PMC4932659", "type": [ "Usage" ], "version": "10.0", "note": null, "metadata": { "title": "Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases", "abstract": "Translational medicine is a domain turning results of basic life science research into new tools and methods in a clinical environment, for example, as new diagnostics or therapies. Nowadays, the process of translation is supported by large amounts of heterogeneous data ranging from medical data to a whole range of -omics data. It is not only a great opportunity but also a great challenge, as translational medicine big data is difficult to integrate and analyze, and requires the involvement of biomedical experts for the data processing. We show here that visualization and interoperable workflows, combining multiple complex steps, can address at least parts of the challenge. In this article, we present an integrated workflow for exploring, analysis, and interpretation of translational medicine data in the context of human health. Three Web services - tranSMART, a Galaxy Server, and a MINERVA platform - are combined into one big data pipeline. Native visualization capabilities enable the biomedical experts to get a comprehensive overview and control over separate steps of the workflow. The capabilities of tranSMART enable a flexible filtering of multidimensional integrated data sets to create subsets suitable for downstream processing. A Galaxy Server offers visually aided construction of analytical pipelines, with the use of existing or custom components. A MINERVA platform supports the exploration of health and disease-related mechanisms in a contextualized analytical visualization system. We demonstrate the utility of our workflow by illustrating its subsequent steps using an existing data set, for which we propose a filtering scheme, an analytical pipeline, and a corresponding visualization of analytical results. The workflow is available as a sandbox environment, where readers can work with the described setup themselves. Overall, our work shows how visualization and interfacing of big data processing services facilitate exploration, analysis, and interpretation of translational medicine data.", "date": "2016-06-01T00:00:00Z", "citationCount": 38, "authors": [ { "name": "Satagopam V." }, { "name": "Gu W." }, { "name": "Eifes S." }, { "name": "Gawron P." }, { "name": "Ostaszewski M." }, { "name": "Gebel S." }, { "name": "Barbosa-Silva A." }, { "name": "Balling R." }, { "name": "Schneider R." } ], "journal": "Big Data" } }, { "doi": "10.1016/j.envpol.2019.04.005", "pmid": "30991279", "pmcid": null, "type": [], "version": "13.1.1", "note": null, "metadata": { "title": "Genes associated with Parkinson's disease respond to increasing polychlorinated biphenyl levels in the blood of healthy females", "abstract": "Polychlorinated biphenyls (PCBs) are a class of widespread environmental pollutants, commonly found in human blood, that have been suggested to be linked to the occurrence of sporadic Parkinson's disease (PD). It has been reported that some non-coplanar PCBs accumulate in the brains of female PD patients. To improve our understanding of the association between PCB exposure and PD risk we have applied whole transcriptome gene expression analysis in blood cells from 594 PCB-exposed subjects (369 female, 225 male). Interestingly, we observe that in females, blood levels of non-coplanar PCBs appear to be associated with expression levels of PD-specific genes. However, no such association was detected in males. Among the 131 PD-specific genes affected, 39 have been shown to display similar changes in expression levels in the substantia nigra of deceased PD patients. Especially among the down-regulated genes, transcripts of genes involved in neurotransmitter vesicle-related functions were predominant. Capsule: Plasma PCB levels are associated with gene expression changes in females only, resulting in brain-related genes changing in blood cells of healthy individuals exposed to PCBs.", "date": "2019-07-01T00:00:00Z", "citationCount": 5, "authors": [ { "name": "Bohler S." }, { "name": "Krauskopf J." }, { "name": "Espin-Perez A." }, { "name": "Gebel S." }, { "name": "Palli D." }, { "name": "Rantakokko P." }, { "name": "Kiviranta H." }, { "name": "Kyrtopoulos S.A." }, { "name": "Balling R." }, { "name": "Kleinjans J." } ], "journal": "Environmental Pollution" } } ], "credit": [], "owner": "mjostaszewski", "additionDate": "2019-08-26T14:34:55Z", "lastUpdate": "2025-04-14T09:01:54.711218Z", "editPermission": { "type": "group", "authors": [ "sascha.herzinger" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OpenCloning", "description": "An Open-Source web application to plan and document cloning and genome engineering", "homepage": "https://opencloning.org/", "biotoolsID": "opencloning", "biotoolsCURIE": "biotools:opencloning", "version": [], "otherID": [], "relation": [ { "biotoolsID": "pydna", "type": "uses" }, { "biotoolsID": "biopython", "type": "uses" }, { "biotoolsID": "primer3", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0491", "term": "Pairwise sequence alignment" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3095", "term": "Nucleic acid design" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0365", "term": "Restriction digest" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0230", "term": "Sequence generation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3203", "term": "Chromatogram visualisation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0573", "term": "Map drawing" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3925", "term": "Network visualisation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web API", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3912", "term": "Genetic engineering" }, { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" }, { "uri": "http://edamontology.org/topic_3895", "term": "Synthetic biology" } ], "operatingSystem": [], "language": [ "Python", "JavaScript" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "UK" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/manulera/OpenCloning", "type": [ "Repository" ], "note": null }, { "url": "https://opencloning.org/", "type": [ "Service" ], "note": "Hosted web app" }, { "url": "https://github.com/manulera/OpenCloning_backend", "type": [ "Repository" ], "note": "Backend code" }, { "url": "https://github.com/manulera/OpenCloning_frontend", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/manulera/OpenCloning", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Manuel Lera-Ramirez", "email": "manulera14@gmail.com", "url": "https://github.com/manulera", "orcidid": "https://orcid.org/0000-0002-8666-9746", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "manulera", "additionDate": "2025-04-11T20:52:47.895200Z", "lastUpdate": "2025-04-11T20:53:03.390161Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "metapr2", "description": "The metaPR2 database contains processed 18S rRNA metabarcodes that are annotated with the PR2 reference sequence database. Version 2.0 of the database contains 41 datasets corresponding to more than 6,000 samples and 90,000 ASVs. The database is accessible through both a web-based interface (https://app.metapr2.org) and an R package.", "homepage": "https://app.metapr2.org/", "biotoolsID": "metapr2", "biotoolsCURIE": "biotools:metapr2", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "vaulot", "additionDate": "2025-04-11T14:04:51.838757Z", "lastUpdate": "2025-04-11T14:04:51.841101Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Protists Ribosomal Reference Database", "description": "The PR2 reference sequence database was initiated in 2010 in the frame of the BioMarks project from work that had developed in the previous ten years in the Plankton Group of the Station Biologique of Roscoff. It aims to provide a reference database of carefully annotated 18S rRNA sequences using nine unique taxonomic fields (from domain to species). At present, it contains over 240,000 sequences. Although it focuses on protists, it also contains sequences from metazoa, fungi and plants as well a limited set of 16S sequences from plastids and bacteria. Several metadata fields are available for many sequences, including geo-localisation, whether it originates from a culture or a natural sample, host type etc… The annotation of PR2 is performed by experts from each taxonomic groups.", "homepage": "https://app.pr2-database.org/", "biotoolsID": "pr2-reference", "biotoolsCURIE": "biotools:pr2-reference", "version": [ "5.1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_4038", "term": "Metabarcoding" } ], "operatingSystem": [], "language": [ "R" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/pr2database/pr2database/releases", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/pr2database/pr2database/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://pr2-database.org/", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://github.com/pr2database/pr2database/releases", "type": "Downloads page", "note": null, "version": "5.1.0" } ], "documentation": [ { "url": "https://pr2database.github.io/pr2database/articles/pr2database.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gks1160", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The Protist Ribosomal Reference database (PR2): A catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy", "abstract": "The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136866 sequences are nuclear encoded, 45708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists. © The Author(s) 2012.", "date": "2013-01-01T00:00:00Z", "citationCount": 1456, "authors": [ { "name": "Guillou L." }, { "name": "Bachar D." }, { "name": "Audic S." }, { "name": "Bass D." }, { "name": "Berney C." }, { "name": "Bittner L." }, { "name": "Boutte C." }, { "name": "Burgaud G." }, { "name": "De Vargas C." }, { "name": "Decelle J." }, { "name": "Del Campo J." }, { "name": "Dolan J.R." }, { "name": "Dunthorn M." }, { "name": "Edvardsen B." }, { "name": "Holzmann M." }, { "name": "Kooistra W.H.C.F." }, { "name": "Lara E." }, { "name": "Le Bescot N." }, { "name": "Logares R." }, { "name": "Mahe F." }, { "name": "Massana R." }, { "name": "Montresor M." }, { "name": "Morard R." }, { "name": "Not F." }, { "name": "Pawlowski J." }, { "name": "Probert I." }, { "name": "Sauvadet A.-L." }, { "name": "Siano R." }, { "name": "Stoeck T." }, { "name": "Vaulot D." }, { "name": "Zimmermann P." }, { "name": "Christen R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [], "owner": "vaulot", "additionDate": "2025-04-11T13:56:02.037873Z", "lastUpdate": "2025-04-11T14:01:09.249274Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RDMkit", "description": "RDMkit is the Research Data Management toolkit for Life Sciences, providing best practices and guidelines to for FAIR (Findable, Accessible, Interoperable and Reusable) data management.", "homepage": "https://rdmkit.elixir-europe.org", "biotoolsID": "rdmkit", "biotoolsCURIE": "biotools:rdmkit", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data", "Interoperability", "Training" ], "elixirNode": [ "UK", "Norway", "Belgium", "Germany", "Finland", "Spain" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/elixir-europe/rdmkit", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://zenodo.org/record/5110061", "type": "Downloads page", "note": null, "version": null } ], "documentation": [], "publication": [], "credit": [], "owner": "munazah", "additionDate": "2022-11-03T14:53:22.145643Z", "lastUpdate": "2025-04-11T13:03:16.201584Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "avida", "description": "Avida is a software platform that mirrors key aspects of biological evolution, making it a useful twin for evolutionary studies.", "homepage": "https://github.com/devosoft/avida", "biotoolsID": "avida", "biotoolsCURIE": "biotools:avida", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "Miguel", "additionDate": "2025-04-11T12:25:53.238464Z", "lastUpdate": "2025-04-11T12:25:53.241076Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PLAZA 4.0", "description": "Integrative resource for functional, evolutionary and comparative plant genomics.\n\nPLAZA is an access point for plant comparative genomics, centralizing genomic data produced by different genome sequencing initiatives.\n\nThis intermediate update of the PLAZA platform, with a focus on the Monocots, became necessary due to substantial annotation updates to species present in the 4.0 PLAZA instances.", "homepage": "https://bioinformatics.psb.ugent.be/plaza", "biotoolsID": "plaza_4.0", "biotoolsCURIE": "biotools:plaza_4.0", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0553", "term": "Gene tree construction" }, { "uri": "http://edamontology.org/operation_0558", "term": "Phylogenetic tree annotation" }, { "uri": "http://edamontology.org/operation_0567", "term": "Phylogenetic tree visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [ "BIG N2N", "VIB", "UGent" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://bioinformatics.psb.ugent.be/plaza/documentation", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/NAR/GKX1002", "pmid": "29069403", "pmcid": "PMC5753339", "type": [], "version": null, "note": null, "metadata": { "title": "PLAZA 4.0: An integrative resource for functional, evolutionary and comparative plant genomics", "abstract": "PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. Each PLAZA instance contains structural and functional gene annotations, gene family data and phylogenetic trees and detailed gene colinearity information. A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework. This version consists of two new instances (Dicots 4.0 and Monocots 4.0) providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes. The total number of species across both instances nearly doubles from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia). The new PLAZA instances can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians to optimally leverage the power of the PLAZA platform.", "date": "2018-01-01T00:00:00Z", "citationCount": 338, "authors": [ { "name": "Van Bel M." }, { "name": "Diels T." }, { "name": "Vancaester E." }, { "name": "Kreft L." }, { "name": "Botzki A." }, { "name": "Van De Peer Y." }, { "name": "Coppens F." }, { "name": "Vandepoele K." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Klaas Vandepoele", "email": "klaas.vandepoele@ugent.vib.be", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "bits@vib.be", "additionDate": "2020-09-03T19:08:44Z", "lastUpdate": "2025-04-11T09:29:36.505334Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "CellBinDB", "description": "We have released a large-scale, multimodal annotated dataset for cell segmentation, CellBinDB. Based on CellBinDB, we designed a benchmarking pipeline to benchmark eight of the most advanced and widely used cell segmentation techniques/methods, and further analyzed the impact of four cell morphology indicators and image gradients on the segmentation results.", "homepage": "https://github.com/STOmics/cs-benchmark", "biotoolsID": "cellbindb", "biotoolsCURIE": "biotools:cellbindb", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "shican", "additionDate": "2025-04-10T03:18:36.031624Z", "lastUpdate": "2025-04-10T03:18:59.657512Z", "editPermission": { "type": "private", "authors": [] }, "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": "Hi-cGAN", "description": "A software to predict Hi-C matrices based on ChIP-seq histone data using a cGAN approach.", "homepage": "https://github.com/joachimwolff/Hi-cGAN", "biotoolsID": "hi-cgan", "biotoolsCURIE": "biotools:hi-cgan", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "joachimwolff", "additionDate": "2025-04-09T09:58:29.019039Z", "lastUpdate": "2025-04-09T09:59:16.835262Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MuDoGeR", "description": "The Multi-Domain Genome Recovery v1.0 (MuDoGeR v1.0) framework is a tool developed to help users to recover Metagenome-Assembled Genomes and Uncultivated Viral Genomes from whole-genome sequence (WGS) samples simultaneously. The MuDoGeR v1.0 framework acts as a wrapper for several tools. It was designed to be an easy-to-use tool that outputs ready-to-use comprehensive files.", "homepage": "https://github.com/mdsufz/MuDoGeR", "biotoolsID": "mudoger", "biotoolsCURIE": "biotools:mudoger", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" }, { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Shell", "R", "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/mdsufz/MuDoGeR", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1111/1755-0998.13904", "pmid": "37994269", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy", "abstract": "Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored for those familiar with Unix command-line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination. We tested MuDoGeR using 24 individual-isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. While MuDoGeR can recover eukaryotic viral sequences, its characterization is predominantly skewed towards bacterial and archaeal viruses, reflecting the field's current state. However, acting as a dynamic wrapper, the MuDoGeR is designed to constantly incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR. Additionally, MuDoGeR is also available as a Singularity container.", "date": "2024-02-01T00:00:00Z", "citationCount": 5, "authors": [ { "name": "Rocha U." }, { "name": "CoelhoKasmanas J." }, { "name": "Kallies R." }, { "name": "Saraiva J.P." }, { "name": "Toscan R.B." }, { "name": "Stefanic P." }, { "name": "Bicalho M.F." }, { "name": "BorimCorrea F." }, { "name": "Basturk M.N." }, { "name": "Fousekis E." }, { "name": "VianaBarbosa L.M." }, { "name": "Plewka J." }, { "name": "Probst A.J." }, { "name": "Baldrian P." }, { "name": "Stadler P.F." } ], "journal": "Molecular Ecology Resources" } } ], "credit": [ { "name": "Ulisses Rocha", "email": "ulisses.rocha@ufz.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2024-04-16T14:14:05.166974Z", "lastUpdate": "2025-04-09T07:23:51.614291Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MarineMetagenomeDB", "description": "MarineMetagenomeDB provides standardized and manually curated metadata for 11,449 marine metagenomes from SRA and MG-RAST. It enables users to search, filter, visualize, and download metadata through a web application equipped with quick and advanced search options, interactive map selection, and export tools. The database enhances data findability and reuse for comparative and large-scale meta-analyses in marine microbiome research.", "homepage": "https://webapp.ufz.de/marmdb/", "biotoolsID": "marinemetagenomedb", "biotoolsCURIE": "biotools:marinemetagenomedb", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3837", "term": "Metagenomic sequencing" }, { "uri": "http://edamontology.org/topic_3277", "term": "Sample collections" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s40793-022-00449-7", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "andersonavilasantos", "additionDate": "2025-04-08T12:40:26.806570Z", "lastUpdate": "2025-04-08T12:44:37.167081Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AnimalAssociatedMetagenomeDB", "description": "The AnimalAssociatedMetagenomeDB (AAMDB) provides standardized and manually curated metadata for 10,885 non-human, animal-associated metagenomes collected from public repositories such as SRA and MG-RAST. It allows users to search, filter, visualize, and export metadata through an interactive web application featuring quick and advanced search options, geographic map-based selection, and support for raw data download. The tool facilitates the discovery and reuse of metagenomic data in biodiversity and microbiome studies.", "homepage": "https://webapp.ufz.de/aamdb/", "biotoolsID": "animalassociatedmetagenomedb", "biotoolsCURIE": "biotools:animalassociatedmetagenomedb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3837", "term": "Metagenomic sequencing" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3277", "term": "Sample collections" } ], "operatingSystem": [], "language": [ "R" ], "license": null, "collectionID": [ "NFDI4Microbiota" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s42523-023-00267-3", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "andersonavilasantos", "additionDate": "2025-04-08T12:16:36.396210Z", "lastUpdate": "2025-04-08T12:38:13.124276Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CheckM2", "description": "Rapid assessment of genome bin quality using machine learning.\n\nCheckM2 uses two distinct machine learning models to predict genome completeness. The 'general' gradient boost model is able to generalize well and is intended to be used on organisms not well represented in GenBank or RefSeq (roughly, when an organism is novel at the level of order, class or phylum). The 'specific' neural network model is more accurate when predicting completeness of organisms more closely related to the reference training set (roughly, when an organism belongs to a known species, genus or family). CheckM2 uses a cosine similarity calculation to automatically determine the appropriate completeness model for each input genome, but you can also force the use of a particular completeness model, or get the prediction outputs for both. There is only one contamination model (based on gradient boost) which is applied regardless of taxonomic novelty and works well across all cases.", "homepage": "https://github.com/chklovski/CheckM2", "biotoolsID": "checkm2", "biotoolsCURIE": "biotools:checkm2", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_0194", "term": "Phylogenomics" }, { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "GPL-3.0", "collectionID": [ "NFDI4Microbiota" ], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.nature.com/articles/s41592-023-01940-w", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://doi.org/10.5281/zenodo.14897628", "type": "Biological data", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/chklovski/CheckM2", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1038/s41592-023-01940-w", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "Kasmanas", "additionDate": "2025-04-08T11:23:25.060891Z", "lastUpdate": "2025-04-08T11:23:25.063938Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Coreprofiler", "description": "CoreProfiler is a cgMLST (core genome multilocus sequence typing) software that identifies alleles in bacterial genome assemblies by comparing them to a reference allele scheme. It detects both exact matches to known alleles and potential novel alleles using a two-step BLAST-based approach, enabling robust and reproducible strain genotyping.", "homepage": "https://gitlab.com/ifb-elixirfr/abromics/coreprofiler", "biotoolsID": "coreprofiler", "biotoolsCURIE": "biotools:coreprofiler", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3840", "term": "Multilocus sequence typing" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://gitlab.com/ifb-elixirfr/abromics/coreprofiler/-/blob/main/README.md?ref_type=heads", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.5281/ZENODO.8282656", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1016/S0022-2836(05)80360-2", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Basic local alignment search tool", "abstract": "A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straight-forward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity. © 1990, Academic Press Limited. All rights reserved.", "date": "1990-01-01T00:00:00Z", "citationCount": 79275, "authors": [ { "name": "Altschul S.F." }, { "name": "Gish W." }, { "name": "Miller W." }, { "name": "Myers E.W." }, { "name": "Lipman D.J." } ], "journal": "Journal of Molecular Biology" } } ], "credit": [], "owner": "clsiguret", "additionDate": "2025-04-08T08:17:22.895529Z", "lastUpdate": "2025-04-08T08:22:57.038047Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OptimJV3", "description": "Optimize parameters of JARVIS3 - a genomic compressor - for compression of genomic sequences", "homepage": "https://github.com/cobilab/OptimJV3", "biotoolsID": "optimjv3", "biotoolsCURIE": "biotools:optimjv3", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "ritaferrolho", "additionDate": "2025-04-03T15:58:10.986044Z", "lastUpdate": "2025-04-03T15:58:10.988726Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PSIPRED", "description": "The PSIPRED Protein Analysis Workbench unites many available analysis tools into a single web based framework. An excellent tool for prediction of secondary structure, with access to GenTHREADER for protein fold recognition and MEMSAT-2 transmembrane topology prediction.", "homepage": "http://bioinf.cs.ucl.ac.uk/psipred/", "biotoolsID": "psipred", "biotoolsCURIE": "biotools:psipred", "version": [], "otherID": [ { "value": "RRID:SCR_018546", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0469", "term": "Protein secondary structure prediction (turns)" }, { "uri": "http://edamontology.org/operation_0303", "term": "Protein fold recognition" }, { "uri": "http://edamontology.org/operation_0267", "term": "Protein secondary structure prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" }, { "uri": "http://edamontology.org/topic_3542", "term": "Protein secondary structure" }, { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://bioinf.cs.ucl.ac.uk/index.php?id=779", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/16.4.404", "pmid": "10869041", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "The PSIPRED protein structure prediction server", "abstract": "The PSIPRED protein structure prediction server allows users to submit a protein sequence, perform a prediction of their choice and receive the results of the prediction both textually via e-mail and graphically via the web. The user may select one of three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version of a widely used transmembrane topology prediction method; or GenTHREADER, a sequence profile based fold recognition method. Availability: Freely available to non-commercial users at http://globin.bio.warwick.ac.uk/psipred/.", "date": "2000-01-01T00:00:00Z", "citationCount": 3053, "authors": [ { "name": "McGuffin L.J." }, { "name": "Bryson K." }, { "name": "Jones D.T." } ], "journal": "Bioinformatics" } }, { "doi": "10.1006/jmbi.1999.3091", "pmid": "10493868", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Protein secondary structure prediction based on position-specific scoring matrices", "abstract": "A two-stage neural network has been used to predict protein secondary structure based on the position specific scoring matrices generated by PSI-BLAST. Despite the simplicity and convenience of the approach used, the results are found to be superior to those produced by other methods, including the popular PHD method according to our own benchmarking results and the results from the recent Critical Assessment of Techniques for Protein Structure Prediction experiment (CASP3), where the method was evaluated by stringent blind testing. Using a new testing set based on a set of 187 unique folds, and three-way cross-validation based on structural similarity criteria rather than sequence similarity criteria used previously (no similar folds were present in both the testing and training sets) the method presented here (PSIPRED) achieved an average Q3 score of between 76.5% to 78.3% depending on the precise definition of observed secondary structure used, which is the highest published score for any method to date. Given the success of the method in CASP3, it is reasonable to be confident that the evaluation presented here gives a fair indication of the performance of the method in general.", "date": "1999-09-17T00:00:00Z", "citationCount": 4685, "authors": [ { "name": "Jones D.T." } ], "journal": "Journal of Molecular Biology" } }, { "doi": "10.1093/nar/gkt381", "pmid": "23748958", "pmcid": "PMC3692098", "type": [], "version": null, "note": null, "metadata": { "title": "Scalable web services for the PSIPRED Protein Analysis Workbench.", "abstract": "Here, we present the new UCL Bioinformatics Group's PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/.", "date": "2013-01-01T00:00:00Z", "citationCount": 1109, "authors": [ { "name": "Buchan D.W." }, { "name": "Minneci F." }, { "name": "Nugent T.C." }, { "name": "Bryson K." }, { "name": "Jones D.T." } ], "journal": "Nucleic acids research" } } ], "credit": [ { "name": "psipred team", "email": "psipred@cs.ucl.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Bijay", "additionDate": "2017-03-25T16:29:49Z", "lastUpdate": "2025-04-03T08:22:35.616168Z", "editPermission": { "type": "group", "authors": [ "zhouwj", "Bijay", "Yunus" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RAMClustR", "description": "A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.", "homepage": "https://github.com/cbroeckl/RAMClustR", "biotoolsID": "ramclustr", "biotoolsCURIE": "biotools:ramclustr", "version": [ "1.2.2", "1.3.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3557", "term": "Imputation" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_3432", "term": "Clustering" }, { "uri": "http://edamontology.org/operation_3465", "term": "Correlation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_3113", "term": "Sample annotation" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://umsa.cerit-sc.cz/root?tool_id=toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.3.0+galaxy0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1021/ac501530d", "pmid": "24927477", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "RAMClust: A novel feature clustering method enables spectral-matching-based annotation for metabolomics data", "abstract": "Metabolomic data are frequently acquired using chromatographically coupled mass spectrometry (MS) platforms. For such datasets, the first step in data analysis relies on feature detection, where a feature is defined by a mass and retention time. While a feature typically is derived from a single compound, a spectrum of mass signals is more a more-accurate representation of the mass spectrometric signal for a given metabolite. Here, we report a novel feature grouping method that operates in an unsupervised manner to group signals from MS data into spectra without relying on predictability of the in-source phenomenon. We additionally address a fundamental bottleneck in metabolomics, annotation of MS level signals, by incorporating indiscriminant MS/MS (idMS/MS) data implicitly: feature detection is performed on both MS and idMS/MS data, and feature-feature relationships are determined simultaneously from the MS and idMS/MS data. This approach facilitates identification of metabolites using in-source MS and/or idMS/MS spectra from a single experiment, reduces quantitative analytical variation compared to single-feature measures, and decreases false positive annotations of unpredictable phenomenon as novel compounds. This tool is released as a freely available R package, called RAMClustR, and is sufficiently versatile to group features from any chromatographic-spectrometric platform or feature-finding software. © 2014 American Chemical Society.", "date": "2014-07-15T00:00:00Z", "citationCount": 201, "authors": [ { "name": "Broeckling C.D." }, { "name": "Afsar F.A." }, { "name": "Neumann S." }, { "name": "Ben-Hur A." }, { "name": "Prenni J.E." } ], "journal": "Analytical Chemistry" } } ], "credit": [ { "name": "Corey Broeckling", "email": "Corey.Broeckling@ColoState.EDU", "url": null, "orcidid": "https://orcid.org/0000-0002-6158-827X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "recetox-specdatri", "additionDate": "2021-09-22T08:33:22.081093Z", "lastUpdate": "2025-04-02T11:37:27.390711Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "neXtProt", "description": "neXtProt was an innovative knowledge platform dedicated to human proteins. This resource contained a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein-coding genes found in the human genome. The content of neXtProt was continuously extended so as to provide many more carefully selected data sets and analysis tools. neXtProt data and tools have been archived.", "homepage": "https://www.expasy.org/archives/nextprot", "biotoolsID": "nextprot", "biotoolsCURIE": "biotools:nextprot", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" }, { "uri": "http://edamontology.org/topic_3120", "term": "Protein variants" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "Rare Disease", "Proteomics" ], "maturity": "Legacy", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Data" ], "elixirNode": [ "Switzerland" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/calipho-sib/", "type": [ "Repository" ], "note": "neXtProt software repository with issue tracking" }, { "url": "https://twitter.com/nextprot_news", "type": [ "Social media" ], "note": "neXtProt release news, publications, presentations, tips and more. DM us with feedback!" }, { "url": "https://www.expasy.org/resources/nextprot", "type": [ "Software catalogue" ], "note": "neXtProt entry in Expasy" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkz995", "pmid": "31724716", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The neXtProt knowledgebase in 2020: Data, tools and usability improvements", "abstract": "The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describe the incorporation of three new data sets that provide expression, function, protein-protein binary interaction, post-translational modifications (PTM) and variant information. New SPARQL query examples illustrating uses of the new data were added. neXtProt has continued to develop tools for proteomics. We have improved the peptide uniqueness checker and have implemented a new protein digestion tool. Together, these tools make it possible to determine which proteases can be used to identify trypsin-resistant proteins by mass spectrometry. In terms of usability, we have finished revamping our web interface and completely rewritten our API. Our SPARQL endpoint now supports federated queries. All the neXtProt data are available via our user interface, API, SPARQL endpoint and FTP site, including the new PEFF 1.0 format files. Finally, the data on our FTP site is now CC BY 4.0 to promote its reuse.", "date": "2020-01-01T00:00:00Z", "citationCount": 155, "authors": [ { "name": "Zahn-Zabal M." }, { "name": "Michel P.-A." }, { "name": "Gateau A." }, { "name": "Nikitin F." }, { "name": "Schaeffer M." }, { "name": "Audot E." }, { "name": "Gaudet P." }, { "name": "Duek P.D." }, { "name": "Teixeira D." }, { "name": "De Laval V.R." }, { "name": "Samarasinghe K." }, { "name": "Bairoch A." }, { "name": "Lane L." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkr1179", "pmid": "22139911", "pmcid": "PMC3245017", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "NeXtProt: A knowledge platform for human proteins", "abstract": "neXtProt (http://www.nextprot.org/) is a new human protein-centric knowledge platform. Developed at the Swiss Institute of Bioinformatics (SIB), it aims to help researchers answer questions relevant to human proteins. To achieve this goal, neXtProt is built on a corpus containing both curated knowledge originating from the UniProtKB/Swiss-Prot knowledgebase and carefully selected and filtered high-throughput data pertinent to human proteins. This article presents an overview of the database and the data integration process. We also lay out the key future directions of neXtProt that we consider the necessary steps to make neXtProt the one-stop-shop for all research projects focusing on human proteins. © The Author(s) 2011.", "date": "2012-01-01T00:00:00Z", "citationCount": 168, "authors": [ { "name": "Lane L." }, { "name": "Argoud-Puy G." }, { "name": "Britan A." }, { "name": "Cusin I." }, { "name": "Duek P.D." }, { "name": "Evalet O." }, { "name": "Gateau A." }, { "name": "Gaudet P." }, { "name": "Gleizes A." }, { "name": "Masselot A." }, { "name": "Zwahlen C." }, { "name": "Bairoch A." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "SIB Swiss Institute of Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Support", "email": "support@nextprot.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Pascale Gaudet", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0003-1813-6857", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "SIB", "additionDate": "2015-01-21T13:30:06Z", "lastUpdate": "2025-04-02T08:05:19.163091Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "mzahn", "LanfearJ" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "csdR", "description": "Differential gene coexpression analysis based on the Conserved, Specific, and Differentiated (CSD) method", "homepage": "https://almaaslab.github.io/csdR/", "biotoolsID": "csdr", "biotoolsCURIE": "biotools:csdr", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0204", "term": "Gene regulation" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.bioconductor.org/packages/release/bioc/html/csdR.html", "type": [ "Software catalogue" ], "note": null }, { "url": "https://github.com/AlmaasLab/csdR", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s12859-022-04605-1", "pmid": "35183100", "pmcid": "PMC8858518", "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "csdR, an R package for differential co-expression analysis", "abstract": "Background: Differential co-expression network analysis has become an important tool to gain understanding of biological phenotypes and diseases. The CSD algorithm is a method to generate differential co-expression networks by comparing gene co-expressions from two different conditions. Each of the gene pairs is assigned conserved (C), specific (S) and differentiated (D) scores based on the co-expression of the gene pair between the two conditions. The result of the procedure is a network where the nodes are genes and the links are the gene pairs with the highest C-, S-, and D-scores. However, the existing CSD-implementations suffer from poor computational performance, difficult user procedures and lack of documentation. Results: We created the R-package csdR aimed at reaching good performance together with ease of use, sufficient documentation, and with the ability to play well with other tools for data analysis. csdR was benchmarked on a realistic dataset with 20,645 genes. After verifying that the chosen number of iterations gave sufficient robustness, we tested the performance against the two existing CSD implementations. csdR was superior in performance to one of the implementations, whereas the other did not run. Our implementation can utilize multiple processing cores. However, we were unable to achieve more than ∼ 2.7 parallel speedup with saturation reached at about 10 cores. Conclusion: The results suggest that csdR is a useful tool for differential co-expression analysis and is able to generate robust results within a workday on datasets of realistic sizes when run on a workstation or compute server.", "date": "2022-12-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Pettersen J.P." }, { "name": "Almaas E." } ], "journal": "BMC Bioinformatics" } } ], "credit": [], "owner": "japet", "additionDate": "2025-03-31T08:50:20.800385Z", "lastUpdate": "2025-03-31T09:00:57.202555Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Species Search Engine - KISSE", "description": "KISSE is a species search engine that utilizes collagen sequences from eight different species to identify unknown samples.", "homepage": "https://kisse.serve.scilifelab.se/app/kisse", "biotoolsID": "kisse", "biotoolsCURIE": "biotools:kisse", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/hassanakthv/SIPMS", "type": "Source code", "note": null, "version": null } ], "documentation": [], "publication": [], "credit": [], "owner": "egonw", "additionDate": "2025-03-27T13:31:15.690258Z", "lastUpdate": "2025-03-28T21:26:36.097092Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Titania", "description": "Suite for In Silico Property Prediction and NAM-Based Modeling", "homepage": "https://enaloscloud.novamechanics.com/EnalosWebApps/titania/", "biotoolsID": "titania", "biotoolsCURIE": "biotools:titania", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3438", "term": "Calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2301", "term": "SMILES string" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [] } ], "note": "calculate boiling point", "cmd": "calculate boiling point" } ], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "egonw", "additionDate": "2025-03-27T13:48:04.671506Z", "lastUpdate": "2025-03-28T21:26:03.296975Z", "editPermission": { "type": "group", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WeSA", "description": "WeSA, (weighted socioaffinity), is a statistical score which can rank results from protein experiments of the bait-prey type, e.g. affinity purification, immunoprecipitation or proximity labelling.\n\nYou can enter lists of interacting proteins according to the results of your experiment. Input your raw data before any filtering is done.\n\nAs a result you will get a re-ordered list of scores which allows one to understand which interactions are more likely than others based on what previous experiments can add to your data.", "homepage": "https://wesa.russelllab.org/", "biotoolsID": "we_sa", "biotoolsCURIE": "biotools:we_sa", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3957", "term": "Protein interaction experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/russelllab/wesa", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://wesa.russelllab.org/help", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkae423", "pmid": "38795065", "pmcid": "PMC11223876", "type": [], "version": null, "note": null, "metadata": { "title": "WeSA: A web server for improving analysis of affinity proteomics data", "abstract": "Protein-protein interaction experiments still yield many false positive interactions. The socioaffinity metric can distinguish true protein-protein interactions from noise based on available data. Here, we present WeSA (Weighted SocioAffinity), which considers large datasets of interaction proteomics data (IntAct, BioGRID, the BioPlex) to score human protein interactions and, in a statistically robust way, flag those (even from a single experiment) that are likely to be false positives. ROC analysis (using CORUM-PDB positives and Negatome negatives) shows that WeSA improves over other measures of interaction confidence. WeSA shows consistently good results over all datasets (up to: AUC = 0.93 and at best threshold: TPR = 0.84, FPR = 0.11, Precision = 0.98). WeSA is freely available without login (wesa.russelllab.org). Users can submit their own data or look for organized information on human protein interactions using the web server. Users can either retrieve available information for a list of proteins of interest or calculate scores for new experiments. The server outputs either pre-computed or updated WeSA scores for the input enriched with information from databases. The summary is presented as a table and a network-based visualization allowing the user to remove those nodes/edges that the method considers spurious.", "date": "2024-07-05T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Shtetinska M.M." }, { "name": "Gonzalez-Sanchez J.-C." }, { "name": "Beyer T." }, { "name": "Boldt K." }, { "name": "Ueffing M." }, { "name": "Russell R.B." } ], "journal": "Nucleic Acids Research" } } ], "credit": [], "owner": "Pub2Tools", "additionDate": "2025-03-28T11:13:12.813456Z", "lastUpdate": "2025-03-28T12:14:32.901305Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ChemFH", "description": "An integrated online platform developed for the screening and prediction of potential frequent drug hitters, thus improving the efficiency of drug R&D in colloidal aggregate, firefly luciferase reporter enzyme inhibition, fluorescence, chemical reactivity, and promiscuity. ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery.", "homepage": "https://chemfh.scbdd.com/", "biotoolsID": "chemfh", "biotoolsCURIE": "biotools:chemfh", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3938", "term": "Virtual screening" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2301", "term": "SMILES string" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1696", "term": "Drug report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1712", "term": "Chemical structure image" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Script", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0209", "term": "Medicinal chemistry" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "JavaScript" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/antwiser/ChemFH", "type": [ "Repository" ], "note": null }, { "url": "https://chemfh.scbdd.com/", "type": [ "Other" ], "note": "Webpage of the tool" } ], "download": [ { "url": "https://github.com/antwiser/ChemFH/releases/tag/ChemFH-1.0.0", "type": "Source code", "note": null, "version": "1.0.0" } ], "documentation": [ { "url": "https://github.com/antwiser/ChemFH/blob/main/README.md", "type": [ "General" ], "note": null }, { "url": "https://chemfh.scbdd.com/documentation/#/", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkae424", "pmid": "38783035", "pmcid": "PMC11223804", "type": [ "Method" ], "version": "1.0.0", "note": "High-throughput screening rapidly tests an extensive array of chemical compounds to identify hit compounds for specific biological targets in drug discovery. However, false-positive results disrupt hit compound screening, leading to wastage of time and resources. To address this, we propose ChemFH, an integrated online platform facilitating rapid virtual evaluation of potential false positives, including colloidal aggregators, spectroscopic interference compounds, firefly luciferase inhibitors, chemical reactive compounds, promiscuous compounds, and other assay interferences. ChemFH is freely available via https://chemfh.scbdd.com/.", "metadata": { "title": "ChemFH: An integrated tool for screening frequent false positives in chemical biology and drug discovery", "abstract": "High-throughput screening rapidly tests an extensive array of chemical compounds to identify hit compounds for specific biological targets in drug discovery. However, false-positive results disrupt hit compound screening, leading to wastage of time and resources. To address this, we propose ChemFH, an integrated online platform facilitating rapid virtual evaluation of potential false positives, including colloidal aggregators, spectroscopic interference compounds, firefly luciferase inhibitors, chemical reactive compounds, promiscuous compounds, and other assay interferences. By leveraging a dataset containing 823 391 compounds, we constructed high-quality prediction models using multi-task directed message-passing network (DMPNN) architectures combining uncertainty estimation, yielding an average AUC value of 0.91. Furthermore, ChemFH incorporated 1441 representative alert substructures derived from the collected data and ten commonly used frequent hitter screening rules. ChemFH was validated with an external set of 75 compounds. Subsequently, the virtual screening capability of ChemFH was successfully confirmed through its application to five virtual screening libraries. Furthermore, ChemFH underwent additional validation on two natural products and FDA-approved drugs, yielding reliable and accurate results. ChemFH is a comprehensive, reliable, and computationally efficient screening pipeline that facilitates the identification of true positive results in assays, contributing to enhanced efficiency and success rates in drug discovery. ChemFH is freely available via https://chemfh.scbdd.com/.", "date": "2024-07-05T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Shi S." }, { "name": "Fu L." }, { "name": "Yi J." }, { "name": "Yang Z." }, { "name": "Zhang X." }, { "name": "Deng Y." }, { "name": "Wang W." }, { "name": "Wu C." }, { "name": "Zhao W." }, { "name": "Hou T." }, { "name": "Zeng X." }, { "name": "Lyu A." }, { "name": "Cao D." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Jiacai Yi", "email": "yjc@nudt.edu.cn", "url": "https://github.com/antwiser", "orcidid": "https://orcid.org/0000-0001-6823-1882", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "National University of Defense Technology, Changsha, Hunan" } ], "owner": "etepf22", "additionDate": "2025-03-28T11:01:52.929561Z", "lastUpdate": "2025-03-28T12:04:07.529430Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "LncRNAway", "description": "A web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs", "homepage": "https://www.lncrnaway.com", "biotoolsID": "lncrnaway", "biotoolsCURIE": "biotools:lncrnaway", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0230", "term": "Sequence generation" }, { "uri": "http://edamontology.org/operation_0308", "term": "PCR primer design" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1033", "term": "Ensembl gene ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1026", "term": "Gene symbol" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_2305", "term": "GFF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_0972", "term": "Text mining report" }, "format": [] } ], "note": "Design of sgRNA for lncRNA knockout; Primer design for PCR and qPCR to knockout detection.", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.lncrnaway.com", "type": [ "Service" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkae383", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "LncRNAway: A web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs", "abstract": "Thousands of long noncoding RNAs (lncRNAs) have been annotated via high-throughput RNA sequencing, yet only a small fraction have been functionally investigated. Genomic knockout is the mainstream strategy for studying the biological function of protein-coding genes and lncRNAs, whereas the complexity of the lncRNA locus, especially the natural antisense lncRNAs (NAT-lncRNAs), presents great challenges. Knocking out lncRNAs often results in unintended disruptions of neighboring protein-coding genes and small RNAs, leading to ambiguity in observing phenotypes and interpreting biological function. To address this issue, we launched LncRNAway, a user-friendly web tool based on the BESST (branchpoint to 3' splicing site targeting) method, to design sgRNAs for lncRNA knockout. LncRNAway not only provides specific and effective lncRNA knockout guidelines but also integrates genotyping primers and quantitative PCR primers designing, thereby streamlining experimental procedures of lncRNA function study. LncRNAway is freely available at https://www.lncrnaway.com.", "date": "2024-07-05T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Zhang S." }, { "name": "Wang S." }, { "name": "Lu F." }, { "name": "Bie L." }, { "name": "Luo Y." }, { "name": "Sun J." }, { "name": "Zhang Y." }, { "name": "Wang Y." }, { "name": "Zhang Y." }, { "name": "Lyu Q.R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Chongqing General Hospital, Chongqing University, Lyu Lab", "email": "qlyu@cqu.edu.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "inespinheiro", "additionDate": "2025-03-28T11:01:27.681477Z", "lastUpdate": "2025-03-28T11:54:36.402981Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "IsoVis", "description": "A webserver for visualization and annotation of alternative RNA isoforms", "homepage": "https://isomix.org/isovis/", "biotoolsID": "isovis", "biotoolsCURIE": "biotools:isovis", "version": [ "v1.10" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2877", "term": "Protein complex" }, "format": [ { "uri": "http://edamontology.org/format_2305", "term": "GFF" }, { "uri": "http://edamontology.org/format_2306", "term": "GTF" }, { "uri": "http://edamontology.org/format_3003", "term": "BED" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [] } ], "note": "isoform stack", "cmd": "--" } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_4019", "term": "Biosciences" } ], "operatingSystem": [ "Linux", "Windows" ], "language": [ "JavaScript" ], "license": "MPL-2.0", "collectionID": [ "IsoVis" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "UK" ], "elixirCommunity": [], "link": [ { "url": "https://isomix.org/isovis/", "type": [ "Other" ], "note": "a webserver" }, { "url": "https://github.com/ClarkLaboratory/IsoVis?tab=MPL-2.0-1-ov-file", "type": [ "Repository" ], "note": null }, { "url": "https://academic.oup.com/nar/article/52/W1/W341/7665639", "type": [ "Other" ], "note": "Nucleic Acids Research" } ], "download": [ { "url": "https://github.com/ClarkLaboratory/IsoVis.git", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://isovis.gandallab.org/tutorial/", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "owner": "Kvetoslava_Mahutova", "additionDate": "2025-03-28T11:20:32.972026Z", "lastUpdate": "2025-03-28T11:41:10.718643Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DDMut-PPI", "description": "A deep learning model that efficiently and accurately predicts the changes in PPI binding free energy upon single and multiple point mutations.", "homepage": "https://biosig.lab.uq.edu.au/ddmut_ppi/", "biotoolsID": "ddmut-ppi", "biotoolsCURIE": "biotools:ddmut-ppi", "version": [], "otherID": [], "relation": [ { "biotoolsID": "tensorflow", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0276", "term": "Protein interaction network analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "note": "Single Prediction - Job Submission", "cmd": "$ curl https://biosig.lab.uq.edu.au/ddmut_ppi/api/single -X POST -i -F pdb_file=@/home/ubuntu/1cse.pdb -F mutation=L45G -F chain=I -F reverse=True" } ], "toolType": [ "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" } ], "operatingSystem": [ "Linux" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://biosig.lab.uq.edu.au/ddmut_ppi/datasets", "type": "Biological data", "note": null, "version": null } ], "documentation": [ { "url": "https://biosig.lab.uq.edu.au/ddmut_ppi/api", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkae412", "pmid": "38783112", "pmcid": "PMC11223791", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "DDMut-PPI: Predicting effects of mutations on protein-protein interactions using graph-based deep learning", "abstract": "Protein-protein interactions (PPIs) play a vital role in cellular functions and are essential for therapeutic development and understanding diseases. However, current predictive tools often struggle to balance efficiency and precision in predicting the effects of mutations on these complex interactions. To address this, we present DDMut-PPI, a deep learning model that efficiently and accurately predicts changes in PPI binding free energy upon single and multiple point mutations. Building on the robust Siamese network architecture with graph-based signatures from our prior work, DDMut, the DDMut-PPI model was enhanced with a graph convolutional network operated on the protein interaction interface. We used residue-specific embeddings from ProtT5 protein language model as node features, and a variety of molecular interactions as edge features. By integrating evolutionary context with spatial information, this framework enables DDMut-PPI to achieve a robust Pearson correlation of up to 0.75 (root mean squared error: 1.33 kcal/mol) in our evaluations, outperforming most existing methods. Importantly, the model demonstrated consistent performance across mutations that increase or decrease binding affinity. DDMut-PPI offers a significant advancement in the field and will serve as a valuable tool for researchers probing the complexities of protein interactions. DDMut-PPI is freely available as a web server and an application programming interface at https://biosig.lab.uq.edu.au/ddmut_ppi.", "date": "2024-07-05T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Zhou Y." }, { "name": "Myung Y." }, { "name": "Rodrigues C.H.M." }, { "name": "Ascher D.B." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": null, "email": null, "url": "https://biosig.lab.uq.edu.au/contact", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "TomasGeraldes", "additionDate": "2025-03-28T11:04:18.911217Z", "lastUpdate": "2025-03-28T11:05:03.279672Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "prolfquapp", "description": "A command-line tool for differential expression analysis in quantitative proteomics", "homepage": "https://github.com/prolfqua/prolfquapp", "biotoolsID": "prolfquapp", "biotoolsCURIE": "biotools:prolfquapp", "version": [ "0.1.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3741", "term": "Differential protein expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": "./prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANN\n# and again you run the version within the docker container with\n# ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANN" }, { "operation": [ { "uri": "http://edamontology.org/operation_2428", "term": "Validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3914", "term": "Quality control report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0571", "term": "Expression data visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/prolfqua/prolfquapp", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/prolfqua/prolfquapp/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/prolfqua/prolfquapp/releases/tag/0.1.6", "type": "Downloads page", "note": null, "version": "0.1.6" } ], "documentation": [ { "url": "https://github.com/prolfqua/prolfquapp/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jproteome.4c00911", "pmid": null, "pmcid": null, "type": [], "version": "0.0.6", "note": null, "metadata": { "title": "prolfquapp ─ A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics", "abstract": "Mass spectrometry is a cornerstone of quantitative proteomics, enabling relative protein quantification and differential expression analysis (DEA) of proteins. As experiments grow in complexity, involving more samples, groups, and identified proteins, interactive differential expression analysis tools become impractical. The prolfquapp addresses this challenge by providing a command-line interface that simplifies DEA, making it accessible to nonprogrammers and seamlessly integrating it into workflow management systems. Prolfquapp streamlines data processing and result visualization by generating dynamic HTML reports that facilitate the exploration of differential expression results. These reports allow for investigating complex experiments, such as those involving repeated measurements or multiple explanatory variables. Additionally, prolfquapp supports various output formats, including XLSX files, SummarizedExperiment objects and rank files, for further interactive analysis using spreadsheet software, the exploreDE Shiny application, or gene set enrichment analysis software, respectively. By leveraging advanced statistical models from the prolfqua R package, prolfquapp offers a user-friendly, integrated solution for large-scale quantitative proteomics studies, combining efficient data processing with insightful, publication-ready outputs.", "date": "2025-02-07T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Wolski W.E." }, { "name": "Grossmann J." }, { "name": "Schwarz L." }, { "name": "Leary P." }, { "name": "Turker C." }, { "name": "Nanni P." }, { "name": "Schlapbach R." }, { "name": "Panse C." } ], "journal": "Journal of Proteome Research" } } ], "credit": [], "owner": "n.m.palmblad@lumc.nl", "additionDate": "2025-02-28T15:04:33.594183Z", "lastUpdate": "2025-03-28T10:18:25.715685Z", "editPermission": { "type": "group", "authors": [ "thatmariia" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WorkflowHub", "description": "WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows.\n\nThe registry supports any workflow in its native repository.\n\nWorkflowHub aims to facilitate discovery and re-use of workflows in an accessible and interoperable way. 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