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Published by Oxford University Press on behalf of Nucleic Acids Research.The CUPP platform includes a web server for functional annotation and sub-grouping of carbohydrate active enzymes (CAZymes) based on a novel peptide-based similarity assessment algorithm, i.e. protein grouping according to Conserved Unique Peptide Patterns (CUPP). This online platform is open to all users and there is no login requirement. The web server allows the user to perform genome-based annotation of carbohydrate active enzymes to CAZy families, CAZy subfamilies, CUPP groups and EC numbers (function) via assessment of peptide-motifs by CUPP. The web server is intended for functional annotation assessment of the CAZy inventory of prokaryotic and eukaryotic organisms from genomic DNA (up to 30MB compressed) or directly from amino acid sequences (up to 10MB compressed). The custom query sequences are assessed using the CUPP annotation algorithm, and the outcome is displayed in interactive summary result pages of CAZymes. The results displayed allow for inspection of members of the individual CUPP groups and include information about experimentally characterized members. 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Pangenomes may be represented as graphical structures, e.g. compacted colored de Bruijn graphs, which offer a low memory usage and facilitate reference-free sequence comparisons. While sequence-to-graph mapping to graphical pangenomes has been studied for some time, no local alignment search tool in the vein of BLAST has been proposed yet. Results: We present a new heuristic method to find maximum scoring local alignments of a DNA query sequence to a pangenome represented as a compacted colored de Bruijn graph. Our approach additionally allows a comparison of similarity among sequences within the pangenome. We show that local alignment scores follow an exponential-tail distribution similar to BLAST scores, and we discuss how to estimate its parameters to separate local alignments representing sequence homology from spurious findings. An implementation of our method is presented, and its performance and usability are shown. Our approach scales sublinearly in running time and memory usage with respect to the number of genomes under consideration. 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"ira", "additionDate": "2026-02-17T16:25:26.383789Z", "lastUpdate": "2026-02-17T16:31:30.082840Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "WikiPathways", "description": "WikiPathways is a database of biological pathways maintained by and for the scientific community.", "homepage": "https://www.wikipathways.org/", "biotoolsID": "wikipathways", "biotoolsCURIE": "biotools:wikipathways", "version": [], "otherID": [], "relation": [ { "biotoolsID": "bridgedb", "type": "uses" }, { "biotoolsID": "rwikipathways", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2497", "term": "Pathway or network analysis" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "output": [ { "data": { "uri": 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"Repository" ], "note": "GitHub Organization" }, { "url": "https://fosstodon.org/@wikipathways", "type": [ "Social media" ], "note": null } ], "download": [ { "url": "https://data.wikipathways.org/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://www.wikipathways.org/index.php/WikiPathways", "type": [ "General" ], "note": null }, { "url": "http://www.wikipathways.org/index.php/Help:WikiPathways_Webservice", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkv1024", "pmid": "26481357", "pmcid": "PMC4702772", "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1371/journal.pone.0006447", "pmid": "19649250", "pmcid": "PMC2714472", "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkaa1024", "pmid": "33211851", "pmcid": "PMC7779061", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkx1064", "pmid": "29136241", "pmcid": "PMC5753270", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkad960", "pmid": "37941138", "pmcid": "PMC10767877", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Martina Kutmon", "email": "martina.kutmon@maastrichtuniversity.nl", "url": "http://www.wikipathways.org/index.php/WikiPathways:About", "orcidid": "https://orcid.org/0000-0002-7699-8191", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Egon Willighagen", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-7542-0286", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Alexander R. Pico", "email": "apico@gladstone.ucsf.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ChrisEvelo", "additionDate": "2017-07-20T18:33:51Z", "lastUpdate": "2026-02-17T12:05:57.404853Z", "editPermission": { "type": "group", "authors": [ "ChrisEvelo", "egonw" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GENSCAN", "description": "A tool for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms.", "homepage": "http://hollywood.mit.edu/GENSCAN.html", "biotoolsID": "mit_splice_predictor", "biotoolsCURIE": "biotools:mit_splice_predictor", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0433", "term": "Splice site prediction" }, { "uri": "http://edamontology.org/operation_2454", "term": "Gene prediction" }, { "uri": "http://edamontology.org/operation_0446", "term": "Exonic splicing enhancer prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_0114", "term": "Gene structure" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Other", "collectionID": [ "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://hollywood.mit.edu/GENSCANinfo.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1006/jmbi.1997.0951", "pmid": "9149143", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Prediction of complete gene structures in human genomic DNA", "abstract": "We introduce a general probabilistic model of the gene structure of human genomic sequences which incorporates descriptions of the basic transcriptional, translational and splicing signals, as well as length distributions and compositional features of exons, introns and intergenic regions. Distinct sets of model parameters are derived to account for the many substantial differences in gene density and structure observed in distinct C + G compositional regions of the human genome. in addition, new models of the donor and acceptor splice signals are described which capture potentially important dependencies between signal positions. The model is applied to the problem of gene identification in a computer program, GENSCAN, which identifies complete exon/intron structures of genes in genomic DNA. Novel features of the program include the capacity to predict multiple genes in a sequence, to deal with partial as well as complete genes, and to predict consistent sets of genes occurring on either or both DNA strands. GENSCAN is shown to have substantially higher accuracy than existing methods when tested on standardized sets of human and vertebrate genes, with 75 to 80% of exons identified exactly. The program is also capable of indicating fairly accurately the reliability of each predicted exon. Consistently high levels of accuracy are observed for sequences of differing C + G content and for distinct groups of vertebrates.", "date": "1997-04-25T00:00:00Z", "citationCount": 2866, "authors": [ { "name": "Burge C." }, { "name": "Karlin S." } ], "journal": "Journal of Molecular Biology" } } ], "credit": [ { "name": "Chris Burge", "email": "cburge@mit.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-09-26T07:53:16Z", "lastUpdate": "2026-02-17T10:10:41.059540Z", "editPermission": { "type": "group", "authors": [ "mojtaba5" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "VISTA", "description": "Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.", "homepage": "http://genome.lbl.gov/vista/index.shtml", "biotoolsID": "vista", "biotoolsCURIE": "biotools:vista", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0491", "term": "Pairwise sequence alignment" }, { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" }, { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" }, { "uri": "http://edamontology.org/operation_0496", "term": "Global alignment" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0749", "term": "Transcription factors and regulatory sites" }, { "uri": "http://edamontology.org/topic_0654", "term": "DNA" }, { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [ "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://genome.lbl.gov/vista/help.shtml", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btg459", "pmid": "15033870", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments", "abstract": "Motivation: The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing number of genomic sequence datasets being generated for an ever-increasing number of organisms. To be efficient these visualization algorithms must support the ability to accommodate consistently a wide range of evolutionary distances in a comparison framework based upon phylogenetic relationships. Results: We have developed Phylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing a similarity measure for multiple DNA sequences. The complexity of visual presentation is effectively organized using a framework based upon interspecies phylogenetic relationships. The phylogenetic organization supports rapid, user-guided interspecies comparison. To aid in navigation through large sequence datasets, Phylo-VISTA leverages concepts from VISTA that provide a user with the ability to select and view data at varying resolutions. The combination of multiresolution data visualization and analysis, combined with the phylogenetic framework for interspecies comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments. © Oxford University Press 2004; all rights reserved.", "date": "2004-03-22T00:00:00Z", "citationCount": 34, "authors": [ { "name": "Shah N." }, { "name": "Couronne O." }, { "name": "Pennacchio L.A." }, { "name": "Brudno M." }, { "name": "Batzoglou S." }, { "name": "Bethel E.W." }, { "name": "Rubin E.M." }, { "name": "Hamann B." }, { "name": "Dubchak I." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/nar/gkm279", "pmid": "17488840", "pmcid": "PMC1933192", "type": [], "version": null, "note": null, "metadata": { "title": "Multiple whole genome alignments and novel biomedical applications at the VISTA portal", "abstract": "The VISTA portal for comparative genomics is designed to give biomedical scientists a unified set of tools to lead them from the raw DNA sequences through the alignment and annotation to the visualization of the results. The VISTA portal also hosts the alignments of a number of genomes computed by our group, allowing users to study the regions of their interest without having to manually download the individual sequences. Here we describe various algorithmic and functional improvements implemented in the VISTA portal over the last 2 years. The VISTA Portal is accessible at http://genome.lbl.gov/vista. © 2007 The Author(s).", "date": "2007-07-01T00:00:00Z", "citationCount": 26, "authors": [ { "name": "Brudno M." }, { "name": "Poliakov A." }, { "name": "Minovitsky S." }, { "name": "Ratnere I." }, { "name": "Dubchak I." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/bioinformatics/btg1005", "pmid": "12855437", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Glocal alignment: Finding rearrangements during alignment", "abstract": "Motivation: To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. The two main classes of pain/vise alignments are global alignment, where one string is transformed into the other, and local alignment, where all locations of similarity between the two strings are returned. Global alignments are less prone to demonstrating false homology as each letter of one sequence is constrained to being aligned to only one letter of the other. Local alignments, on the other hand, can cope with rearrangements between non-syntenic, orthologous sequences by identifying similar regions in sequences; this, however, comes at the expense of a higher false positive rate due to the inability of local aligners to take into account overall conservation maps. Results: In this paper we introduce the notion of glocal alignment, a combination of global and local methods, where one creates a map that transforms one sequence into the other while allowing for rearrangement events. We present Shuffle-LAGAN, a glocal alignment algorithm that is based on the CHAOS local alignment algorithm and the LAGAN global aligner, and is able to align long genomic sequences. To test Shuffle-LAGAN we split the mouse genome into BAC-sized pieces, and aligned these pieces to the human genome. We demonstrate that Shuffle-LAGAN compares favorably in terms of sensitivity and specificity with standard local and global aligners. From the alignments we conclude that about 9% of human/mouse homology may be attributed to small rearrangements, 63% of which are duplications. Availability: Our systems, supplemental information, and the alignment of the human and mouse genomes using Shuffle-LAGAN are available at http://lagan.stanford.edu/glocal. © Oxford University Press 2003; all rights reserved.", "date": "2003-12-01T00:00:00Z", "citationCount": 238, "authors": [ { "name": "Brudno M." }, { "name": "Malde S." }, { "name": "Poliakov A." }, { "name": "Do C.B." }, { "name": "Couronne O." }, { "name": "Dubchak I." }, { "name": "Batzoglou S." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/bioinformatics/16.11.1046", "pmid": "11159318", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Vista: Visualizing global DNA sequence alignments of arbitrary length", "abstract": "VISTA is a program for visualizing global DNA sequence alignments of arbitrary length. It has a clean output, allowing for easy identification of similarity, and is easily configurable, enabling the visualization of alignments of various lengths at different levels of resolution. It is currently available on the web, thus allowing for easy access by all researchers.", "date": "2000-01-01T00:00:00Z", "citationCount": 736, "authors": [ { "name": "Mayor C." }, { "name": "Brudno M." }, { "name": "Schwartz J.R." }, { "name": "Poliakov A." }, { "name": "Rubin E.M." }, { "name": "Frazer K.A." }, { "name": "Pachter L.S." }, { "name": "Dubchak I." } ], "journal": "Bioinformatics" } }, { "doi": "10.1101/gr.789803", "pmid": "12529311", "pmcid": "PMC430967", "type": [], "version": null, "note": null, "metadata": { "title": "AVID: A global alignment program.", "abstract": "In this paper we describe a new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments. We have also performed a quantitative comparison of AVID with other popular alignment tools. To this end, we have established a format for the representation of alignments and methods for their comparison. These formats and methods should be useful for future studies. The tools we have developed for the alignment comparisons, as well as the AVID program, are publicly available. See Web Site References section for AVID Web address and Web addresses for other programs discussed in this paper.", "date": "2003-01-01T00:00:00Z", "citationCount": 350, "authors": [ { "name": "Bray N." }, { "name": "Dubchak I." }, { "name": "Pachter L." } ], "journal": "Genome research" } }, { "doi": "10.1101/gr.926603", "pmid": "12654723", "pmcid": "PMC430158", "type": [], "version": null, "note": null, "metadata": { "title": "LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA", "abstract": "To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. We present LAGAN, a system for rapid global alignment of two homologous genomic sequences, and Multi-LAGAN, a system for multiple global alignment of genomic sequences. We tested our systems on a data set consisting of greater than 12 Mb of high-quality sequence from 12 vertebrate species. All the sequence was derived from the genomic region orthologous to an ∼1.5-Mb region on human chromosome 7q31.3. We found that both LAGAN and Multi-LAGAN compare favorably with other leading alignment methods in correctly aligning protein-coding exons, especially between distant homologs such as human and chicken, or human and fugu. Multi-LAGAN produced the most accurate alignments, while requiring just 75 minutes on a personal computer to obtain the multiple alignment of all 12 sequences. Multi-LAGAN is a practical method for generating multiple alignments of long genomic sequences at any evolutionary distance. Our systems are publicly available at http://lagan.stanford.edu.", "date": "2003-04-01T00:00:00Z", "citationCount": 803, "authors": [ { "name": "Brudno M." }, { "name": "Do C.B." }, { "name": "Cooper G.M." }, { "name": "Kim M.F." }, { "name": "Davydov E." }, { "name": "Green E.D." }, { "name": "Sidow A." }, { "name": "Batzoglou S." } ], "journal": "Genome Research" } }, { "doi": "10.1093/nar/gkh458", "pmid": "15215394", "pmcid": "PMC441596", "type": [], "version": null, "note": null, "metadata": { "title": "VISTA: Computational tools for comparative genomics", "abstract": "Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.Ibl.gov/vista/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, to submit their own sequences of interest to several VISTA servers for various types of comparative analysis and to obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein. © Oxford University Press 2004; all rights reserved.", "date": "2004-07-01T00:00:00Z", "citationCount": 1303, "authors": [ { "name": "Frazer K.A." }, { "name": "Pachter L." }, { "name": "Poliakov A." }, { "name": "Rubin E.M." }, { "name": "Dubchak I." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkl822", "pmid": "17130149", "pmcid": "PMC1716724", "type": [], "version": null, "note": null, "metadata": { "title": "VISTA Enhancer Browser - A database of tissue-specific human enhancers", "abstract": "Despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo. This paucity of enhancer collections with defined activities has thus hindered computational approaches for the genome-wide prediction of enhancers and their functions. To fill this void, we utilize comparative genome analysis to identify candidate enhancer elements in the human genome coupled with the experimental determination of their in vivo enhancer activity in transgenic mice [L. A. Pennacchio et al. (2006) Nature, in press]. These data are available through the VISTA Enhancer Browser (http://enhancer.lbl.gov) This growing database currently contains over 250 experimentally tested DNA fragments, of which more than 100 have been validated as tissue-specific enhancers. For each positive enhancer, we provide digital images of whole-mount embryo staining at embryonic day 11.5 and an anatomical description of the reporter gene expression pattern. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to a particular tissue, or download entire collections of enhancers with a defined tissue specificity or conservation depth. These experimentally validated training sets are expected to provide a basis for a wide range of downstream computational and functional studies of enhancer function. © 2007 Oxford University Press.", "date": "2007-01-01T00:00:00Z", "citationCount": 589, "authors": [ { "name": "Visel A." }, { "name": "Minovitsky S." }, { "name": "Dubchak I." }, { "name": "Pennacchio L.A." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Vista Support", "email": "Vista@lbl.gov", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-03-24T09:34:05Z", "lastUpdate": "2026-02-17T10:10:39.922919Z", "editPermission": { "type": "group", "authors": [ "mojtaba5" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)", "description": "The tool performs a DICOM quality check in terms of correct number of files per sequence, corrupted files, precise directory hierarchy, separated dynamic series merging them, interest series filtering/selection by specific series description lists and diffusion sequence identification by b-values. It applies the desired changes to the dataset and generates a report containing information about the selected sequences, corrupted files, missing files and merged files.\n\nStatus: Deployed", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "biotoolsID": "dicom_file_integrity_checker_by_gibi230", "biotoolsCURIE": "biotools:dicom_file_integrity_checker_by_gibi230", "version": [ "2.0.0", "2.1.0", "2.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "For Data Holders (ingestion-tools)", "cmd": "docker run -it --rm --name my-container \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n -v \"<config_path>:/config\" \\\n harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_file_integrity_checker:latest" }, { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "For Data Users (processing-tools)", "cmd": "docker run -it --rm --name my-container \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n harbor.eucaim.cancerimage.eu/processing-tools/dicom_file_integrity_checker:latest \\\n /app/entrypoint.sh --config-string \"{'QA': {'sequence_selection': ['ALL'], 'modality_selection': ['ALL'], 'input_directory': 'dataset_id'}}\"" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" }, { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "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 }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "type": [ "Software catalogue" ], "note": "Link to EUCAIM's Harbor for Data Holders" }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/dicom_file_integrity_checker/artifacts-tab", "type": [ "Software catalogue" ], "note": "Link to EUCAIM's Harbor for Data Users" } ], "download": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "type": "Container file", "note": "EUCAIM user needed", "version": "2.1.0" } ], "documentation": [ { "url": "https://drive.eucaim.cancerimage.eu/s/LAKqSQZY4Bjqz5W", "type": [ "User manual" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/EEqjraK574HrwMf", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=oUebkjLYeSs&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=3", "type": [ "Training material" ], "note": null } ], "publication": [], "credit": [ { "name": "GIBI230 - HULAFE", "email": "gibi230@iislafe.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "Adrian Galiana-Bordera", "email": "adrian_galiana@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8324-8284", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Documentor" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "pedromiguel_martinez_HULAFE", "additionDate": "2025-04-15T17:42:40.968987Z", "lastUpdate": "2026-02-16T17:32:26.457200Z", "editPermission": { "type": "group", "authors": [ "casopon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "vvv2_display", "description": "Display SNP proportions (vardict outputs), CDS (vadr annotations) of an assembly/genome, coverage depth (samtools depth), in png image and a tsv file, filtering results to summarize analyses (alignment, variant calling, annotation).", "homepage": "https://github.com/ANSES-Ploufragan/vvv2_display", "biotoolsID": "vvv2_display", "biotoolsCURIE": "biotools:vvv2_display", "version": [ "0.2.5.0" ], "otherID": [ { "value": "doi:10.3390/v17101385", "type": "doi", "version": "0.2.4.0" } ], "relation": [ { "biotoolsID": "ggplot2", "type": "uses" }, { "biotoolsID": "pysam", "type": "uses" }, { "biotoolsID": "R", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0287", "term": "Base position variability plotting" }, { "uri": "http://edamontology.org/operation_3184", "term": "Sequence assembly visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": 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-x signif_snp_res.vcf" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0781", "term": "Virology" } ], "operatingSystem": [ "Linux" ], "language": [ "R", "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ANSES-Ploufragan/vvv2_display", "type": [ "Repository" ], "note": null }, { "url": "https://toolshed.g2.bx.psu.edu/view/ftouzain/vvv2_display/fcd3aa68bd39", "type": [ "Other" ], "note": "Galaxy wrapper" }, { "url": "https://workflowhub.eu/search?q=vvv2", "type": [ "Other" ], "note": "Listing of Galaxy workflow performing all steps:\n- alignment on ref/assembly\n- annotation of ref/assembly\n- coputation of coverage depth\n- vardict variant calling\n- vvv2_display synthesis\n\nOne can be found for each sequencing technology (Illumina SE/Proton, Illumina PE, nanopore, pacbio" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.3390/v17101385", "pmid": "41157655", "pmcid": "PMC12567792", "type": [ "Primary" ], "version": "0.2.4.0", "note": "published in Viruses journal", "metadata": null } ], "credit": [ { "name": "Fabrice Touzain", "email": "fabrice.touzain@anses.fr", "url": "https://github.com/ANSES-Ploufragan/vvv2_display", "orcidid": "https://orcid.org/0000-0002-1103-2425", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Dr. in Bioinformatics at ANSES (\"Swine virology, innovation and genomics\" Unit, Bioinformatics Team)" } ], "owner": "fabrice", "additionDate": "2026-02-12T16:06:53.794717Z", "lastUpdate": "2026-02-12T16:07:53.280544Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Segmentation evaluation", "description": "This tool calculates segmentation metrics (Dice score, intersection over union, Hausdorff distance, and normalised surface distance) between two sets of masks. 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For more options please run `uv run eval_segmentation --help`", "cmd": "uv run eval_segmentation \\\n --pred test_data/predicted/ \\\n --gt test_data/groundtruth/ \\\n --output test.json \\\n --n_classes 2 \\\n --verbose \\\n --params '{\"normalised_surface_distance\": {\"max_distance\": 100.0}}'" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_3444", "term": "MRI" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/josegcpa/eucaim-metrics/tree/master", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/josegcpa/eucaim-metrics/tree/master", "type": [ "Quick start guide", "API documentation" ], "note": null } ], "publication": [], "credit": [ { "name": "José Guilherme de Almeida", "email": "jose.almeida@research.fchampalimaud.org", "url": null, "orcidid": "https://orcid.org/0000-0002-1887-0157", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "Nickolas Papanikolaou", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3298-2072", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "josegcpa", "additionDate": "2026-02-12T14:54:22.759092Z", "lastUpdate": "2026-02-12T15:01:23.363666Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PathoFact2", "description": "An Integrative Pipeline for Antimicrobial Resistance Genes, Virulence Factors, Toxin-associated proteins, and Biosynthetic Gene Clusters Prediction in Metagenomes", "homepage": "https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2", "biotoolsID": "pathofact2", "biotoolsCURIE": "biotools:pathofact2", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3482", "term": "Antimicrobial resistance prediction" }, { "uri": "http://edamontology.org/operation_3461", "term": "Virulence prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0925", "term": "Sequence assembly" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_4013", "term": "Antimicrobial resistance" } ], "operatingSystem": [ "Linux" ], "language": [ "Python", "R", "Bash" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2", "type": [ "Repository" ], "note": null }, { "url": "https://zenodo.org/records/14192463", "type": [ "Repository" ], "note": null }, { "url": "https://zenodo.org/records/17647372", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Luis F. Delgado", "email": "luis.delgado@uni.lu", "url": null, "orcidid": "https://orcid.org/0000-0001-7850-5285", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Júlia Ortís Sunyer", "email": "julia.ortissunyer@uni.lu", "url": null, "orcidid": "https://orcid.org/0000-0002-2714-7067", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Paul Wilmes", "email": "paul.wilmes@uni.lu", "url": null, "orcidid": "https://orcid.org/0000-0002-6478-2924", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "julia8", "additionDate": "2026-02-12T09:37:33.991999Z", "lastUpdate": "2026-02-12T14:58:55.997656Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Foldcomp", "description": "A library and format for compressing and indexing large protein structure sets.", "homepage": "https://foldcomp.foldseek.com", "biotoolsID": "foldcomp", "biotoolsCURIE": "biotools:foldcomp", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_0249", "term": "Protein geometry calculation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_3489", "term": "Database management" }, { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/btad153", "pmid": "36961332", "pmcid": "PMC10085514", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Martin Steinegger", "email": "martin.steinegger@snu.ac.kr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Chan019", "additionDate": "2023-04-20T14:28:02.353577Z", "lastUpdate": "2026-02-11T06:23:47.889831Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Randmice", "description": "Randmice is an online tool that optimize randomization of animals for in vivo experiences by minimizing heterogeneity between groups.", "homepage": "https://randmice.com", "biotoolsID": "randmice", "biotoolsCURIE": "biotools:randmice", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3679", "term": "Animal study" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "sylvain", "additionDate": "2026-02-09T20:42:59.408390Z", "lastUpdate": "2026-02-09T20:46:20.459289Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Liana+", "description": "LIANA+ is a scalable framework for inference of cell‑cell communication (CCC) from single-cell and spatially resolved omics data. 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LIANA+ accepts AnnData/MuData formats and interfaces with single‑cell ecosystems like scverse for flexible, interoperable workflows.", "homepage": "https://liana-py.readthedocs.io/en/latest/", "biotoolsID": "liana", "biotoolsCURIE": "biotools:liana", "version": [ "1.7.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0313", "term": "Expression profile clustering" }, { "uri": "http://edamontology.org/operation_2939", "term": "Principal component visualisation" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [ { "uri": "http://edamontology.org/format_3590", "term": "HDF5" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3768", "term": "Clustered expression profiles" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_4028", "term": "Single-cell sequencing" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" } ], "operatingSystem": [], "language": [ "Python" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/saezlab/liana-py", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://liana-py.readthedocs.io/en/latest/api.html", "type": [ "API documentation" ], "note": null }, { "url": "https://liana-py.readthedocs.io/en/latest/installation.html", "type": [ "Installation instructions" ], "note": null }, { "url": "https://liana-py.readthedocs.io/en/latest/notebooks/index.html", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1038/s41556-024-01469-w", "pmid": "39223377", "pmcid": "PMC11392821", "type": [], "version": "1.7.1", "note": "The growing availability of single-cell and spatially resolved transcriptomics has led to the development of many approaches to infer cell-cell communication, each capturing only a partial view of the complex landscape of intercellular signalling. 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HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Maria Beser-Robles", "email": "maria_beser@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-0072-5525", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Support" ], "note": null }, { "name": "Adrian Galiana-Bordera", "email": "adrian_galiana@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8324-8284", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T12:09:16.704255Z", "lastUpdate": "2026-02-03T11:47:01.186875Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MR-based DIPG tumour detection and segmentation (EUCAIM-SW-020_T-01-02-003)", "description": "The tool performs an automatic segmentation of the possible DIPG tumours on MR images. 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