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{ "count": 9508, "next": "?page=2", "previous": null, "list": [ { "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": "http://edamontology.org/format_3603", "term": "PNG" } ] }, { "data": { "uri": "http://edamontology.org/data_3779", "term": "Annotated text" }, "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" } ] } ], "note": "Inputs:\n- tbl pass vadr annotation file\n- tbl fail vadr annotation file\n- seqstat vadr output file\n- vcf vardict-java variant calling results (all)\n- samtools depth text file (coverage depth of an alignment)\nOutputs:\n- png summary file with all info\n- tsv file of indexed significant variant (index showed on png figure)\n- [optional] vcf file of significant variants only", "cmd": "vvv2_display.py -p vadr_pass_annotation.tbl -f vadr_fail_annotation.tbl -s vadr_seqstat.txt -n vardict-java_res.vcf -o samtools_depth_out.txt -r signif_snp_annot_res.png -u signif_snp_res.tsv -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. It can be used to quickly calculate a number of metrics for segmentation models.", "homepage": "https://github.com/josegcpa/eucaim-metrics/tree/master", "biotoolsID": "segmentation_evaluation", "biotoolsCURIE": "biotools:segmentation_evaluation", "version": [ "v0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "This is the core command which can be used to calculate image segmentation metrics. 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": "Metagenomic operational taxonomic units (mOTUs)", "description": "Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.", "homepage": "https://motu-tool.org/", "biotoolsID": "motus", "biotoolsCURIE": "biotools:motus", "version": [ "2.5.1" ], "otherID": [], "relation": [ { "biotoolsID": "gtdb", "type": "uses" }, { "biotoolsID": "motus-db", "type": "uses" } ], "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": "Taxonomic profiling from shotgun metagenomes Quality-filtered shotgun metagenomic reads A taxonomic profiling matrix with species in rows and samples in columns; each entry m_{i,j} indicates the number of reads from sample j mapped to marker genes of species i", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": "GPL-3.0", "collectionID": [ "de.NBI" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/motu-tool/mOTUs", "type": [ "Repository" ], "note": null }, { "url": "https://motus-db.org/", "type": [ "Other" ], "note": "Database for mOTUs profiler" } ], "download": [ { "url": "https://motu-tool.org/download.html", "type": "Biological data", "note": null, "version": null }, { "url": "https://github.com/motu-tool", "type": "Source code", "note": null, "version": null }, { "url": "https://anaconda.org/bioconda/motus", "type": "Container file", "note": "MBT:Container", "version": null } ], "documentation": [ { "url": "https://motu-tool.org/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s40168-022-01410-z", "pmid": "36464731", "pmcid": "PMC9721005", "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkae1004", "pmid": "39526369", "pmcid": "PMC11701688", "type": [ "Primary" ], "version": null, "note": "mOTUs-db paper", "metadata": null } ], "credit": [ { "name": "European Molecular Biology Laboratory (EMBL)", "email": null, "url": "https://www.embl.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "HD-HuB", "email": null, "url": "https://www.hd-hub.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "http://www.bork.embl.de/software/mOTU/contact.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Shinichi Sunagawa", "email": "ssunagawa@ethz.ch", "url": null, "orcidid": "http://orcid.org/0000-0003-3065-0314", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "hdhub", "additionDate": "2016-02-11T12:02:14Z", "lastUpdate": "2026-02-12T14:33:33.330556Z", "editPermission": { "type": "group", "authors": [ "vashokan" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "metabuli", "description": "Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid", "homepage": "https://metabuli.steineggerlab.com", "biotoolsID": "metabuli", "biotoolsCURIE": 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"Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [], "license": "BSD-3-Clause", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/sourmash-bio/sourmash", "type": [ "Repository" ], "note": "github repository" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.12688/f1000research.19675.1", "pmid": "31508216", "pmcid": "PMC6720031", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "C. 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Omics Fusion provides a collection of new and established tools and visualization methods to support researchers in exploring omics data, validating results or understanding how to adjust experiments in order to make new discoveries. It is easily extendible and new visualization methods are added continuously. 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"credit": [ { "name": null, "email": null, "url": "https://github.com/lifs-tools/jmzTab-m", "orcidid": "https://orcid.org/0000-0002-6540-6875", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "de.NBI_Service_Team", "additionDate": "2018-06-21T08:37:35Z", "lastUpdate": "2026-02-03T10:26:12.147063Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "decompTumor2Sig", "description": "R package for identification of mutational signatures active in individual tumors. It decomposes an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor.", "homepage": "http://rmpiro.net/decompTumor2Sig/", "biotoolsID": "decompTumor2Sig", "biotoolsCURIE": "biotools:decompTumor2Sig", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0239", "term": "Sequence motif recognition" }, { "uri": "http://edamontology.org/operation_1812", "term": "Parsing" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/rmpiro/decompTumor2Sig/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/rmpiro/decompTumor2Sig", "type": [ "Repository" ], "note": null }, { "url": "https://bioconductor.org/packages/release/bioc/html/decompTumor2Sig.html", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://rmpiro.net/index.html#downloads", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/rmpiro/decompTumor2Sig/blob/master/decompTumor2Sig-manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-019-2688-6", "pmid": "30999866", "pmcid": "PMC6472187", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "DecompTumor2Sig: Identification of mutational signatures active in individual tumors", "abstract": "© 2019 The Author(s).Background: The somatic mutations found in a tumor have in most cases been caused by multiple mutational processes such as those related to extrinsic carcinogens like cigarette smoke, and those related to intrinsic processes like age-related spontaneous deamination of 5-methylcytosine. The effect of such mutational processes can be modeled by mutational signatures, of which two different conceptualizations exist: the model introduced by Alexandrov et al., Nature 500:415-421, 2013, and the model introduced by Shiraishi et al., PLoS Genetics 11(12):e1005657, 2015. The initial identification and definition of mutational signatures requires large sets of tumor samples. Results: Here, we present decompTumor2Sig, an easy to use R package that can decompose an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor. Until now, such tools were available only for Alexandrov signatures. We demonstrate the correctness and usefulness of our approach with three test cases, using somatic mutations from 21 breast cancer genomes, from 435 tumor genomes of ten different tumor entities, and from simulated tumor genomes, respectively. Conclusions: The decompTumor2Sig package is freely available and has been accepted for inclusion in Bioconductor.", "date": "2019-04-18T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Kruger S." }, { "name": "Piro R.M." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Prof. Dr. Rosario M. 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Computational methods in this area rely on high quality validation datasets which are usually manually assembled. Due to the increase in published structures as well as the increasing demand for specially tailored validation datasets, automatic procedures should be adopted. Results StructureProfiler is a new tool for automatic, objective and customizable profiling of X-ray protein structures based on the most frequently applied selection criteria currently in use to assemble benchmark datasets. As examples, four dataset configurations (Astex, Iridium, Platinum, combined), all results of the combined tests and the list of all PDB Ids passing the combined criteria set are attached in theSupplementary Material.", "date": "2019-03-01T00:00:00Z", "citationCount": 4, "authors": [ { "name": "Meyder A." }, { "name": "Kampen S." }, { "name": "Sieg J." }, { "name": "Fahrrolfes R." }, { "name": "Friedrich N.-O." }, { "name": "Flachsenberg F." }, { "name": "Rarey M." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Matthias Rarey", "email": "rarey@zbh.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ehrt", "additionDate": "2019-07-06T06:35:25Z", "lastUpdate": "2025-12-23T14:50:37.487104Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EDIA", "description": "Easily interpretable electron density score for individual atoms. It quantifies the electron density support of each single atom by computing a weighted sum over an oversampled electron density grid in the proximity of the atom. Atomic EDIA values can also be combined with the help of the power mean to compute EDIA_m, an electron density score for small molecules, fragments, or residues.", "homepage": "http://proteinsplus.zbh.uni-hamburg.de/#edia", "biotoolsID": "edia", "biotoolsCURIE": "biotools:edia", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0321", "term": "Protein model validation" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1461", "term": "Protein-ligand complex" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": "Score for structure quality assessment on a global or atomistic level", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_2828", "term": "X-ray diffraction" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "de.NBI", "COVID-19" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "http://proteinsplus.zbh.uni-hamburg.de/help/index", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jcim.7b00391", "pmid": "28981269", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures", "abstract": "© 2017 American Chemical Society.Macromolecular structures resolved by X-ray crystallography are essential for life science research. While some methods exist to automatically quantify the quality of the electron density fit, none of them is without flaws. Especially the question of how well individual parts like atoms, small fragments, or molecules are supported by electron density is difficult to quantify. While taking experimental uncertainties correctly into account, they do not offer an answer on how reliable an individual atom position is. A rapid quantification of this atomic position reliability would be highly valuable in structure-based molecular design. To overcome this limitation, we introduce the electron density score EDIA for individual atoms and molecular fragments. EDIA assesses rapidly, automatically, and intuitively the fit of individual as well as multiple atoms (EDIAm) into electron density accompanied by an integrated error analysis. The computation is based on the standard 2fo - fc electron density map in combination with the model of the molecular structure. For evaluating partial structures, EDIAm shows significant advantages compared to the real-space R correlation coefficient (RSCC) and the real-space difference density Z score (RSZD) from the molecular modeler's point of view. Thus, EDIA abolishes the time-consuming step of visually inspecting the electron density during structure selection and curation. It supports daily modeling tasks of medicinal and computational chemists and enables a fully automated assembly of large-scale, high-quality structure data sets. Furthermore, EDIA scores can be applied for model validation and method development in computer-aided molecular design. In contrast to measuring the deviation from the structure model by root-mean-squared deviation, EDIA scores allow comparison to the underlying experimental data taking its uncertainty into account.", "date": "2017-10-23T00:00:00Z", "citationCount": 33, "authors": [ { "name": "Meyder A." }, { "name": "Nittinger E." }, { "name": "Lange G." }, { "name": "Klein R." }, { "name": "Rarey M." } ], "journal": "Journal of Chemical Information and Modeling" } } ], "credit": [ { "name": "University of Hamburg - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "rarey-office@zbh.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ehrt", "additionDate": "2016-11-28T10:07:17Z", "lastUpdate": "2025-12-23T14:50:31.055029Z", "editPermission": { "type": "group", "authors": [ "Bietz", "ehrt" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Image Duplicates Checker", "description": "Detects duplicate or visually similar DICOM series using a tiered approach that combines metadata analysis, hash-based comparison, and pixel-level similarity metrics.\nIdeal for:\n1. 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Detecting duplicates even after post-processing (e.g., denoising, filtering).\n\nFor scenarios requiring strict, image-level deduplication based on pixel content, fully agnostic to metadata changes, consider using [https://bio.tools/image_duplicate_check_tool]", "homepage": "https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologies", "biotoolsID": "dicom_image_similarity-duplicate_checker", "biotoolsCURIE": "biotools:dicom_image_similarity-duplicate_checker", "version": [ "2.0" ], "otherID": [], "relation": [ { "biotoolsID": "data_integration_quality_check_tool_diqct", "type": "includedIn" } ], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "eucaim" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/deduplication_tool", "type": [ "Repository" ], "note": "Link to the Harbor image" } ], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/10GsrgRCeyrZrdus04iI-967llth0o9yE/edit?usp=drive_link&ouid=108776251279939449410&rtpof=true&sd=true", "type": [ "General" ], "note": null } ], "publication": [], "credit": [], "owner": "difoto", "additionDate": "2025-05-28T23:55:08.439649Z", "lastUpdate": "2025-12-23T13:24:16.938179Z", "editPermission": { "type": "group", "authors": [ "authEucaim" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Spatial Proteomics", "description": "End-to-end spatial proteomics analysis workflow with QuPath integration. Our workflow consists of cell segmentation, batch correction, unsupervised clustering, validation of clusters on the image, and cell type clustering results visualization.", "homepage": "https://github.com/BioDepot/SpatialProteomics", "biotoolsID": "spatial_proteomics", "biotoolsCURIE": "biotools:spatial_proteomics", "version": [], "otherID": [ { "value": "RRID:SCR_027835", "type": "rrid", "version": null } ], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [], "operatingSystem": [], "language": [ "Python", "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://youtu.be/vHjdCAZQhfE", "type": [ "Other" ], "note": "Demo video" } ], "download": [ { "url": "https://github.com/BioDepot/SpatialProteomics", "type": "Source code", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1101/2025.05.23.655879", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": "1", "note": null, "metadata": null } ], "credit": [ { "name": "Ling-Hong Hung", "email": "lhhung@uw.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-5209-2248", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Ka Yee Yeung", "email": "kayee@uw.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-1754-7577", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "Bryce Fukuda", "email": "fukudab@uw.edu", "url": null, "orcidid": "https://orcid.org/0009-0003-7203-5261", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null } ], "owner": "kayee", "additionDate": "2025-12-23T00:16:25.679615Z", "lastUpdate": "2025-12-23T00:29:13.711774Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }