Phylo-MoviesPhylo-Movies is an open-source React and Flask web application, also available as a desktop app, for inspecting ordered phylogenetic tree series. It computes and visualizes subtree-prune-and-regraft transition frames between consecutive trees, helping users see which taxa or subtrees move across sliding-window analyses, bootstrap replicates, and curated tree-series comparisons. The viewer includes timeline playback, tree comparison, MSA context, coloring, analytics, image export, and recording tools.https://enesberksakalli.github.io/phylo-movies/phylo-moviesbiotools:phylo-movies0.98.1Desktop applicationWeb applicationhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0092Data visualisationWindowsMacLinuxPythonJavaScriptTypeScriptMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_0324Phylogenetic tree analysishttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAVisualizes ordered phylogenetic tree series as animated transition movies with comparison, MSA context, movement analytics, image export, and recording support.https://github.com/enesBerkSakalli/phylo-moviesRepositorySource code repository.https://enesberksakalli.github.io/phylo-movies/demo/ServiceStatic browser demo with precomputed example movies.https://github.com/enesBerkSakalli/phylo-movies/issuesIssue trackerhttps://github.com/enesBerkSakalli/phylo-moviesSource codeSource checkout for full web application and backend workflows.0.98.1https://github.com/enesBerkSakalli/phylo-movies/releases/tag/v0.98.1BinariesDesktop convenience builds for macOS, Windows, and Linux.0.98.1https://enesberksakalli.github.io/phylo-movies/manual/User manualResearcher-facing manual.https://github.com/enesBerkSakalli/phylo-movies/blob/main/README.mdGeneralProject overview, installation, usage, citation, and links.https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/getting-started.mdInstallation instructionsLocal source-checkout setup instructions.https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/api.mdAPI documentationBackend API documentation.10.64898/2026.04.01.715821PrimarybioRxiv preprint describing the Phylo-Movies method and examples.10.5281/zenodo.20488923Primary0.98.1Archived software release on Zenodo.Enes Berk Sakallienes@lbi-netmed.athttps://github.com/enesBerkSakalliPersonDeveloperPrimary contactCorresponding software contact.Simon E. HaendelerPersonDeveloperArndt von HaeselerPersonDeveloperHeiko A. SchmidtPersonDeveloperLacunaWhen a stroke, tumor, or other focal brain injury damages tissue, understanding its consequences requires placing the lesion within the broader organization of the brain. Lacuna is an open-source toolbox that uses normative reference data from healthy individuals, including connectivity datasets and anatomical atlases, to characterize lesions beyond their anatomical location.
Users provide lesion masks in MNI space, and Lacuna automatically retrieves reference data, performs required processing steps, and generates BIDS-organized outputs. Designed for multicenter research, it standardizes workflows, scales from single cases to large cohorts, supports HPC deployment through containers, and records provenance for reproducible lesion analyses.https://github.com/m-petersen/lacunalacunabiotools:lacunahttp://edamontology.org/topic_3334NeurologyLinuxMacPythonBashOpen accesshttps://lacuna-py.readthedocs.io/en/latest/Command-line optionsProteinsPlusThe ProteinsPlus web server aims to support life scientists in working with protein structures. Protein structures are the key to understanding protein function. They are an important resource in many biotechnological application areas from pharmaceutical research to biocatalysis. ProteinsPlus focuses on protein-ligand interactions. The server provides support for the initial steps of dealing with protein structures, namely structure search, quality assessment, and preprocessing. JAMDA enables users to perform an on-the-fly molecular docking of up to five molecules. The poses can then be visualized in 2D (PoseView, PoseEdit). Furthermore, advanced options, such as protein pocket detection (DoGSite), prediction of water molecule positions (WarPP), protein structure ensemble generation (SIENA), prediction of metal coordination (METALizer), the analysis of solvent channels in protein crystals (LifeSoaks), or the categorization of protein-protein-interfaces (HyPPI) are supported.https://proteins.plusproteinsplusbiotools:proteinsplusWeb serviceWeb APIhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFprediction of protonation states and tautomers and placement of hydrogen atomshttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_1844Protein geometry validationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFquality profiling for protein-ligand complexeshttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0384Accessible surface calculationhttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFcalculating bottleneck radii for crystal solvent channelshttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFatom-level assessment of the electron density fit for structures solved by X-ray crystallographyhttp://edamontology.org/operation_2949Protein-protein interaction analysishttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBprotein-protein interface classification (permanent, transient, crystal artifact)http://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_1197InChIhttp://edamontology.org/format_1196SMILEShttp://edamontology.org/format_3816Mol2http://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFprotein-ligand docking for small moleculeshttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFsmall molecule binding site detectionhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFsmall molecule binding site detection and druggability assessmenthttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF2D interaction diagram drawing and editinghttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFmetal complex geometry predictionhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF2D interaction diagram drawinghttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFstructural single-residue substitution search and analysishttp://edamontology.org/operation_2844Structure clusteringhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFPDB mining and protein binding site ensemble generationhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0306Text mininghttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFtextual, numerical, and chemical 3D searches in the PDBhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFwater molecule placementhttps://proteins.plusServicehttps://proteins.plus/help/indexGeneraldogsitescorerincludesdogsite3includesediaincludessienaincludesmetalizerincludesstructureprofilerincludesjamdaincludesgeomineincludesmicrominerincludesposeeditincludesposeviewincludesprotossincludeslifesoaksincludesppiincludes10.1093/nar/gkx33328472372PMC5570178Primary10.1093/nar/gkaa23532297936PMC7319454Usage10.1093/nar/gkac30535489057PMC9252762Usage10.1093/nar/gkaf37740326518PMC12230695UsageProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderMicroMinerMicroMiner assists in identifying single-residue substitutions in protein structure databases. It searches protein residue environments with local sequence and structural similarity based on the SIENA methodology. Users can search for structural mutation in the entire PDB, their in-house structure collection, or (subsets of) the AlphaFold Database. They can use the method to explore the mutation landscape of proteins with experimental or predicted structures. MicroMiner can be applied to single domains or even protein-protein or protein-ligand interfaces. Several filter options to simplify downstream analysis are available.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/microminer.htmlmicrominerbiotools:microminerCommand-line toolWeb servicehttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0091BioinformaticsMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFstructural single-residue substitution search and analysishttps://proteins.plusServiceA web service to run MicroMiner calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneralsienauses10.1093/bib/bbad357Primaryproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service Issuessoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderJAMDAJAMDA enables the preparation of individual protein structures and the docking of small molecules in preprocessed binding sites of choice. JAMDA simplifies the process of protein-ligand docking by automatic preprocessing protocols for the protein and binding sites of interest. The JAMDAscore scoring function retrieved 75% of the native poses in the three highest-ranked solutions for high-quality protein-ligand complexes with default settings. Individual configurations for protein preparation are available, e.g., considering protein ensembles, relevant binding site water molecules, or cofactors. A user-defined number of input conformations for the ligands of interest can be generated fully automated using Conformator. Alternatively, users can also provide externally prepared ligand conformers.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/jamda.htmljamdabiotools:jamdaWeb serviceCommand-line toolhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0082Structure predictionWindowsMacLinuxOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_1196SMILEShttp://edamontology.org/format_3816Mol2http://edamontology.org/format_3814SDFhttp://edamontology.org/format_1197InChIhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFprotein-ligand docking for small moleculeshttps://proteins.plusServiceA web service to run JAMDA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneralprotossuses10.1021/acs.jcim.3c01573Primary10.1002/jcc.26522Method10.1021/acs.jcim.0c01095MethodProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderGeoMineGeoMine enables the automated mining of protein-ligand binding sites. Based on individually designed queries, users can search for spatial interaction patterns in huge collections of protein-ligand complexes and binding pockets. The regularly updated GeoMine database relies on the free database systems SQLite and PostgreSQL. It supports radius-based pockets (based on ligands and predicted pockets (based on DoGSite3) for query generation. The query management is based on XML (for the REST service) or JSON in the GUI mode. Its output consists of the query-based superpositions of the matched binding sites and statistics on matching points, distances, and angles.https://www.zbh.uni-hamburg.de/forschung/amd/software/geomine.htmlgeominebiotools:geomineWeb serviceWeb APIhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3336Drug discoveryLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0306Text mininghttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFtextual, numerical, and chemical 3D searches in the PDBhttps://proteins.plusServiceA web service to run GeoMine calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://proteins.plus/help/geomine_restServiceA web API to run GeoMine calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://proteins.plus/help/indexGeneraldogsite3usesprotossuses10.1093/bioinformatics/btaa69332735322Usage10.1021/acs.jcim.6b00561Method10.1021/acs.jmedchem.1c01046Primary10.1007/s10822-024-00563-3UsageProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderStructureProfilerThree-dimensional protein structures play a vital role in drug design. Structure-based design necessitates an in-depth examination of the available quality data before using the structure in computational experiments and for method evaluation. StructureProfiler assists in automatically profiling sets of protein-ligand complex structures based on multiple quality indicators, ranging from model characteristics, e.g., the R factor, and active site features, e.g., bond length deviations, to ligand properties such as electron density support and the validity of torsion angles.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/structureprofiler.htmlStructureProfilerbiotools:StructureProfilerWeb serviceWeb APICommand-line toolhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3572Data quality managementhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_1317Structural biologyLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_1844Protein geometry validationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFquality profiling for protein-ligand complexeshttps://proteins.plusServiceA web service to run StructureProfiler calculations for protein structures stored in the Protein Data Bank.https://proteins.plus/help/structurechecker_restServiceA web API to run StructureProfiler calculations for protein structures stored in the Protein Data Bank.https://uhh.de/naomiSoftware catalogueLink to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinarieshttps://proteins.plus/help/indexGeneral10.1093/bioinformatics/bty69230124779PrimaryProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderWarPPWarPP predicts the position and orientation of water molecules in small-molecule binding sites. It places and scores water molecules in binding sites of crystallographic structures based on EDIAscorer results and interaction geometries as known from experimentally solved protein structures. WarPP was validated on a high-quality set of 1,500 protein-ligand complexes, containing 20,000 crystallographically observed water molecules. It is sufficiently fast for high-throughput analyses. It correctly places water molecules in approx. 80% of the cases. Users can export the predictions as PDB files for, e.g., molecular docking with JAMDA.https://www.zbh.uni-hamburg.de/forschung/amd/software/warpp.htmlwarppbiotools:warppCommand-line toolWeb APIWeb servicehttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3534Protein binding sitesMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFwater molecule placementhttps://proteins.plusServiceA web service to run WarPP calculations for protein structures stored in the Protein Data Bank.https://proteins.plus/help/warpp_restServiceA web API to run WarPP calculations for protein structures stored in the Protein Data Bank.https://uhh.de/naomiSoftware catalogueLink to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinarieshttps://proteins.plus/help/indexGeneral10.1021/acs.jcim.8b0027130036062PrimaryProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderLifeSoaksLifeSoaks was designed to find solvent channels in macromolecular structures solved by X-ray crystallography. It predicts their accessibility by molecules through an automated annotation of so-called bottleneck radii. It simplifies the process of manually checking a crystal structure for solvent channels. Bottleneck radii can be calculated for solvent channels and small molecule binding sites. The tool is ideally suited for channel analyses before the actual soaking experiments to select the most promising experimental conditions and crystal forms. LifeSoaks runs fully automated and will finish within seconds to minutes for moderately sized crystals.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/lifesoaks.htmllifesoaksbiotools:lifesoaksWeb serviceCommand-line toolhttp://edamontology.org/topic_2828X-ray diffractionhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0091BioinformaticsWindowsMacLinuxOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0384Accessible surface calculationhttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFcalculating bottleneck radii for crystal solvent channelshttps://proteins.plusServiceA web service to run LifeSoaks calculations for protein structures stored in the Protein Data Bank.https://uhh.de/naomi.deSoftware catalogueA link to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneral10.1107/S205979832300582XPrimaryProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderMETALizerMETALizer predicts the coordination geometry of metal ions in metalloproteins. Users can compare potential coordination geometries to those found in the examined structure. The predicted coordination geometries and the observed metal interaction distances can be interactively compared to statistics calculated based on the PDB.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/metalizer.htmlmetalizerbiotools:metalizerWeb serviceWeb APIhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0123Protein propertiesWindowsMacLinuxOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFmetal complex geometry predictionhttps://proteins.plusServiceA web service to run METALizer calculations for protein structures stored in the Protein Data Bank.https://proteins.plus/help/metalizer_restServiceA web API to run METALizer calculations for protein structures stored in the Protein Data Bank.https://proteins.plus/help/indexGeneral10.1093/nar/gkaa235PrimaryProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderEDIAscorerThe electron density score for individual atoms (EDIA) quantifies the electron density fit of each atom in a crystallographically resolved structure. Multiple EDIA values can be combined using the power mean to compute the EDIAm, i.e., the electron density score for a group of several atoms. It enables users to score a set of atoms, such as a ligand, a residue, or an active site.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/ediascorer.htmlediabiotools:ediaWeb serviceCommand-line toolWeb APIhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_2828X-ray diffractionhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2275Molecular modellingWindowsMacLinuxOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFatom-level assessment of the electron density fit for structures solved by X-ray crystallographyhttps://proteins.plusServiceA web service to run EDIAscorer calculations for protein structures stored in the Protein Data Bank.https://proteins.plus/help/edia_restServiceA web API to run EDIAscorer calculations for protein structures stored in the Protein Data Bank.https://uhh.de/naomiSoftware catalogueA link to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinarieshttps://proteins.plus/help/indexGeneralstructureprofilerusedBy10.1021/acs.jcim.7b0039128981269PrimaryProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.deSupportNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.deSupportUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956ProviderHyPPIHyPPI classifies a protein-protein complex based on its interaction type into permanent, transient, or crystal artifact. Permanent protein-protein complexes are only stable in their complexed state. Their subunits would denature upon dissociation of the protein-protein complex. Transient protein-protein complexes are stable in the complexed as well as in the monomeric form, depending on the necessary function of the complex. Crystal artifacts have no biological function and are artificially formed during the crystallization process. The discrimination is performed using two characteristics of the protein-protein complex, the hydrophobicity of the interface (ΔGhydrophobic) and the quotient of interface area ratios (IF-quotient). The IF-quotient considers whether the protein-protein interface is symmetric.https://proteins.plus/help/ppippibiotools:ppiWeb serviceWeb APIhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0602Molecular interactions, pathways and networksLinuxWindowsMacOtherde.NBIde.NBI-biodataLegacyFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_2949Protein-protein interaction analysishttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBprotein-protein interface classification (permanent, transient, crystal artifact)https://proteins.plusServiceA web service to run HyPPI calculations for protein structures stored in the Protein Data Bank or uploaded structures.https://proteins.plus/help/ppi_restServiceA web API to run HyPPI calculations for protein structures stored in the Protein Data Bank or uploaded structures.https://proteins.plus/help/indexGeneral10.1007/s10822-012-9626-223269578Method10.1093/nar/gkx333PrimaryUsageProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderSIENASIENA is a software pipeline enabling the fully automated construction of protein structure ensembles from the PDB. Starting with a single query structure, all binding sites with high sequence similarity are extracted from the PDB, aligned, and superimposed. SIENA also handles complicated cases, such as comparing binding sites at protein domain interfaces or within multimeric proteins.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/siena.htmlsienabiotools:sienaWeb serviceWeb APICommand-line toolhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0128Protein interactionsLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_2844Structure clusteringhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFPDB mining and protein binding site ensemble generationhttps://proteins.plusServiceA web service to run SIENA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://proteins.plus/help/siena_restServiceA web API to run SIENA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://uhh.de/naomiSoftware catalogueA link to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneralproteinsplusincludedIn10.1021/acs.jcim.5b0058826759067MethodPrimary10.1021/acs.jcim.5b0021026098831MethodProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderPoseEditPoseEdit automatically generates 2D diagrams of protein-ligand complexes, focusing on the interactions between protein and ligand. Interactions between molecules are estimated by an underlying interaction model that relies on atom types and simple geometric criteria. The structure mining tool GeoMine also uses this model to describe binding sites. In addition, users can manipulate the diagrams by translating, rotating, mirroring parts of the structure, adding additional interactions, or removing them. Furthermore, users can add individual labels or adjust available labels. Users can download the final 2D diagrams for a binding site of interest in JSON or SVG format.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/poseedit.htmlposeeditbiotools:poseeditWeb serviceWeb APIhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3534Protein binding sitesWindowsMacLinuxOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF2D interaction diagram drawing and editinghttps://proteins.plusServiceA web service to run PoseEdit calculations for protein-ligand complexes.https://proteins.plus/help/poseview2_restServiceA web API to run PoseEdit calculations for protein-ligand complexes.https://proteins.plus/help/indexGeneralgeomineusedByprotossuses10.1007/s10822-023-00522-437515714PMC10440272PrimaryProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderPoseViewPoseView automatically generates 2D diagrams of protein-ligand complexes, focusing on the interactions between protein and ligand. Interactions between molecules are estimated by an underlying interaction mode that relies on atom types and simple geometric criteria. It adheres to the conventions of chemical structure diagram generation. The quality of the resulting diagrams is comparable to manually drawn examples from books and scientific publications.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/poseview.htmlposeviewbiotools:poseviewWeb APIWeb servicehttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3534Protein binding sitesMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF2D interaction diagram drawinghttps://proteins.plusServiceA web service to run PoseView calculations for protein-ligand complexes.https://proteins.plus/help/poseview_restServiceA web API to run PoseView calculations for protein-ligand complexes.https://proteins.plus/help/indexGeneral10.1021/ml100164p24900245PMC4007829Primary10.1093/bioinformatics/btl15016632493Benchmarking study10.1002/cmdc.20070001017436259Benchmarking study10.1021/ci049958u15154775MethodProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956ProviderProtossProtoss is a fully automated hydrogen atom placement tool for protein-ligand complexes. It adds missing hydrogen atoms to protein structures and detects reasonable protonation states, tautomeric states, and hydrogen coordinates of both protein and ligand molecules by optimizing the hydrogen bond network.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/protoss.htmlprotossbiotools:protossWeb APIWeb servicehttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0082Structure predictionMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFprediction of protonation states and tautomers and placement of hydrogen atomshttps://proteins.plusServiceA web service to run Protoss calculations.https://proteins.plus/help/protoss_restServiceA web API to run Protoss calculations.https://proteins.plus/help/indexGeneralgeomineusedByjamdausedBy10.1186/1758-2946-6-1224694216PMC4019353Primary10.1186/1758-2946-1-1320298519PMC3225823OtherProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderDoGSiteScorerDoGSiteScorer is a grid-based automated pocket detection and analysis tool. It applies a Difference of Gaussian filter to detect potential binding pockets and splits them into sub-pockets. The method solely uses the 3D structure of the protein. Global properties, describing the size, shape, and chemical features of the predicted (sub-)pockets, are calculated. Per default, a simple druggability score based on a linear combination of the three descriptors describing volume, hydrophobicity, and enclosure is provided for each (sub-)pocket. Furthermore, a subset of meaningful descriptors is incorporated in a support vector machine (libsvm) to predict the (sub-)pocket druggability score (values are between zero and one). The higher the score, the more druggable the pocket is estimated to be.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/dogsitescorer.htmldogsitescorerbiotools:dogsitescorerWeb APIWeb servicehttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0123Protein propertiesMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFsmall molecule binding site detection and druggability assessmenthttps://proteins.plusServiceA web service to run DoGSiteScorer calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://proteins.plus/help/dogsite_restServiceA web API to run DoGSiteScorer calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://proteins.plus/help/indexGeneral10.1021/ci100241y20945875MethodPrimary10.1093/bioinformatics/bts31022628523MethodProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderDoGSite3DoGSite3 was developed for predicting robust and reliable small molecule binding sites and computing their geometrical and chemical descriptors. It is based on the grid-based DoGSite algorithm for predicting pockets and their sub-pockets. The new tool is largely rotation- and translation-invariant due to a normalization procedure before binding site prediction. Known ligands in the structure can be used to bias the grid by sufficiently buried ligand fragments. The output encompasses novel chemical binding site descriptors considering solvent accessibility. Compared to its predecessor, it shows increased robustness through comprehensive parameter optimization. DoGSite3 runs finish within seconds.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/dogsite3.htmldogsite3biotools:dogsite3Command-line toolWeb APIWeb servicehttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0123Protein propertiesMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFsmall molecule binding site detectionhttps://proteins.plusServiceA web service to run DoGSite3 calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://proteins.plus/help/dogsite3_restServiceA web API to run DoGSite3 calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://uhh.de/naomiSoftware catalogueLink to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneralgeomineusedBy10.1021/acs.jcim.3c0033637130052PrimaryProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderOBIToolsSet of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.https://git.metabarcoding.org/obitools/obitools/wikis/homeobitoolsbiotools:obitoolsCommand-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_3168SequencingLinuxWindowsMacPythonhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/obitools-scripts-and-library-for-sequence-analysis.htmlSoftware cataloguehttp://metabarcoding.org//obitools/doc/welcome.html#installing-the-obitoolsGeneral10.1111/1755-0998.1242825959493Eric Coissaceric.coissac@inria.frhttp://metabarcoding.org/obitoolsPersonPrimary contactPredictProteinPredictProtein is a protein sequence analysis and structure prediction tool. Users provide a protein sequence, and PredictProtein reports similar sequences, PROSITE sequence motifs, and various types of structure prediction information. You can also use META PredictProtein to submit a sequence to one web form and query several other servers at once, retrieving the results by e-mail.http://ppopen.rostlab.orgpredictproteinbiotools:predictproteinWeb applicationhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0166Protein structural motifs and surfaceshttp://edamontology.org/topic_0078ProteinsLinuxWindowsMachttp://edamontology.org/operation_0468Protein secondary structure prediction (helices)http://edamontology.org/operation_0303Protein fold recognitionhttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://edamontology.org/operation_0474Protein structure predictionhttps://open.predictprotein.org/tutorialsGeneral10.1093/nar/gkg57212824314PMC16897810.1093/nar/gkh37715215403PMC44151510.1093/nar/gkg50812824312PMC168915PredictProtein Supporthelp@predictprotein.orgPersonPrimary contactSNAPThe Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.https://korflab.ucdavis.edu/software.htmlsnapbiotools:snapCommand-line toolhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_3053GeneticsLinuxChttp://edamontology.org/operation_2454Gene predictionhttps://www.mybiosoftware.com/snap-20130216-gene-prediction-tool.htmlSoftware cataloguehttps://korflab.ucdavis.edu/software.htmlGeneral10.1186/1471-2105-5-5915144565PMC421630ifkorf@ucdavis.eduhttps://korflab.ucdavis.edu/PersonPrimary contactFlavoTyperFlavoTyper is a bioinformatics tool that performs in silico serotyping of Flavobacterium psychrophilum genome assemblies.https://forge.inrae.fr/eric.duchaud/flavotyperflavotyperbiotools:flavotyperCommand-line toolWeb servicehttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_3397Veterinary medicineMacLinuxPythonApache-2.0EmergingOpen accesshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_0925Sequence assemblyhttp://edamontology.org/format_1929FASTAhttps://flavotyper-125bcf.pages-forge.inrae.fr/User manualMONAI LabelMONAI Label is an intelligent open source image labeling and learning tool that enables users to create annotated datasets and build AI annotation models for clinical evaluation. MONAI Label enables application developers to build labeling apps in a serverless way, where custom labeling apps are exposed as a service through the MONAI Label Server.https://monai.readthedocs.io/projects/label/en/latest/monai_labelbiotools:monai_label0.8.5Web applicationhttp://edamontology.org/topic_3303MedicineLinuxWindowsPythonApache-2.0MatureFree of chargehttp://edamontology.org/operation_3553Image annotation10.1007/978-3-031-17027-0_2DeepConsensusDeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.https://github.com/google/deepconsensusdeepconsensusbiotools:deepconsensus1.2.0Command-line toolhttp://edamontology.org/topic_3307Computational biologyLinuxPythonBSD-3-ClauseMatureFree of chargehttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_0850Sequence setdeepconsensus run --subreads_to_ccs=shard_id.subreads_to_ccs.bam --ccs_bam=shard_id.ccs.bam --checkpoint=model/checkpoint --output=shard_id.output.fastq10.1038/s41587-022-01435-736050551DAZZ_DBA database system designed to store, organize, and manage large-scale nucleotide sequencing read data (like PacBio reads) for the Dazzler genome assemblerhttps://github.com/thegenemyers/DAZZ_DBdazz_dbbiotools:dazz_db1.0Command-line toolhttp://edamontology.org/topic_3307Computational biologyLinuxCOtherLegacyFree of chargehttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/data_2887Nucleic acid sequence record1. fasta2DB [-v] <path:db> ( -f<file> | -i[<name>] | <input:fasta> ... )SigmaCVAuto-generates clean, customizable academic CVs from open research data (OpenAlex, ORCID, Crossref, DataCite, Open Editors Plus). A single canonical CV object drives every output format (HTML, PDF, DOCX, LaTeX, Markdown); citations render through CSL; and the account holder is matched by persistent identifier (ORCID / OpenAlex ID) rather than name string. Free for individuals, open-source, and FAIR by design.https://sigmacv.orgsigmacvbiotools:sigmacv0.1.0Web applicationMacWindowsLinuxJavaScriptTypeScriptApache-2.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_0226Annotationhttps://github.com/BasileChretien/sigmacvRepositoryhttps://github.com/BasileChretien/sigmacv/issuesIssue trackerhttps://github.com/BasileChretien/sigmacvSource codehttps://github.com/BasileChretien/sigmacv#readmeGeneral10.5281/zenodo.20594123Other0.1.0Basile Chrétienchretien.basile.jean.bernard.u4@s.mail.nagoya-u.ac.jphttps://orcid.org/0000-0002-7483-2489DeveloperMaintainerPrimary contactPDB-REDO databank of optimised macromolecular structuresDatabank of optimised macromolecular structures. PDB-REDO entries are refined, rebuilt and validated with one consistent protocol using the equivalent entry in the Protein Data Bank and its experimental data. PDB-REDO entries typically have higher structural quality and a better fit to the experimental data.https://pdb-redo.eupdb-redobiotools:pdb-redoDatabase portalhttp://edamontology.org/topic_0081Structure analysisLinuxWindowsMacFreeware3D-BioInfo3D-BioInfo-Nucleic-AcidDRCAT3D-BioInfo-Protein-Ligand-InteractionsINSTRUCT3D-BioInfo-Structure-FunctionMatureFree of chargeOpen accessData3D-BioInfohttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1127PDB IDhttps://github.com/PDB-REDO/pdb-redo-mainRepositoryRepository for main software pipelinehttps://github.com/PDB-REDO/libpdb-redoRepositoryLibrary code for pdb-redo toolshttps://github.com/PDB-REDO/pdb-redo-session-managerRepositoryRepository for the web interface including the APIhttps://pdb-redo.eu/download-info.htmlDownloads pagehttps://pdb-redo.euGeneral10.1107/s090744491105451522505269PMC332260810.1107/s002188980900878422477769PMC324681910.1107/s090744490803759119171973PMC263163110.1107/s205225251801055230224962PMC612664810.1002/pro.335329168245PMC5818736Method7Algorithms for homology restrains; new databank10.1093/bioinformatics/btr59022034521PMC3232375MethodAlgorithms for model rebuilding10.1016/j.jmb.2016.02.00226869101MethodAlgorithms for correction and completion of N-glycosylation sites10.1107/s205979831601303627710932PMC505313710.1107/s205979831900387530988258PMC6465985Robbie P. Joostenr.joosten@nki.nlhttps://orcid.org/0000-0002-2323-2686PersonPrimary contactDeveloperGert Vriendvriend@cmbi.ru.nlPersonProject initiatorAnastassis Perrakisa.perrakis@nki.nlhttps://orcid.org/0000-0002-1151-6227PersonPrimary contactMaarten Hekkelmanm.hekkelman@nki.nlPersonDeveloperBart van BeusekomPersonContributorKrista JoostenPersonContributorNetherlands Organization for Scientific Research (NWO)Funding agencyVarious grants (Veni, Vidi, TOP)West-Life Horizon 2020ConsortiumiNEXTConsortiumWouter TouwPersonContributorThe Netherlands Cancer InstituteInstituteProviderCCP4https://www.ccp4.ac.ukProjectContributorFinancial and other supportGRNsightWeb application and service for visualizing small- to medium-scale models of gene regulatory networks. It automatically lays out either an unweighted or weighted network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges and has general applicability.http://dondi.github.io/GRNsight/grnsightbiotools:grnsight7.8.0Web applicationhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0204Gene regulationLinuxWindowsMacJavaScriptBSD-3-ClauseMatureFree of chargehttp://edamontology.org/operation_1781Gene regulatory network analysishttp://edamontology.org/operation_3083Pathway or network visualisationGRNsight automatically lays out a network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. When a user uploads a spreadsheet with an unweighted adjacency matrix, GRNsight automatically lays out the graph using black lines and pointed arrowheads. When a user uploads a spreadsheet with a weighted adjacency matrix, GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (positive for activation or negative for repression) and magnitude of the weight parameter. Nodes are rectangular and support gene labels of up to 12 characters. The edges are arcs, which become straight lines when the nodes are close together. Self-regulatory edges are indicated by a loop on the lower-right side of a node. Visualizations can be modified by sliders that adjust D3.js's force graph layout parameters and through manual node dragging.https://github.com/dondi/GRNsightRepositoryhttps://github.com/dondi/GRNsight/archive/refs/heads/main.zipSource codehttp://dondi.github.io/GRNsight/documentation.htmlGeneral10.7717/peerj-cs.85Other10.5281/zenodo.7411630OtherAlex MillerPersonDeveloperJia Celyne GarciaPersonDeveloperCindy TongPersonDeveloperAmelie DinhPersonDeveloperMilka ZekariasPersonDeveloperNgoc Kim Ngan TranPersonDeveloperCecilia ZaragozaPersonDeveloperA’Kaia PhelpsPersonDeveloperOna O. IgbinedionPersonDeveloperAhmad R. MersaghianPersonDeveloperIan M. GreenPersonDeveloperLauren L. AmparoPersonDeveloperAlexia M. FillerPersonDeveloperKevin B. PattersonPersonDeveloperJohn L. LopezPersonDeveloperJustin Kyle T. TorresPersonDeveloperEileen ChoePersonDeveloperJen ShinPersonDeveloperMihir SamdarshiPersonDeveloperAnindita VarshneyaPersonDeveloperNicole A. AnguianoPersonDeveloperBritain J. SouthwickPersonDeveloperBen G. FitzpatrickPersonDeveloperLoyola Marymount UniversityInstituteProviderNSF award 0921038; LMU Rains Research Assistant Program; LMU Summer Undergraduate Research ProgramFunding agencyContributorlmu.eduInstituteProviderKam D. Dahlquistkdahlquist@lmu.eduPersonPrimary contactJohn David N. Dionisiodondi@lmu.eduhttps://orcid.org/0000-0001-8655-4693PersonPrimary contactMol Biology ToolsMol Biology Tools is a free browser-based collection of molecular biology utilities for routine sequence analysis, primer design, Sanger sequencing primer planning, cloning setup, and wet-lab calculations. The site includes tools for PCR primer design, Sanger primer design and primer walking, primer binding checks, restriction site analysis, reverse complement generation, ORF and protein translation, codon optimization, ligation calculations, molarity calculations, dilution calculations, and multi-solute solution recipe preparation. The tools run in the browser and are intended for quick experimental planning without requiring logins or server-side sequence upload.https://molbiologytools.com/mol_biology_toolsbiotools:mol_biology_toolsWeb servicehttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3297Biotechnologyhttp://edamontology.org/topic_3895Synthetic biologyWindowsMaciOSLinuxAndroidJavaScriptProprietaryEmergingFree of chargehttp://edamontology.org/operation_0308PCR primer designhttps://molbiologytools.com/Software catalogueRepositoryLanding page with all tools listed.https://molbiologytools.com/faqOtherSearchable FAQ covering primer design, Sanger sequencing, restriction sites, sequence checks, molarity, dilution, ligation, and connected tool workflows.https://molbiologytools.com/primer_designServicePCR primer design tool for raw DNA, FASTA, or GenBank templates, with primer length or target Tm modes and optional restriction-enzyme overhang planning.https://molbiologytools.com/primer_binding_checkerServicePrimer binding checker for linear or circular DNA templates, including binding positions, amplicon size, strand direction, and product checks.https://molbiologytools.com/restriction_site_analyzerServiceRestriction enzyme site analyzer for linear or circular DNA, FASTA, or GenBank input, with enzyme cut-site detection and sequence-to-primer workflow links.https://molbiologytools.com/molarity_calculatorServiceMolarity calculator and multi-solute recipe builder for lab solutions, molecular weight, percent w/v, compound search, 1X recipes, and stock-multiplier outputs.https://molbiologytools.com/ligation_calculatorServiceDNA ligation calculator for cloning setup, vector mass, insert length, insert-to-vector molar ratio, and insert mass calculation.https://molbiologytools.com/help_guidesQuick start guideDr. Rohit P Jamesrpjscience@gmail.comhttps://orcid.org/0009-0003-9347-2014PersonPrimary contactDeveloperMaintainerProviderDr. Rohit P James graduated from IIT Bombay. He works on biocatalysis and enzyme engineering.AutoDock VinaAutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.http://vina.scripps.edu/autodock_vinabiotools:autodock_vina1.1.2RRID:SCR_011958rridDesktop applicationhttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_2275Molecular dockingLinuxWindowsMacC++http://edamontology.org/operation_0478Molecular dockinghttp://www.mybiosoftware.com/autodock-vina-1-1-2-molecular-docking-virtual-screening-program.htmlSoftware cataloguehttp://vina.scripps.edu/manual.htmlUser manual10.1002/jcc.2133419499576PMC3041641Primaryhttp://olegtrott.com/PersonPrimary contactRExPrimerA web application that provides many functionalities for improved PCR primer design.http://www4a.biotec.or.th/rexprimer/rexprimerbiotools:rexprimerWeb applicationhttp://edamontology.org/topic_3511Nucleic acid sites, features and motifshttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0632Probes and primersLinuxWindowsMacPythonhttp://edamontology.org/operation_0308PCR primer designhttp://www.mybiosoftware.com/rexprimer-web-based-application-for-primer-design.htmlSoftware cataloguehttp://www4a.biotec.or.th/rexprimer/help/User_Manual.htmlUser manual10.1186/1471-2164-10-s3-s419958502PMC2788391chumpol.nga@biotec.or.thhttp://www4a.biotec.or.th/GIPersonPrimary contactEGAEuropean genome-phenome Archive (EGA) - service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.https://ega-archive.org/egabiotools:egaWeb APIWeb applicationDatabase portalhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0607Laboratory information managementhttp://edamontology.org/topic_3263Data securityhttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacJavaRD-connectRare DiseaseMatureFree of chargeOpen accessDataSpainhttp://edamontology.org/operation_3431Depositionhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/data_2383EGA accessionhttps://ega-archive.org/General10.1038/ng.3312PrimaryEMBL-EBI DatabasesInstituteProviderhelpdesk@ega-archive.orgPersonPrimary contactPHYLIPComprehensive set of programs for phylogenetic analyses; available for PC and Mac; source code available for easy compiling in UNIX.http://evolution.genetics.washington.edu/phylip.htmlphylipbiotools:phylipRRID: SCR_006244rridWeb applicationhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_3300PhysiologyLinuxWindowsMacCBSD-3-ClauseAnimal and Crop Genomicshttp://edamontology.org/operation_0552Phylogenetic tree bootstrappinghttp://edamontology.org/operation_0557Phylogenetic tree distances calculationhttp://edamontology.org/operation_0547Phylogenetic tree generation (maximum likelihood and Bayesian methods)http://edamontology.org/operation_0545Phylogenetic tree generation (parsimony methods)http://edamontology.org/operation_0324Phylogenetic tree analysishttp://evolution.genetics.washington.edu/phylip/phylip.htmlGeneral10.1371/journal.pone.001399921085574PMC298155310.1385/1-59259-192-2:24310547839Joe Felsensteinjoe@gs.washington.eduhttp://evolution.gs.washington.edu/felsenstein.htmlPersonPrimary contactCalibraCurveA highly useful and flexible tool for calibration of targeted MS‐based measurements. CalibraCurve enables an automated batch-mode determination of dynamic linear ranges and quantification limits for both targeted proteomics and similar assays. The software uses a variety of measures to assess the accuracy of the calibration and provides intuitive visualizations.https://github.com/mpc-bioinformatics/CalibraCurvecalibracurvebiotools:calibracurve2.0WorkflowScriptDesktop applicationPlug-inhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3678Experimental design and studiesLinuxWindowsMacRBSD-3-ClauseBioInfra.Protde.NBICUBiMed.RUBMatureFree of chargeOpen accessToolsProteomicsGermanyhttp://edamontology.org/operation_2945Analysishttp://edamontology.org/data_2526Text datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/operation_0337Visualisationhttps://github.com/mpc-bioinformatics/CalibraCurveRepositoryhttps://github.com/mpc-bioinformatics/CalibraCurveDownloads page2.0https://github.com/mpc-bioinformatics/CalibraCurveInstallation instructionsCitation instructionsGeneralUser manualTraining materialTerms of use10.1002/pmic.20190014332086983Primary2.0PD Dr. Martin Eisenachermartin.eisenacher@rub.dePersonProviderPrimary contactIf contacting use "SPARROW" in subject line to avoid mail deluge.de.NBIhttps://www.denbi.de/ProjectProviderMaintainerSupportService provision and maintenance funded by de.NBI.Dr. Michael Kohlmichael.kohl@rub.dePersonDevelopermaeparsermaeparser is a parser for Schrodinger Maestro files.https://github.com/schrodinger/maeparsermaeparserbiotools:maeparserv1.3.3Libraryhttp://edamontology.org/topic_1317Structural biologyLinuxMacC++MITMaturehttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/data_0883StructureLongTRTandem repeat genotyping with long reads, being a modified version of HipSTR.https://github.com/gymrek-lab/LongTRLongTRbiotools:LongTRv1.2Command-line toolhttp://edamontology.org/topic_0797Comparative genomicshttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_4056Long-read sequencingLinuxMacPythonC++CShellGPL-2.0Maturehttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_3003BEDhttp://edamontology.org/format_2572BAM10.1186/s13059-024-03319-238965568PMC11229021influentialA comprehensive R package for identifying and ranking influential nodes in biological and other complex networks. The package implements the Integrated Value of Influence (IVI), Experimental data-based Integrative Ranking (ExIR), SIRIR, and numerous network centrality measures, enabling network topology analysis, influential node detection, feature prioritization, and candidate biomarker discovery. It also provides functions for network reconstruction, centrality assessment, visualization, and analysis of relationships between centrality measures.https://asalavaty.github.io/influential/influentialbiotools:influentialLibraryhttp://edamontology.org/topic_3307Computational biologyLinuxWindowsMacRGPL-3.0Maturehttp://edamontology.org/operation_2495Expression analysishttp://edamontology.org/operation_3927Network analysisIdentification of influential nodes
Network centrality analysis
Feature prioritization and ranking
Network reconstruction
Biomarker candidate discovery
Topological network analysis
Integrative rankingivi()
exir()https://github.com/asalavaty/influentialRepositorySource codehttps://asalavaty.github.io/influential/OtherDocumentationhttps://github.com/asalavaty/influentialDownloads pagehttps://cran.r-project.org/package=influentialDownloads pageCRAN Versionhttps://asalavaty.github.io/influential/articles/Vignettes.htmlUser manual10.1016/j.patter.2020.10005233205118PMC7660386PrimaryCellSeekrCellSeekr is a customizable discovery platform for the exploration and identification of immune signatures in a variety of tumors, patient and treatment settings through scRNAseq data analysis.http://cellseekr.comcellseekrbiotools:cellseekrWeb servicehttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3400Allergy, clinical immunology and immunotherapeuticshttp://edamontology.org/topic_0804Immunologyhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_2229Cell biologyMacWindowsLinuxFree of chargeOpen accesshttp://edamontology.org/operation_3800RNA-Seq quantificationhttp://edamontology.org/operation_0313Expression profile clusteringhttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/operation_0337Visualisationhttp://cellseekr.com/documentationUser manualSandro Matoseviccontact@cellseekr.compathogensurveillancePathogensurveillance is a population genomics pipeline for pathogen identification, variant detection, and biosurveillance. The pipeline accepts paths to raw reads for one or more organisms and creates reports in the form of an interactive HTML document. Significant features include the ability to analyze unidentified eukaryotic and prokaryotic samples, creation of reports for multiple user-defined groupings of samples, automated discovery and downloading of reference assemblies from NCBI RefSeq, and rapid initial identification based on k-mer sketches followed by a more robust multi gene phylogeny and SNP-based phylogeny.https://nf-co.re/pathogensurveillance/pathogensurveillancebiotools:pathogensurveillance1.1.0Command-line toolhttp://edamontology.org/topic_0622GenomicsLinuxGroovyRBashMITEmergingFree of chargeOpen accesshttps://github.com/nf-core/pathogensurveillanceRepositoryhttps://github.com/nf-core/pathogensurveillance/issuesIssue trackerhttps://github.com/nf-core/pathogensurveillance/archive/refs/tags/1.1.0.tar.gzSource code1.1.0https://nf-co.re/pathogensurveillanceUser manualCluster based harmonization (EUCAIM-SW-044_T-01-03-006)The tool is designed to perform radiomics harmonization on large and heterogeneous datasets, where the risk of over-harmonization is present. Instead of directly applying harmonization based on predefined batch labels, the tool first identifies groups of batches that share similar characteristics through clustering of the radiomics data. It then performs harmonization using these cluster-derived labels. The tool allows the harmonization of radiomics variables using two methods: (1) original ComBat (Rabinovic, 2007) method, where each original batch group is considered for the harmonization process and (2) cluster-based ComBat method, where batch groups with similar radiomics characteristics form clusters and the latter are being considered for the harmonization process.https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/cluster_based_harmonization/info-tabcluster_based_harmonizationbiotools:cluster_based_harmonization1.1.0Libraryhttp://edamontology.org/topic_0219Data curation and archivalhttp://edamontology.org/topic_3382ImagingMacWindowsLinuxPythonCC-BY-NC-ND-4.0EUCAIMEmergingFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_3432Clusteringhttp://edamontology.org/data_2526Text datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3620xlsxhttp://edamontology.org/data_2526Text datahttp://edamontology.org/format_3464JSONdocker run --rm --cpus CPUS -v input_path:/input -v output_path:/output -v config_path:/config harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0 --config /config/config.jsonhttp://edamontology.org/operation_3432Clusteringhttp://edamontology.org/data_2526Text datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3620xlsxdocker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0 --file_path /input/data.xlsx --identifier patient_id --start_col original_shape_Elongation --end_col lbp-3D-k_ngtdm_Strength --batch_col software_versions --output_dir /output/results --min_clusters 2 --max_clusters 100 --results full --approach soft --small_groups mergehttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/cluster_based_harmonization/artifacts-tabSoftware cataloguehttps://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/Social mediahttps://drive.eucaim.cancerimage.eu/s/Kz3jfQYQZjezpxKUser manualhttps://drive.eucaim.cancerimage.eu/s/5bMA2jsZTfS8eoZTerms of usehttps://www.youtube.com/watch?v=0GJqNJv-Qf8&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=31Training materialhttps://drive.eucaim.cancerimage.eu/s/LkczHCMZH5nd8QRGeneralGIBI230 - HULAFEeucaim_project@iislafe.esInstituteProviderAikaterini Vrakaaikaterini_vraka@iislafe.eshttps://orcid.org/0000-0001-5984-904XPersonDeveloperPedro-Miguel Martínez-Gironéspedromiguel_martinez@iislafe.eshttps://orcid.org/0000-0002-9506-9451PersonPrimary contactSupport2D Digital Mammography Harmonization (EUCAIM-SW-046_T-01-03-008)This preprocessing tool is design for 2D digital mammograms in DICOM format. It standardizes and harmonizes images through a configurable pipeline that includes spatial reorientation, pseudo-3D stacking, isotropic resampling, intensity normalization, optional denoising, contrast enhancement, and mask processing (if available).https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/2d_digital_mammography_harmonization/info-tab2d_digital_mammography_harmonizationbiotools:2d_digital_mammography_harmonization1.1.0Libraryhttp://edamontology.org/topic_0219Data curation and archivalhttp://edamontology.org/topic_3316Computer sciencehttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_3071Data managementLinuxMacWindowsPythonCC-BY-NC-ND-4.0EUCAIMEmergingFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_3464JSONdocker run -it --rm --name container_name -v "<input_path>:/input" -v "<output_path>:/output" -v "<config_path>:/config" harbor.eucaim.cancerimage.eu/processing-tools/2d_digital_mammography_harmonization:1.1.0 /app/entrypoint.sh --config /config/config.jsonhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formatCommand Argumentsdocker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processing-tools/2d_digital_mammography_harmonization:1.1.0 --input_directory dataset_id --output_directory gaussian_output --num_workers 4 --series_number 2301101 --series_description_suffix _harmonized --zscore_enabled true --zscore_p_low 1.0 --zscore_p_high 99.0 --denoise_method gaussian --gaussian_ksize 3 --gaussian_sigma 0.8 --clahe_enabled true --clahe_clip_limit 0.01https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/2d_digital_mammography_harmonization/artifacts-tabSoftware cataloguehttps://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/Social mediahttps://drive.eucaim.cancerimage.eu/s/CC3yJTjPz9N7GggUser manualhttps://drive.eucaim.cancerimage.eu/s/rdHWqMkNf7frQRYTerms of usehttps://www.youtube.com/watch?v=IrZhMp2lB7g&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=13Training materialGIBI230 - HULAFEeucaim_project@iislafe.esManuel Marfil-Trujillomanuel_marfil@iislafe.esPersonDeveloperPedro-Miguel Martinez-Gironespedromiguel_martinez@iislafe.eshttps://orcid.org/0000-0002-9506-9451PersonPrimary contactSupportCarina Soler-Ponscarina_soler@iislafe.eshttps://orcid.org/0009-0000-2991-1391PersonSupportCT-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-022_T-01-02-005)The tool performs by deep learning an automatic segmentation of the possible neuroblastoma tumours on Contrast Enhanced CT images (CE-CTs). Model architecture is Unet-based with residual operations, atrous dilation convolution and specific batch generator. It applies preprocessing steps as RAS conversion, resizing, z-score normalization, patching; and postprocessing operations. It takes DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ct-based_neuroblastoma_tumour_detection_and_segmentation/info-tabct-based_neuroblastoma_tumour_detection_and_segmentationbiotools:ct-based_neuroblastoma_tumour_detection_and_segmentation2.0.0Libraryhttp://edamontology.org/topic_3365Data architecture, analysis and designhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3474Machine learningMacWindowsLinuxPythonCC-BY-NC-ND-4.0EUCAIMMatureFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/format_3549niihttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_3752CSVdocker run --rm --gpus all \
-v /path/to/input:/input \
-v /path/to/output:/output \
harbor.eucaim.cancerimage.eu/processing-tools/ct-based_neuroblastoma_tumour_detection_and_segmentation:2.0.0 \
--series_csv /output/config/series_to_segment.csv \
--output_dir /outputhttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ct-based_neuroblastoma_tumour_detection_and_segmentation/info-tabSoftware cataloguehttps://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/Social mediahttps://drive.eucaim.cancerimage.eu/s/GxJrJPrYBnzecqTTerms of usehttps://www.youtube.com/watch?v=JQ0dtAE_6uc&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=37Training material10.3390/app11083508UsageGIBI230 - HULAFEeucaim_project@iislafe.esInstituteProviderPedro-Miguel Martinez-Gironespedromiguel_martinez@iislafe.eshttps://orcid.org/0000-0002-9506-9451PersonPrimary contactDeveloperSupportAdrian Galiana-Borderaadrian_galiana@iislafe.eshttps://orcid.org/0000-0002-8324-8284PersonDeveloperCarina Soler-Ponscarina_soler@iislafe.eshttps://orcid.org/0009-0000-2991-1391PersonSupportLuis Marti-Bonmatiluis_marti@iislafe.eshttps://orcid.org/0000-0002-8234-010XPersonProviderMR-based glioblastoma tumour detection and segmentation (EUCAIM-SW-021_T-01-02-004)The tool performs an automatic segmentation of the possible glioblastoma tumours on MRI images and its subregions: necrosis (Intratumoral necrotic core), edema (Peritumoral vasogenic edema), enhancing (Contrast-enhancing tumor region), total (Total tumor including edema and necrosis by a single model) and total-fused (Total tumor fusioning of necrosis+edema+enhancing). It applies preprocessing steps as skull stripping, intra-patient registration, z-score normalization, patching, among others. It takes DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/info-tabmr-based_glioblastoma_tumour_detection_and_segmentationbiotools:mr-based_glioblastoma_tumour_detection_and_segmentation2.1.1Libraryhttp://edamontology.org/topic_3365Data architecture, analysis and designhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3474Machine learningMacWindowsLinuxPythonCC-BY-NC-ND-4.0EUCAIMMatureFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/format_3549niihttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_3752CSVdocker run --rm --gpus all \
-v /path/to/input:/input \
-v /path/to/output:/output \
harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest \
--series-selector /input/config/series.csv \
--target total \
--emit-config truehttp://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/format_3549niihttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_3752CSVdocker run --rm --gpus all \
-v /path/to/input:/input \
-v /path/to/output:/output \
harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest \
--series-list '[{"dataset_id":"DS001","patient_id":"PAT001","study_id":"ST001","series_path":"/input/DICOM/DS001/PAT001/ST001/T1_POST"}]' \
--target total-fused \
--emit-config truehttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/info-tabSoftware cataloguehttps://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/Social mediahttps://pubmed.ncbi.nlm.nih.gov/38849632/Generalhttps://drive.eucaim.cancerimage.eu/s/otrYTickHjDxnkPTerms of usehttps://www.youtube.com/watch?v=8_OJPTQUKAw&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=22Training material10.1007/s11548-024-03205-zPrimaryGIBI230 - HULAFEeucaim_project@iislafe.esInstituteProviderMaria Beser-Roblesmaria_beser@iislafe.eshttps://orcid.org/0000-0002-0072-5525PersonDeveloperPedro-Miguel Martinez-Gironespedromiguel_martinez@iislafe.eshttps://orcid.org/0000-0002-9506-9451PersonPrimary contactDeveloperSupportAdrian Galiana-Borderaadrian_galiana@iislafe.eshttps://orcid.org/0000-0002-8324-8284PersonDeveloperCarina Soler-Ponscarina_soler@iislafe.eshttps://orcid.org/0009-0000-2991-1391PersonSupportLeonor Cerda-Alberichleonor_cerda@iislafe.eshttps://orcid.org/0000-0002-5567-4278PersonProviderLuis Marti-Bonmatiluis_marti@iislafe.eshttps://orcid.org/0000-0002-8234-010XPersonProviderMR-based DIPG tumour detection and segmentation (EUCAIM-SW-020_T-01-02-003)The tool performs an automatic segmentation of the possible DIPG tumours on MR images. DIPG (Diffuse Intrinsic Pontine Glioma), or more recently, DMG (Diffuse Midline Glioma) is a H3 K27M–mutant pediatric brainstem cancer detected in T1W and Flair/T2-weighted magnetic resonance images. The tool includes a complete workflow from DICOM images to DICOM seg tumoral masks.https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/info-tabmr-based_dipg_tumour_detection_and_segmentationbiotools:mr-based_dipg_tumour_detection_and_segmentation2.0.0Libraryhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3365Data architecture, analysis and designMacWindowsLinuxPythonCC-BY-NC-ND-4.0EUCAIMMatureFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/format_3549niihttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3464JSONdocker run --rm --gpus all \
-v /path/to/input:/input \
-v /path/to/output:/output \
harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest \
--series-selector /input/config/series.csvhttp://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/format_3549niidocker run --rm --gpus all \
-v /path/to/input:/input -v /path/to/output:/output harbor.eucaim.cancerimage.eu/processing-tools/mr-based_dipg_tumour_detection_and_segmentation:latest \
--json-args '{"dataset_id":"DS1","patient_id":"P1","study_id":"S1","sequences":{"T1w":"/input/DICOM/DS1/P1/S1/T1","FLAIR":"/input/DICOM/DS1/P1/S1/FLAIR"}}'https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/info-tabSoftware cataloguehttps://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/Social mediahttps://link.springer.com/article/10.1007/s10278-025-01557-9Generalhttps://drive.eucaim.cancerimage.eu/s/5CL2H8tyMDzFHexTerms of usehttps://www.youtube.com/watch?v=f3DPS56z6oI&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=36Training material10.1007/s10278-025-01557-9PrimaryGIBI230 - HULAFEeucaim_project@iislafe.esInstituteProviderMatias Fernandez-Patonmatias_fernandez@iislafe.eshttps://orcid.org/0000-0001-9374-1411PersonDeveloperPedro-Miguel Martinez-Gironespedromiguel_martinez@iislafe.eshttps://orcid.org/0000-0002-9506-9451PersonPrimary contactDeveloperDocumentorSupportAdrian Galiana-Borderaadrian_galiana@iislafe.eshttps://orcid.org/0000-0002-8324-8284PersonDeveloperCarina Soler-Ponscarina_soler@iislafe.eshttps://orcid.org/0009-0000-2991-1391PersonDocumentorSupportLeonor Cerda-Alberichleonor_cerda@iislafe.eshttps://orcid.org/0000-0002-5567-4278PersonProviderLuis Marti-Bonmatiluis_marti@iislafe.eshttps://orcid.org/0000-0002-8234-010XPersonProviderMR-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-019_T-01-02-002)This tool is specifically designed and validated for automated detection and segmentation of neuroblastic tumours in T2-weighted magnetic resonance images (T2-MR) using deep learning. It processes DICOM or NIfTI input data and outputs in NIFTI or DICOM SEG.
TRAINING & VALIDATION COHORTS:
Initial Development (Veiga-Canuto 2022):
-Training: 106 patients, 5-fold CV (median DSC 0.965 ± 0.018).
-Internal validation: 26 patients (median DSC 0.918 ± 0.067).
-Sources: La Fe (Spain), SIOPEN HR-NBL1/LINES, St. Anna (Austria), Pisa (Italy).
-Mean age: 37.6 ± 39.3 months.
-Median tumor volume: 116,518 mm³.
External Validation (Veiga-Canuto 2023):
-300 patients, 535 independent T2 MRI scans (486 at diagnosis, 49 post-chemotherapy).
-Performance: median DSC 0.997 (0.944–1.000), 94% successful detection.
-Sources: 12 European countries (HR-NBL1/SIOPEN 119, LINES/SIOPEN 107, German Registry 62, others 12).
-Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105), Canon (3).https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/info-tabmr-based_neuroblastoma_tumour_detection_and_segmentationbiotools:mr-based_neuroblastoma_tumour_detection_and_segmentation2.0.0Libraryhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3365Data architecture, analysis and designMacWindowsLinuxPythonCC-BY-NC-ND-4.0EUCAIMMatureFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/format_3549niihttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3464JSONdocker run --rm \
-v "<input_path>:/input" \
-v "<output_path>:/output" \
--gpus all \
harbor.eucaim.cancerimage.eu/processing-tools/mr_based_neuroblastoma_tumour_detection_and_segmentation:2.0.0 \
--mode dicom-seg \
--series-selector /output/config/series_to_segment.csv \
--seg-series-number 2302001 \
--seg-algorithm-name "nnUNet_Neuroblastoma_Primage_training" \
--seg-coordinating-center "EUCAIM Consortium" \
--keep-nifti falsehttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/info-tabSoftware cataloguehttps://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/Social mediahttps://drive.eucaim.cancerimage.eu/s/tS2W8nb38Zs2ZzKUser manualhttps://www.mdpi.com/2072-6694/14/15/3648Generalhttps://drive.eucaim.cancerimage.eu/s/44BxMSNpxwgsZiETerms of usehttps://www.youtube.com/watch?v=c7XOEGRA9aQ&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=12Training material10.3390/cancers14153648Primary10.3390/cancers15051622PrimaryGIBI230 - HULAFEeucaim_project@iislafe.esInstituteProviderLeonor Cerda-Alberichleonor_cerda@iislafe.eshttps://orcid.org/0000-0002-5567-4278PersonDeveloperDiana Veiga Canutodianaveigac@gmail.comhttps://orcid.org/0000-0002-6048-2940PersonDeveloperPedro-Miguel Martinez-Gironespedromiguel_martinez@iislafe.eshttps://orcid.org/0000-0002-9506-9451PersonPrimary contactSupportDocumentorDeveloperCarina Soler-Ponscarina_soler@iislafe.eshttps://orcid.org/0009-0000-2991-1391PersonSupportDocumentorLuis Marti-Bonmatiluis_marti@iislafe.eshttps://orcid.org/0000-0002-8234-010XPersonProviderDenoising-Inhomogeneity Correction Tool (EUCAIM-SW-015_T-01-01-015)The tool is designed to perform a customisable image pre-processing to reduce noise and inhomogeneity field effect, thus improving image quality and reproducibility of radiomics features. This tool consists of two independent steps: one for denoising using one of the 5 integrated filters (Bilateral Filter, Anisotropic Diffusion Filter (ADF), Curvature Flow Filter (CFF), SUSAN and Non Local Means (NLM)), and another for the ANTs N4 and another for the ANT's N4 bias correction filter. The parameter configuration of this tool has been optimised for TW1, T2W, DWI and DCE sequences in neuroblastoma (NB) and paediatric brain tumours, but it can also be configured with some of their parameters using a JSON parameter configuration file.https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/info-tabdenoising-inhomogeneity_correction_toolbiotools:denoising-inhomogeneity_correction_tool1.1.0Libraryhttp://edamontology.org/topic_0219Data curation and archivalMacWindowsLinuxPythonCC-BY-NC-ND-4.0EUCAIMhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_3464JSONdocker run -it --rm --name container_name -v "<input_path>:/input" -v "<output_path>:/output" -v "<config_path>:/config" harbor.eucaim.cancerimage.eu/processing-tools/denoising_inhomogeneity_correction_tool:1.1.0 --config /config/config.jsonhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formatdocker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processin-tools/denoising_inhomogeneity_correction_tool:1.1.0 --paths /input/Dataset/Patient_1/Study/T1W /input/Dataset/Patient_2/Study/T2W --output /output --series_number 2000 --series_description_suffix "_harmonized" --denoising adf --conductance 0.5 --iterations 3 --time_step 0.0625 --n4 --bspline_size 50 --n4_iterations 50 30 --shrink_factor 2https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/artifacts-tabSoftware cataloguehttps://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/Social mediahttps://drive.eucaim.cancerimage.eu/s/wYJ7Fttnk6Dp7gcUser manualhttps://drive.eucaim.cancerimage.eu/s/oseiKoeFZqwoRCATerms of usehttps://www.youtube.com/watch?v=HkHqFGXGEbo&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=9Training material10.1007/s10278-021-00512-834505958PMC8554919Primary10.1186/s41747-020-00150-932246291PMC7125275GIBI230 - HULAFEeucaim_project@iislafe.esInstituteProviderMatias Fernandez-Patonmatias_fernandez@iislafe.eshttps://orcid.org/0000-0001-9374-1411PersonDeveloperPedro-Miguel Martinez-Gironespedromiguel_martinez@iislafe.eshttps://orcid.org/0000-0002-9506-9451PersonPrimary contactDocumentorSupportCarina Soler-Ponscarina_soler@iislafe.eshttps://orcid.org/0009-0000-2991-1391PersonDocumentorSupportLeonor Cerda-Alberichleonor_cerda@iislafe.eshttps://orcid.org/0000-0002-5567-4278PersonProviderLuis Marti-Bonmatiluis_marti@iislafe.eshttps://orcid.org/0000-0002-8234-010XPersonProviderML model for MR series categorisation (EUCAIM-SW-011_T-01-01-011)A tool based on artificial intelligence that is able to perform a categorisation of MRI series by using standardized DICOM tags. The categorisation includes the type of sequence (e.g. spin echo, gradient echo), the weighting (e.g. T1W, T2W, DCE, ...), the presence of fat suppression and the detection of non-relevant / junk series (e.g. localizers, calibrations, screenshots...).https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/info-tabml_model_for_mr_series_categorisationbiotools:ml_model_for_mr_series_categorisation1.1.0Libraryhttp://edamontology.org/topic_3316Computer sciencehttp://edamontology.org/topic_3077Data acquisitionhttp://edamontology.org/topic_3071Data managementLinuxMacWindowsPythonCC-BY-NC-ND-4.0EUCAIMMatureFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_2990Classificationhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formatdocker run -it --rm --name my-container \
-v "<input_path>:/input" \
-v "<output_path>:/output" \
harbor.eucaim.cancerimage.eu/processing-tools/ml_model_for_mr_series_categorisation:<version> \
--config-string "{'output_name': 'classification_results.json'}"https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tabSoftware cataloguehttps://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/Social mediahttps://drive.eucaim.cancerimage.eu/s/rpm56rD5FfXAHybUser manualhttps://drive.eucaim.cancerimage.eu/s/8r3CzyQXrd7ERFpTerms of usehttps://www.youtube.com/watch?v=gudDCiuJIf8&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=11Training material10.1186/s40537-025-01086-wPrimaryGIBI230 - HULAFEeucaim_project@iislafe.esInstituteProviderArmando Gomis-Mayaarmago@alumni.uv.eshttps://orcid.org/0000-0002-9527-8093PersonDeveloperPedro-Miguel Martinez-Gironespedromiguel_martinez@iislafe.eshttps://orcid.org/0000-0002-9506-9451PersonSupportCarina Soler-Ponscarina_soler@iislafe.eshttps://orcid.org/0009-0000-2991-1391PersonSupportLeonor Cerda-Alberichleonor_cerda@iislafe.eshttps://orcid.org/0000-0002-5567-4278PersonContributorLuis Marti-Bonmatiluis_marti@iislafe.eshttps://orcid.org/0000-0002-8234-010XPersonContributorTime Coherence Tool (EUCAIM-SW-001_T-01-01-001)Tool that aims to validate visually the chronological order and logical consistency of dates associated with a patient's medical history. It generates a timeline visualization for each patient from an Excel file and highlights rule violations.
Status : Containerizedhttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/time_coherence_tool/info-tabtime_coherence_toolbiotools:time_coherence_tool1.1.0Libraryhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3316Computer scienceLinuxMacWindowsPythonCC-BY-NC-ND-4.0EUCAIMEmergingFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_2945Data analysishttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3620xlsxdocker run -it --rm --name my-container -v "<input_path>:/input" -v "<output_path>:/output" harbor.eucaim.cancerimage.eu/processing-tools/time_coherence_tool:2.1.0 --config-string "{'data_file': 'my_data.xlsx', 'generate_pdf': 'true'}"https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/time_coherence_tool/artifacts-tabSoftware cataloguehttps://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/Social mediahttps://drive.eucaim.cancerimage.eu/s/M23wDa4RWXenzxXUser manualhttps://drive.eucaim.cancerimage.eu/s/9QbdWjnLBeMYSWRTerms of usehttps://www.youtube.com/watch?v=j4J_UPQqYR4&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=10Training materialGIBI230 - HULAFEeucaim_project@iislafe.esInstituteProviderAdrian Galiana-Borderaadrian_galiana@iislafe.eshttps://orcid.org/0000-0002-8324-8284PersonDeveloperPedro-Miguel Martinez-Gironespedromiguel_martinez@iislafe.eshttps://orcid.org/0000-0002-9506-9451PersonDeveloperSupportCarina Soler-Ponscarina_soler@iislafe.eshttps://orcid.org/0009-0000-2991-1391PersonSupportDICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)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.
Status: Deployedhttps://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/info-tabdicom_file_integrity_checker_by_gibi230biotools:dicom_file_integrity_checker_by_gibi2302.0.02.1.02.1.1Libraryhttp://edamontology.org/topic_3316Computer sciencehttp://edamontology.org/topic_3077Data acquisitionhttp://edamontology.org/topic_3071Data managementLinuxMacWindowsPythonCC-BY-NC-ND-4.0EUCAIMMatureFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_0336Format validationhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_3620xlsxFor Data Holders (ingestion-tools)docker run -it --rm --name my-container \
-v "<input_path>:/input" \
-v "<output_path>:/output" \
-v "<config_path>:/config" \
harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_file_integrity_checker:latesthttp://edamontology.org/operation_0336Format validationhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formatFor Data Users (processing-tools)docker run -it --rm --name my-container \
-v "<input_path>:/input" \
-v "<output_path>:/output" \
harbor.eucaim.cancerimage.eu/processing-tools/dicom_file_integrity_checker:latest \
/app/entrypoint.sh --config-string "{'QA': {'sequence_selection': ['ALL'], 'modality_selection': ['ALL'], 'input_directory': 'dataset_id'}}"https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/Social mediahttps://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tabSoftware catalogueLink to EUCAIM's Harbor for Data Holdershttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/dicom_file_integrity_checker/artifacts-tabSoftware catalogueLink to EUCAIM's Harbor for Data Usershttps://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tabContainer fileEUCAIM user needed2.1.0https://drive.eucaim.cancerimage.eu/s/LAKqSQZY4Bjqz5WUser manualhttps://drive.eucaim.cancerimage.eu/s/EEqjraK574HrwMfTerms of usehttps://www.youtube.com/watch?v=oUebkjLYeSs&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=3Training materialGIBI230 - HULAFEeucaim_project@iislafe.esInstituteProviderPedro-Miguel Martinez-Gironespedromiguel_martinez@iislafe.eshttps://orcid.org/0000-0002-9506-9451PersonPrimary contactDeveloperDocumentorMaintainerAdrian Galiana-Borderaadrian_galiana@iislafe.eshttps://orcid.org/0000-0002-8324-8284PersonDeveloperCarina Soler-Ponscarina_soler@iislafe.eshttps://orcid.org/0009-0000-2991-1391PersonContributorDocumentorLuis Marti-Bonmatiluis_marti@iislafe.eshttps://orcid.org/0000-0002-8234-010XPersonProviderDICOM-SEG AnnotationThis module provides a command line tool to validate DICOM SEG files against predefined requirements specified in an Excel file. It contains components for finding relevant DICOM files, loading and parsing validation requests and applying validation rules. The main validation process checks each DICOM file for compliance with the Type 1, 1C, 2, 2C and 3 attributes specified in the requirements file. A detailed report is generated highlighting issues such as missing, invalid or conditionally required attributes, including file paths and affected DICOM tags. The tool is designed to ensure data integrity and compliance with DICOM standards.https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologiesdicom-seg_annotationbiotools:dicom-seg_annotation0.1Desktop applicationCommand-line toolhttp://edamontology.org/topic_3572Data quality managementLinuxWindowsMacPythonApache-2.0eucaimMatureFree of chargeOpen access (with restrictions)https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/annotation_tool/info-tabRepositoryhttps://drive.eucaim.cancerimage.eu/s/i4D6iMeBCxxHGXzGeneralhttps://drive.eucaim.cancerimage.eu/s/PgS6HJ5pBTk8THWUser manualdata_integration_quality_check_tool_diqctincludedIn