Pepkio Cell Seeding Density CalculatorDerives cells per well and suspension pipette volumes for standard 6-, 12-, 24-, 48-, 96-, and 384-well plates from a hemocytometer stock count, trypan blue viability, and target seeding confluency, with QC flags for low viability and impractical transfers. A browser calculator supports interactive planning with cell-line presets; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured plate tables and shareable run identifiers.https://www.pepkio.com/tools/well-plate-seeding-density-calculatorpepkio-well-plate-seeding-density-calculatorbiotools:pepkio-well-plate-seeding-density-calculator0.1.0Command-line toolLibraryWeb applicationhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3361Laboratory techniqueshttp://edamontology.org/topic_2229Cell biologyPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3434ConversionWeb calculator for bench seeding; Python library and CLI for API-backed automation of the same cell seeding engine.https://github.com/pepkio/pepkio-well-plate-seeding-density-calculatorRepositoryhttps://www.pepkio.com/tools/well-plate-seeding-density-calculatorServicehttps://pypi.org/project/pepkio-well-plate-seeding-density-calculator/OtherPython client on PyPI.https://www.pepkio.com/tools/well-plate-seeding-density-calculatorGeneralhttps://github.com/pepkio/pepkio-well-plate-seeding-density-calculatorUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.Pepkio Standard Curve CalculatorProcesses 96-well plate absorbance data through blank subtraction, regression fitting, and dilution correction to report sample concentrations with QC flags for BCA, Bradford, and ELISA workflows. A browser calculator supports interactive grid entry with CSV and PDF export; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits plate layout and absorbance values and returns model comparison, per-sample concentrations, and shareable run identifiers.https://www.pepkio.com/tools/absorbance-curve-calculatorpepkio-absorbance-curve-calculatorbiotools:pepkio-absorbance-curve-calculator0.1.0Web applicationCommand-line toolLibraryhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3361Laboratory techniqueshttp://edamontology.org/topic_3292BiochemistryPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/operation_3659Regression analysisWeb calculator for plate-based standard-curve fitting; Python library and CLI for API-backed automation of the same absorbance-curve engine.https://github.com/pepkio/pepkio-absorbance-curve-calculatorRepositoryhttps://www.pepkio.com/tools/absorbance-curve-calculatorServicehttps://www.pepkio.com/tools/absorbance-curve-calculatorGeneralhttps://github.com/pepkio/pepkio-absorbance-curve-calculatorUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.Pepkio Tm Annealing Temperature CalculatorEstimates PCR primer melting temperatures and polymerase-specific annealing temperatures from sequence and buffer inputs, with per-pair QC for hairpins, dimers, and Tm balance. A browser calculator supports interactive single-pair and batch entry (up to 200 pairs) with method comparison and export; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic for the API client is hosted remotely; sequences are transmitted for programmatic runs while the web interface performs calculations in the browser.https://www.pepkio.com/tools/tm-annealing-temperature-calculatorpepkio-tm-annealing-temperature-calculatorbiotools:pepkio-tm-annealing-temperature-calculator0.1.0Web applicationCommand-line toolLibraryhttp://edamontology.org/topic_0632Probes and primershttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3361Laboratory techniquesPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_0455Nucleic acid thermodynamic property calculationWeb calculator for in-browser Tm/Ta planning; Python library and CLI for API-backed automation of the same primer thermodynamics engine.https://github.com/pepkio/pepkio-tm-annealing-temperature-calculatorRepositoryhttps://www.pepkio.com/tools/tm-annealing-temperature-calculatorServicehttps://pypi.org/project/pepkio-tm-annealing-temperature-calculator/OtherPython client on PyPI.https://www.pepkio.com/tools/tm-annealing-temperature-calculatorGeneralhttps://github.com/pepkio/pepkio-tm-annealing-temperature-calculatorUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.Pepkio pH Buffer Recipe CalculatorComputes weighed laboratory buffer recipes from target pH, concentration, and volume, accounting for separate preparation and working temperatures when pKa shifts with temperature. Supports calculator mode from dry reagents and stock dilution mode, returning acid and base masses, ionic strength estimates, optional NaCl adjustment, gravimetric and titration routes, and stepwise protocols. A browser calculator supports interactive recipe entry with shareable links; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured recipe tables, compatibility warnings, and shareable run identifiers.https://www.pepkio.com/tools/ph-buffer-recipe-calculatorpepkio-ph-buffer-recipe-calculatorbiotools:pepkio-ph-buffer-recipe-calculator0.1.0Command-line toolLibraryWeb applicationhttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3361Laboratory techniquesPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3434ConversionWeb calculator for bench buffer planning; Python library and CLI for API-backed automation of the same pH buffer recipe engine.https://github.com/pepkio/pepkio-ph-buffer-recipe-calculatorRepositoryhttps://www.pepkio.com/tools/ph-buffer-recipe-calculatorServicehttps://pypi.org/project/pepkio-ph-buffer-recipe-calculator/OtherPython client on PyPI.https://www.pepkio.com/tools/ph-buffer-recipe-calculatorGeneralhttps://github.com/pepkio/pepkio-ph-buffer-recipe-calculatorUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.Pepkio PCR Master Mix CalculatorPlans PCR and qPCR master-mix reagent volumes from stock and final concentrations, reaction counts, and pipetting overage, with consolidated totals when several assays are prepared together. A browser calculator supports interactive recipe entry with printable bench sheets; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured volume tables, dilution warnings, and shareable run identifiers.https://www.pepkio.com/tools/pcr-master-mix-calculatorpepkio-pcr-master-mix-calculatorbiotools:pepkio-pcr-master-mix-calculator0.1.0Web applicationCommand-line toolLibraryhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3361Laboratory techniquesPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3434ConversionWeb calculator for bench planning; Python library and CLI for API-backed automation of the same PCR master-mix engine.https://github.com/pepkio/pepkio-pcr-master-mix-calculatorRepositoryhttps://www.pepkio.com/tools/pcr-master-mix-calculatorServicehttps://pypi.org/project/pepkio-pcr-master-mix-calculator/OtherPython client on PyPI.https://www.pepkio.com/tools/pcr-master-mix-calculatorGeneralhttps://github.com/pepkio/pepkio-pcr-master-mix-calculatorUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.Pepkio Molarity Solution CalculatorComputes laboratory solution preparation parameters—powder mass to weigh, stock and diluent volumes for single dilutions, and multi-step serial concentration tables—with correction for hydrated salts and supplier purity. A browser calculator supports interactive prep planning with saved recipes and shareable links; a Python client and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured protocol steps and shareable run identifiers.https://www.pepkio.com/tools/molarity-solution-calculatorpepkio-molarity-solution-calculatorbiotools:pepkio-molarity-solution-calculator0.1.0Web applicationCommand-line toolLibraryhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3361Laboratory techniqueshttp://edamontology.org/topic_3292BiochemistryPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3434ConversionWeb calculator for powder, dilution, and serial modes; Python library and CLI for API-backed automation of the same solution-prep engine.https://github.com/pepkio/pepkio-molarity-solution-calculatorRepositoryhttps://www.pepkio.com/tools/molarity-solution-calculatorServicehttps://pypi.org/project/pepkio-molarity-solution-calculator/OtherPython client on PyPI.https://www.pepkio.com/tools/molarity-solution-calculatorGeneralhttps://github.com/pepkio/pepkio-molarity-solution-calculatorUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.Pepkio Serial Dilution PlannerPlans geometric serial dilution series for molecular biology and biochemistry workflows, rounding transfer volumes to declared pipette ranges and optional 96- or 384-well plate layouts. A browser calculator supports interactive protocol design; a Python client and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured step tables and shareable run identifiers.https://www.pepkio.com/tools/serial-dilution-plannerpepkio-serial-dilution-plannerbiotools:pepkio-serial-dilution-planner0.1.2doi:10.5281/zenodo.20555991doi0.1.2Command-line toolLibraryWeb applicationhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3361Laboratory techniqueshttp://edamontology.org/topic_3292BiochemistryPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3434ConversionWeb calculator for bench planning; Python library and CLI for API-backed automation of the same dilution engine.https://github.com/pepkio/pepkio-serial-dilution-plannerRepositoryhttps://www.pepkio.com/tools/serial-dilution-plannerServicehttps://doi.org/10.5281/zenodo.20555991OtherArchived client release on Zenodo.https://www.pepkio.com/tools/serial-dilution-plannerGeneralhttps://github.com/pepkio/pepkio-serial-dilution-plannerUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.EGAEuropean 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 accession

http://edamontology.org/data_2531Experiment reporthttp://edamontology.org/format_2331HTML

https://ega-archive.org/General10.1038/ng.3312PrimaryEMBL-EBI DatabasesInstituteProviderhelpdesk@ega-archive.orgPersonPrimary 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_3752CSV

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3591tiff

http://edamontology.org/data_2526Text datahttp://edamontology.org/format_3752CSV

http://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.dePersonDeveloperPrimerPickrPrimerpickr is an open-source tool for rt-PCr primer picking powered by the aggregation of public usage of rt-pcr primers from open source papers. The database is validated with 154 genes and contains over 31,000 genes across 10 species.https://www.primerpickr.comprimerpickrbiotools:primerpickr1.1Web servicehttp://edamontology.org/topic_3519PCR experimenthttp://edamontology.org/topic_0632Probes and primersCC-BY-NC-ND-4.0Free of chargeOpen accesshttp://edamontology.org/operation_0308PCR primer designhttps://www.primerpickr.com/RepositoryMetaProteomeAnalyzer-CloudThe MetaProteomeAnalyzer Cloud (MPA Cloud) is an intuitive, open-source tool for metaproteomics data analysis and interpretation, designed to analyse comprehensive metaproteomics data from tandem mass spectrometry experiments through a web interface.https://mdoa-tools.bi.denbi.de/mpacloud/mpa-cloudbiotools:mpa-cloudWeb servicehttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_4060Metaproteomicshttp://edamontology.org/topic_0121ProteomicsJavaTypeScriptGPL-3.0MatureFree of chargeOpen accessGermanyhttps://gitlab.com/mdoa-group/mpa-websiteRepositoryhttps://gitlab.com/mdoa-group/mpa-cloud-serverRepositoryhttps://mdoa-tools.bi.denbi.de/mpacloud/documentationUser manualmetaproteomeanalyzerisNewVersionOfmpa_portableisNewVersionOf10.1038/s41596-020-0368-73285998410.3389/fmicb.2019.0188331474963PMC670742510.1021/acs.analchem.7b0354429215871PMC575722010.1021/pr501246w25660940Kay SchallertDaniel KautznerBenjamin J. SaalfeldProf. Dr.-Ing. Robert HeyerLudwig KnocheMalte BöttcherCellSeekrCellSeekr 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.comFlexRLA Flexible Model For Record Linkagehttps://github.com/robachowyk/FlexRLflexrlbiotools:flexrl0.1.1Libraryhttp://edamontology.org/topic_3345Data identity and mappingC++RGPL-3.0-or-laterEmergingFree of chargeOpen accesshttps://github.com/robachowyk/FlexRLRepositoryhttps://github.com/robachowyk/FlexRL/issuesIssue trackerhttps://github.com/robachowyk/FlexRL/issuesHelpdeskhttps://github.com/robachowyk/FlexRL/issuesDiscussion forumhttps://github.com/robachowyk/FlexRLSource codehttps://cran.r-project.org/package=FlexRLSoftware packagehttps://rdrr.io/cran/FlexRL/api/API documentationhttps://github.com/robachowyk/FlexRLInstallation instructionsQuick start guideTraining materialUser manual10.1093/jrsssc/qlaf016Primary10.48550/arXiv.2407.06835PreprintKayané Robachhttps://www.amsterdamumc.org/en/research/researchers/kayane-robachhttps://orcid.org/0000-0002-5725-623X05grdyy37PersonPrimary contactVerbexVerbex is a private, on-device Voice-to-ELN iOS app for scientists. It helps researchers capture experiment notes by voice as work happens, organize those notes into scientific sections, and prepare clean, reviewable, ELN-ready scientific records.http://www.verbalexperiment.comverbexbiotools:verbexv1.2ProprietaryEmergingFree of charge (with restrictions)Open accesshttp://www.verbalexperiment.comServicehttps://apps.apple.com/us/app/verbex/id6758427118OtherAppStore Linkekokratiekokrati computes habitat connectivity metrics (PC, IIC, EC(PC), dPC and its decomposition into intra-patch, flux and connector components) for habitat patch networks. Users upload polygon data as GeoPackage or shapefile, set species-specific dispersal parameters, and receive patch importance scores and landscape-level indices. Designed for conservation planners, landscape ecologists and environmental consultants. No installation required.https://app.ekokrati.seekokratibiotools:ekokratihttp://edamontology.org/topic_0610Ecologyhttp://edamontology.org/topic_3050BiodiversityProprietaryEmergingOpen access (with restrictions)http://edamontology.org/operation_3927Network analysishttp://edamontology.org/data_3736Ecological data

http://edamontology.org/data_3736Ecological data

http://edamontology.org/data_3707Biodiversity data

TenDNA DNA Format ConverterTool for converting raw DNA data files between 23andMe, AncestryDNA, MyHeritage, and FamilyTreeDNA formats.https://tendna.com/en/dna-convertertendna_dna_format_converterbiotools:tendna_dna_format_converterdoi:10.5281/zenodo.20185958doi1.0.0Web servicehttp://edamontology.org/topic_0091BioinformaticsWindowsPHPMITFile ExchangeMatureFree of chargeOpen accesshttps://github.com/milaza/dna-raw-data-converter-23andme-myheritage-ancestry/RepositoryOpen-source documentation and source code for the TenDNA DNA Format Converter, including raw DNA format guides, compatibility notes, and conversion examples for 23andMe, AncestryDNA, MyHeritage, and FamilyTreeDNA.https://tendna.com/en/dna-converterServiceThe tool supports DNA file format compatibility, raw genotype data restructuring, and cross-platform conversion for genealogy and personal genomics workflows. Features include: - raw DNA format conversion - compatibility between major consumer DNA services - support for TSV and CSV genotype files - online processing without manual editinghttps://github.com/milaza/dna-raw-data-converter-23andme-myheritage-ancestry/OtherGitHub repository with source code and documentation for raw DNA format conversion between major consumer genomics platforms.10.5281/zenodo.201859581.0.0https://doi.org/10.5281/zenodo.2018595810.6084/m9.figshare.3249303610.6084/m9.figshare.32493036pathogensurveillancePathogensurveillance 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_3464JSON

http://edamontology.org/data_2526Text datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3620xlsx

http://edamontology.org/data_2526Text datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3620xlsx

http://edamontology.org/data_2526Text datahttp://edamontology.org/format_3835TIDE TXT

docker 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_3620xlsx

http://edamontology.org/data_2526Text datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3620xlsx

http://edamontology.org/data_2526Text datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3620xlsx

http://edamontology.org/data_2526Text datahttp://edamontology.org/format_3835TIDE TXT

docker 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_3464JSON

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM format

docker 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 format

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM format

Command 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_3752CSV

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/format_3549nii

docker 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_3752CSV

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/format_3549nii

docker 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_3752CSV

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/format_3549nii

docker 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_3464JSON

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/format_3549nii

docker 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_3549nii

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/format_3549nii

docker 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_3464JSON

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/format_3549nii

docker 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/0000-0002-8234-010XPersonProviderML 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 format

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_3464JSON

docker 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_3620xlsx

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3603PNGhttp://edamontology.org/format_3508PDFhttp://edamontology.org/format_3604SVG

docker 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_3620xlsx

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM format

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_3620xlsxhttp://edamontology.org/format_2331HTML

For 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 format

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM format

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_3620xlsxhttp://edamontology.org/format_2331HTML

For 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/0000-0002-8234-010XPersonProviderVirtual Imaging PlatformVIP is a web portal for medical imaging applications. It allows users to access scientific applications as a service (directly through the web browser with no installation required), as well as distributed computing resources in a transparent manner. It exploits the resources available in the biomed virtual organization of the EGI e-infrastructure to offer an open service to researchers worldwide.https://vip.creatis.insa-lyon.frvirtual_imaging_platformbiotools:virtual_imaging_platform3.0.14.6.1Bioinformatics portalJavaCECILL-BEUCAIMMatureFree of chargeOpen accesshttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_2333Binary formathttps://vip.creatis.insa-lyon.fr/Servicehttps://github.com/virtual-imaging-platform/Source code3.0.1https://hub.docker.com/layers/viplatform/vip-portal/4.6.1/images/sha256-5d47d27c3e285dec287506e2b3c436b343e2c1f92818b7c2cbf39afaed46fbb5Container fileVIP Docker image for development or testing (NOT for production)4.6.1https://github.com/virtual-imaging-platform/VIP-portal/wikiOther10.1109/tmi.2012.222015423014715SKMStress Knowledge Map: A compilation of knowledge on mechanisms underlying responses of plants to stress, the so called stress signalling network.https://skm.nib.si/skmbiotools:skmDatabase portalWeb applicationhttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0780Plant biologyPlant Systems BiologyELIXIR-SIEmergingFree of chargeOpen accessPlant SciencesSystems BiologySloveniahttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/data_2299Gene name

http://edamontology.org/data_2080Database search resultshttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_3619sif

http://edamontology.org/operation_2422Data retrieval

http://edamontology.org/data_0950Mathematical modelhttp://edamontology.org/format_2585SBMLhttp://edamontology.org/format_3619sifhttp://edamontology.org/format_3692SBGN-ML

https://skm.nib.si/contactOtherhttps://skm.nib.si/documentationGeneralgomapmanusesnewt-veuses10.1016/j.xplc.2024.10092038616489PrimaryStress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responsesNational Institute of Biology, Department of Biotechnology and Systems Biologyhttp://www.nib.si/InstituteProviderCarissa Blekercarissarobyn.bleker@nib.sihttps://orcid.org/0000-0003-1617-7145PersonDeveloperMaintainerKristina GrudenPersonContributorŽiva RamšakPersonContributorVid PodpečanDeveloperDICOM-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_diqctincludedInJCVIJCVI is a versatile toolkit for comparative genomics analysis. It is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.https://github.com/tanghaibao/jcvijcvibiotools:jcviCommand-line toolLibraryhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0102MappingWindowsLinuxMacPythonBSD-2-ClauseFree of chargeOpen accesshttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/operation_0337Visualisationhttps://pypi.org/project/jcviRepositoryhttps://github.com/tanghaibao/jcvi/wikiUser manual10.1002/IMT2.21139135687PMC11316928Haibao Tangtanghaibao@gmail.comhttps://orcid.org/0000-0002-3460-8570PersonXingtan Zhangtanger_009@163.comPersonPolySTestRobust statistical testing of quantitative proteomics data. The tool comprises and combines different tests and includes a new method for combined statistics of quantitative and missing values.http://computproteomics.bmb.sdu.dk/app_direct/PolySTestPolySTestbiotools:PolySTestWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_2269Statistics and probabilityLinuxMacRGPL-2.0MatureFree of chargeOpen accessDenmarkhttp://edamontology.org/operation_3664Statistical modellinghttp://edamontology.org/operation_3741Differential protein expression profilinghttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3751DSVhttp://edamontology.org/format_3752CSV

http://edamontology.org/data_3932Q-valuehttp://edamontology.org/format_3752CSV

http://edamontology.org/data_1669P-valuehttp://edamontology.org/format_3752CSV

http://edamontology.org/data_1636Heat maphttp://edamontology.org/format_3604SVG

http://edamontology.org/data_3905Histogramhttp://edamontology.org/format_3604SVG

http://edamontology.org/data_0928Gene expression profilehttp://edamontology.org/format_3752CSV

https://github.com/computproteomics/PolySTestRepository10.1074/mcp.RA119.00177732424025PMC8015005PrimaryImage Duplicates CheckerAutomatically detects duplicate and near-duplicate DICOM image series in large medical imaging datasets. Uses a tiered pipeline combining DICOM metadata analysis, SHA-based pixel hashing, and image similarity metrics (SSIM, cosine, MAD) to identify exact copies, re-exported series, and near-identical acquisitions. All findings are reported for human expert review — no files are modified or deleted automatically. For scenarios requiring strict, image-level deduplication based on pixel content, fully agnostic to metadata changes, consider using [https://bio.tools/image_duplicate_check_tool]https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologiesdicom_image_similarity-duplicate_checkerbiotools:dicom_image_similarity-duplicate_checker2.0Command-line toolhttp://edamontology.org/topic_3572Data quality managementLinuxWindowsMacPythonApache-2.0eucaimMatureFree of chargeOpen access (with restrictions)https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/deduplication_tool/info-tabRepositoryLink to the Harbor imagehttps://drive.eucaim.cancerimage.eu/s/pELEgMjZL4xMWe3Generalhttps://drive.eucaim.cancerimage.eu/s/ZxwyR5GTbSWSYjoUser manualdata_integration_quality_check_tool_diqctincludedInminigraphMinigraph is a sequence-to-graph mapper and graph constructor. For graph generation, it aligns a query sequence against a sequence graph and incrementally augments an existing graph with long query subsequences diverged from the graph.https://github.com/lh3/minigraphminigraphbiotools:minigraphCommand-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0102MappingMacLinuxCJavaScriptMITFree of chargeOpen accesshttp://edamontology.org/operation_2928Alignmenthttps://lh3.github.io/minigraph/GeneralSNP-sitesFinds SNP sites from a multi-FASTA alignment file.https://sanger-pathogens.github.io/snp-sites/snp-sitesbiotools:snp-sites2.5.1Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_2885DNA polymorphismLinuxCGPL-3.0Open accesshttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_3820Relaxed PHYLIP Sequentialhttp://edamontology.org/format_1984FASTA-alnhttp://edamontology.org/format_3016VCF

http://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_3820Relaxed PHYLIP Sequentialhttp://edamontology.org/format_1984FASTA-alnhttp://edamontology.org/format_3016VCF

snp-sites my_alignment.aln snp-sites my_gzipped_alignment.aln.gzhttps://github.com/sanger-pathogens/snp-sitesRepositoryhttps://sanger-pathogens.github.io/snp-sites/General10.1099/mgen.0.00005628348851PMC5320690PrimaryParseSNPA small <720Kb C++ windows utility. That allows you to load Ancestry, 23andMe, FTDNA, or Genes for Good RAW DNA files search them, merge them. covert them to Ancestry format. But also create files from peer reviewed publications to compare with you loaded data to give your genetic disposition for the condition you have entered the data for an statistical risk if OR values are included. Included with the program are example files for Type 2 Diabetes risk factors. (As I have type 2 Diabetes so I could test the results).https://britrobin.github.io/ParseSNP/parsesnp21-26biotools:parsesnp21-261.1.1Desktop applicationhttp://edamontology.org/topic_3577Personalised medicineWindowsC++GPL-3.0EmergingFree of chargeOpen accesshttps://britrobin.github.io/ParseSNP/OtherGit page for easy installer and pdf manual downloadhttps://github.com/BritRobin/ParseSNPRepositoryGitHub repositoryhttps://britrobin.github.io/ParseSNP/Software packageWindows x64 or x86 installer1.1.1https://raw.githubusercontent.com/BritRobin/ParseSNP/master/ParseSNP_Manual.pdfUser manualpdf user manualCompuCell3DCompuCell3D is a multiscale multicellular virtual tissue modeling and simulation environment. CompuCell3D is written in C++ and provides Python bindings for model and simulation development in Python.https://compucell3d.org/SrcBincompucell3dbiotools:compucell3d4.8.0Command-line toolhttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_3307Computational biologyWindowsLinuxMacPythonC++GPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_2426Modelling and simulationhttps://compucell3d.org/SrcBinRepositoryhttps://www.reddit.com/r/CompuCell3D/Discussion forumhttps://compucell3d.org/API documentationhttps://compucell3d.org/TutorialsTraining materialhttps://compucell3d.org/PublicationsCitation instructions10.1016/b978-0-12-388403-9.00013-822482955PMC3612985PrimaryNuclearPhaserNuclearPhaser is a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs. This is an overview of the phasing pipeline for dikaryons.https://github.com/JanaSperschneider/NuclearPhasernuclearphaserbiotools:nuclearphaser1.1Scripthttp://edamontology.org/topic_0622GenomicsLinuxMacPythonGPL-3.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_2403Sequence analysishttps://github.com/JanaSperschneider/NuclearPhaserRepositoryhttps://github.com/JanaSperschneider/NuclearPhaser/blob/main/README.mdQuick start guideJana Sperschneiderhttps://github.com/JanaSperschneidersam2intervalA Python script that converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2intervalsam2intervalbiotools:sam2intervalScripthttp://edamontology.org/topic_0622GenomicsMacWindowsLinuxPythonMITEmergingFree of chargeOpen accessGalaxyhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2573SAM

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2572BAM

https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2intervalRepositoryminicondaMiniconda is a minimal Python distribution that includes the Conda package and environment manager plus only essential dependencies. It provides a lightweight way to create isolated environments and install Python packages as needed, without the large preinstalled package set of Anaconda.https://www.anaconda.com/docs/getting-started/miniconda/mainminicondabiotools:miniconda26.3SuiteCommand-line toolhttp://edamontology.org/topic_4047Software managementWindowsLinuxMacPythonProprietaryMatureFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_3760Service managementhttps://www.anaconda.com/download/successDownloads pagehttps://www.anaconda.com/docs/getting-started/miniconda/mainGeneralEUCAIM ETL toolsetModular toolchain for an extensible and customizable ETL pipeline that extracts, transforms, and loads clinical data and medical imaging metadata, applying dataset-specific mappings to generate outputs compatible with the EUCAIM Common Data Model (CDM). Its design aims to minimize manual data preparation efforts and facilitate customization and integration with other components, such as data quality assurance tools. Containerized, currently supports input datasets in CSV, JSON, XLSX.https://github.com/EUCAIM/etl-toolset/eetl_toolsetbiotools:eetl_toolset0.1.10.1.20.2.1WorkflowLibraryhttp://edamontology.org/topic_3345Data identity and mappinghttp://edamontology.org/topic_0769WorkflowsWindowsLinuxPythonJavaApache-2.0EUCAIMEmergingFree of chargeOpen access (with restrictions)ToolsSpainhttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_3431Data depositionhttp://edamontology.org/operation_0336Format validationhttps://github.com/EUCAIM/etl-toolset/Repositoryhttps://drive.eucaim.cancerimage.eu/s/zXE4xYDm3x3CWtQGeneralTool documentation (updated)tabular_data_curatorusesAlphaFind v2AlphaFind v2 is a tool for fast, structure‑based search for protein structures against the AlphaFold DB (https://alphafold.ebi.ac.uk/) and TED DB (https://ted.cathdb.info/). The tool uses protein‑level embeddings to provide a rapid pre‑filter, with top candidates undergoing TM-Score, RMSD and residue‑level alignments computations. Four complementary search modes are available: (i) whole‑chain search, (ii) pLDDT‑aware search that restricts similarity to high‑confidence regions, (iii) domain search against the TED database, and (iv) multidomain search that combines several chain‑level matches into a single score. Users can restrict queries to a given organism, CATH superfamily or to proteins with experimental structures, and submit queries by UniProt/AlphaFold identifier. Results comprise a ranked list with similarity metrics, rich metadata and an interactive 3‑D superposition view. The service is freely accessible at https://alphafind.ics.muni.cz/.https://alphafind.ics.muni.cz/alphafind_v2biotools:alphafind_v2Web applicationhttp://edamontology.org/topic_0078ProteinsMatureFree of chargeOpen access3D-BioInfoCzech Republichttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/data_1460Protein structure

http://edamontology.org/data_0888Structure similarity score

https://alphafind.ics.muni.cz/Servicehttps://alphafind.ics.muni.cz/manualUser manualalphafindisNewVersionOf10.1093/nar/gkag37242028635PrimaryCirclatorCirclator is a tool to circularize genome assemblies. It will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly.https://sanger-pathogens.github.io/circlator/circlatorbiotools:circlatorCommand-line toolhttp://edamontology.org/topic_0196Sequence assemblyPythonGDMatureFree of chargeOpen accesshttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_0523Mapping assemblyhttps://github.com/sanger-pathogens/circlatorRepository10.1186/S13059-015-0849-026714481PMC4699355Martin Huntmh12@sanger.ac.ukPersonGONetViewStandalone browser-based Gene Ontology network viewer for exploring, filtering, searching, and exporting GO term and gene annotation neighborhoods from locally preprocessed GO OBO and GAF data.https://jonasmarx3007.github.io/GONetView/gonetviewbiotools:gonetview0.1.0Web applicationhttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_0085Functional genomicshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0091BioinformaticsPythonTypeScriptMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3559Ontology visualisationhttp://edamontology.org/data_1176GO concept ID

http://edamontology.org/data_2600Pathway or networkhttp://edamontology.org/format_3508PDFhttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3603PNG

http://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_1026Gene symbolhttps://jonasmarx3007.github.io/GONetView/OtherWeb Application Homepagehttps://github.com/JonasMarx3007/GONetViewRepositoryhttps://github.com/JonasMarx3007/GONetView/blob/main/README.mdGeneralhttps://github.com/JonasMarx3007/GONetView/blob/main/docs/tutorial.mdUser manual10.5281/zenodo.20271711Primary0.1.0Jonas Marxjonas.marx3007@gmx.dePersonDeveloperMaintainerEdinOmics Dash AppAn interactive platform that performs statistical analyses on metabolomics datasets and allows visualising results with ease. The interface gives users autonomy in creating figures suited to their reporting and publication needs.https://github.com/EdinOmics/A-Python-Dash-App-and-cPanel-workflow-to-automate-metabolomics-data-analyses-and-visualisationdash_app_to_automate_metabolomics_data_analysesbiotools:dash_app_to_automate_metabolomics_data_analysesScripthttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0219Data curation and archivalhttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_4019BiosciencesPythonCC-BY-4.0MatureFree of chargeOpen accesshttps://github.com/EdinOmics/A-Python-Dash-App-and-cPanel-workflow-to-automate-metabolomics-data-analyses-and-visualisationRepositoryhttps://github.com/EdinOmics/A-Python-Dash-App-and-cPanel-workflow-to-automate-metabolomics-data-analyses-and-visualisationUser manualOpen Neuroscience GraphThe Open Neuroscience Graph (openneuroscience.org) is an open-access, curated knowledge graph that maps the open science ecosystem in neuroscience as a browsable digital garden. Built from an Obsidian vault and published as a static website using Quartz, the project replaces traditional linear presentation with a networked structure of interlinked Markdown notes. Bidirectional links, full-text search, and an integrated graph visualization allow users to navigate thematic relationships dynamically rather than sequentially. The complete source material is openly available to sustain, replicate and extend the resource, includding all Markdown content, media attachments, Quartz configuration files, and site customizations. Researchers, educators, and open-science practitioners may explore the site directly, download the vault for offline use in Obsidian, or fork the material to build new, derivative knowledge bases. PID=https://doi.org/10.5281/zenodo.20181900https://openneuroscience.orgopen_neuroscience_graphbiotools:open_neuroscience_graph1.0.0doi:10.5281/zenodo.20181900doi1.0.0Database portalhttp://edamontology.org/topic_4019BiosciencesWindowsiOSAndroidLinuxMacJavaScriptCC-BY-4.0EmergingFree of chargeOpen accessTrainingFrancehttps://gitlab.com/icm-institute/dac/opensciencegraphRepositoryhttps://gitlab.com/icm-institute/dac/opensciencegraphSource code1.0.0https://gitlab.com/icm-institute/dac/opensciencegraph/-/blob/main/CONTRIBUTING.md?ref_type=headsContributions policy10.5281/zenodo.20181900Primary1.0.0Stephen Whitmarshstephen.whitmarsh@icm-institute.orghttps://stephenwhitmarsh.comhttps://orcid.org/0000-0002-3969-6565Image Quality Assessment metrics (IQA) for XNAT platformDocker images developped at the Euro-BioImaging MED-Hub and National Research Council (CNR) for the XNAT platform hosted by University of Turin. A suite of four Image Quality Assessment (IQA) metrics designed to evaluate the perceptual quality of preclinical and clinical image datasets within the XNAT platform at the scan and subject levels. The tool outputs Excel files containing the mean and median for each metric and scan, as well as PNG files with corresponding histogram plots.https://github.com/FerielRamdhane/Image-Quality-Assessment-metrics-IQA-for-XNAT-platformimage_quality_assessment_metrics_iqa_for_xnat_platformbiotools:image_quality_assessment_metrics_iqa_for_xnat_platform1.0ScriptCommand-line toolhttp://edamontology.org/topic_3572Data quality managementMacLinuxWindowsPythonMATLABCC-BY-NC-ND-4.0EUCAIMFree of chargeOpen accesshttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM format

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3603PNG

http://edamontology.org/data_1772Scorehttp://edamontology.org/format_3620xlsx

https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/iqaxnat_scan/info-tabRepositoryhttps://drive.eucaim.cancerimage.eu/s/Q7x86RTMiZJdq97GeneralFeriel Romdhaneferielromdhane@yahoo.frhttps://orcid.org/0000-0002-5854-9341Euro-BioImaging ERICpreclinicaldata@eurobioimaging.euhttps://www.eurobioimaging.eu/National Research Councilhttps://www.ibb.cnr.it/NLmCED FilterThe NLmCED (Non Local mean Coherence Enhancing Diffusion) filter is a denoising tool aimed to reduce Rician Noise in 3D MR images. It is a combination between two filters such as the Non-Local mean filter and the Anisotropic Diffusion tensor method with an estimator of Rician noise. The NLmCED filter can benefit from the noise reduction capabilities of the NLM filter while maintaining the edge-preserving characteristics of anisotropic diffusion.https://github.com/FerielRamdhane/NLmCED-Filter/tree/mainnlmced_filterbiotools:nlmced_filter1.0Scripthttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_3444MRIhttp://edamontology.org/topic_3384Medical imagingMacLinuxWindowsPythonMATLABCC-BY-NC-ND-4.0EUCAIMFree of chargeOpen accesshttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM format

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3579JPGhttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/format_3626MAT

https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nlmced/info-tabRepositoryGithub Linkhttps://drive.eucaim.cancerimage.eu/s/L5iwmo6WknyLoWwGeneral10.1504/IJCVR.2018.09001210.1002/mrm.28676Feriel Romdhaneferielromdhane@yahoo.frhttps://orcid.org/0000-0002-5854-9341ExomeFlowExomeFlow is a Python package that provides a complete, automated Whole Exome Sequencing (WES) analysis workflow from raw FASTQ files to functionally annotated variants in a single reproducible CLI command. It aims to be the standard high-level pipeline for WES analysis in Python, combining GATK best-practice variant calling, hard filtering, and ANNOVAR annotation into one modular, maintainable package. It handles cohort-level processing (multiple samples), checkpointing for resumable runs, structured logging, and parallel execution out of the box.https://pypi.org/project/exomeflow/exomeflowbiotools:exomeflow1.0.91.0.8WorkflowCommand-line toolhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_2533DNA mutationLinuxPythonBashFreewareEmergingFree of chargeOpen accesshttps://pypi.org/project/exomeflow/Repositoryhttps://pypi.org/project/exomeflow/Software package1.0.08https://pypi.org/project/exomeflow/Generalfastpusesbio-samtoolsincludesgatk_haplotype_callerincludesRobin Kumaritsrobintomar@gmail.comhttps://pypi.org/project/exomeflow/https://orcid.org/0009-0002-9084-2019PersonDeveloperFrameXploreFrameXplore is a Google Colab notebook that extends ColabFold to automatically identify and correct disulfide bonds in cysteine‑rich protein structures. After a standard ColabFold prediction, it extracts all cysteine residues, computes Cα–Cα and S–S distances, identifies true disulfide bonds using geometric cutoffs (Cα–Cα < 6.5 Å, S–S < 2.5 Å), writes a corrected PDB with proper CONECT records, and provides an interactive 3D view.https://github.com/Vidhusv/FRAMEXPLORERframexplorebiotools:framexplore1.0.0doi:10.5281/zenodo.20135079doiWeb applicationhttp://edamontology.org/topic_4019BiosciencesLinuxMacWindowsPythonMITEmergingFree of chargeOpen accesshttps://github.com/Vidhusv/FRAMEXPLORERRepositoryGitHub repository with source code, documentation, and logohttps://github.com/Vidhusv/FRAMEXPLORER/issuesIssue trackerReport bugs, suggest features, or ask questionshttps://github.com/Vidhusv/FRAMEXPLORER/archive/refs/heads/main.zipSource codeLatest version of the complete repository as a ZIP file1.0.0https://raw.githubusercontent.com/Vidhusv/FRAMEXPLORER/main/FrameXplore.ipynbBinariesDirect download of the Colab notebook (.ipynb file). Can be run locally or uploaded to Google Colab.1.0.0https://github.com/Vidhusv/FRAMEXPLORER/blob/main/README.mdGeneralQuick start guide, example test case, methodology explanation, citation, and repository contents10.1038/s41592-022-01488-135637307PMC9184281PrimaryColabFold: making protein folding accessible to all. Nature Methods, 2022.Vidhu S Vijayvidhuvijay2003@gmail.comhttps://github.com/Vidhusvhttps://orcid.org/0009-0009-1182-2089PersonDeveloperMaintainerMS Bioinformatics student at Amrita Vishwa Vidyapeetham; creator and maintainer of FrameXplore.BIGR xnattoolsxnattools is a python package with a set of modules for performing various operations on data stored in XNAT servers. The main purpose is to provide one standardized platform for running operations on XNAT servers. The package currently contains four tools that use this platform: dicom to nifty conversion, thumbnail generation from dicom, DICOM header data collection, in bulk downloading of a project.https://gitlab.com/radiology/radiomics/xnattoolsbigr_xnattoolsbiotools:bigr_xnattoolsv0.0.1LibraryLinuxMacWindowsPythonApache-2.0EUCAIMEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3096Data editinghttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_3436Aggregationhttps://gitlab.com/radiology/radiomics/xnattoolsSource codev0.0.1xnatpyusesxnatusesMartijn PA Starmansm.starmans@erasmusmc.nlhttps://bigr.nl/member/martijn/https://orcid.org/0000-0001-5086-7153PersonPrimary contactErasmus MCInstituteProvider