REGENIEregenie is a C++ program for whole genome regression modelling of large genome-wide association studies.https://rgcgithub.github.io/regenie/regeniebiotools:regeniev4.1http://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3517GWAS studyhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3474Machine learningRFortranShellC++COtherMatureFree of chargeOpen accesshttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3659Regression analysis10.1038/S41588-021-00870-734017140Jonathan Marchinijonathan.marchini@regeneron.comhttps://orcid.org/0000-0003-0610-8322PersonGeoMineGeoMine 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 Bioinformatics00g30e956InstituteProviderHyPPIHyPPI 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 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 Bioinformatics00g30e956InstituteProviderProtossProtoss 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 Bioinformatics00g30e956InstituteProviderSNAPThe 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 contactMONAI 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/s41587-022-01435-736050551PDB-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 supportopenbabelOpen Babel is a chemical toolbox designed to speak the many languages of chemical data.http://openbabel.org/openbabelbiotools:openbabelopenbabel-3-2-0http://edamontology.org/topic_3314Chemistryhttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_0081Structure analysisRC#ShellPerlCPythonJavaPHPRubyC++ScalaGPL-2.0Maturehttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0883Structurehttps://github.com/openbabel/openbabel/wikiGeneralhttps://openbabel.org/docs/index.htmlUser manual10.1186/1758-2946-3-3321982300PMC3198950SPALNGenome mapping and spliced alignment of cDNA or amino acid sequenceshttps://github.com/ogotoh/spalnspalnbiotools:spalnver.3.0.8bCommand-line toolhttp://edamontology.org/topic_0102MappingCPerlC++GPL-2.0Maturehttp://edamontology.org/operation_2429Mappinghttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_1234Sequence set (nucleic acid)https://github.com/ogotoh/spalnRepositoryhttps://github.com/ogotoh/spalnGeneral10.1093/nar/gkag35742134803PMC1317563310.1093/bioinformatics/btn4601872804310.1093/nar/gks70822848105PMC348821110.1093/bioinformatics/16.3.1901086901210.1093/bioinformatics/btae51739152995PMC1136180910.1007/978-1-0716-1036-7_53328988710.1093/bioinformatics/btl06716500940Osamu Gotohgotoh.osamu.67a@st.kyoto-u.ac.jphttps://orcid.org/0009-0002-6750-1945PersonscenicplusSCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.https://github.com/aertslab/scenicplusscenicplusbiotools:scenicplusv1.0a2http://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0122Structural genomicshttp://edamontology.org/topic_3308TranscriptomicsPythonOtherMatureFree of chargehttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3475TSVhttp://edamontology.org/operation_3927Network analysishttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3475TSVhttp://edamontology.org/operation_3658Statistical inferencehttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3475TSVhttps://scenicplus.readthedocs.io/en/latest/Perturbation_simulation.html#Tutorial:-Perturbation-simulationTraining material10.1038/s41592-023-01938-437443338PMC10482700screen_assemblyScreen a bacterial assembly (contigs/CDS or proteins) for nucleotide or protein sequences.
Pipeline that screens for presence of genes of interest (GOI) in bacterial assemblies. Generates multiple CSVs and plots that describe which genes are present and how variable their sequence is. Can use DNA or protein query sequences (GOIs) and DNA contigs/fastas or protein fastas as database (db) to search in.https://github.com/shimbalama/screen_assemblyscreen_assemblybiotools:screen_assemblyv1ScriptCommand-line toolhttp://edamontology.org/topic_0196Sequence assemblyPythonMITMaturehttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_0925Sequence assemblyhttp://edamontology.org/format_1929FASTAhttps://github.com/shimbalama/screen_assemblyRepositoryhttps://github.com/shimbalama/screen_assembly/wikiGeneral10.1038/s41588-019-0417-831133745PMC6650292PrimaryMark R. Davieshttps://orcid.org/0000-0001-6141-5179PersondsRIPdsRIP is a web platform for optimizing dsRNA sequences for RNAi in pest control and research. It offers tools for identifying effective target genes and minimizing risk to non-target species, based on sequence features identified in Tribolium castaneum.https://dsrip.uni-goettingen.dedsripbiotools:dsriphttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_4055siRNA experimenthttp://edamontology.org/topic_0632Probes and primershttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/operation_2008siRNA duplex predictionhttp://edamontology.org/operation_0308PCR primer designhttp://edamontology.org/operation_0465siRNA binding specificity prediction10.1186/S12915-025-02219-640296100PMC12039203Doga Ceddendoga.cedden@biologie.uni-goettingen.dePersonGregor Buchergbucher1@uni-goettingen.dePersonRExPrimerA 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 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.dePersonDeveloperLongTRTandem 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/s13059-024-03319-238965568PMC11229021MetaProteomeAnalyzer-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 BöttcherMR-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/0000-0002-8234-010XPersonProviderDenoising-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/0000-0002-8234-010XPersonContributorNP-LikenessNatural Product-likeness calculator v-2.1 : calculates natural product-likeness of small molecules based on open-data of natural products.https://github.com/vcnainala/NP-Likenessnp-likenessbiotools:np-likenessCommand-line toolhttp://edamontology.org/topic_0154Small moleculesJavaLGPL-2.0-or-laterFree of charge10.1186/1471-2105-13-10622607271PMC3436723Primary10.1021/ci700286x18034468MethodKalai Vanii Jayaseelankalai@ebi.ac.ukAndreas TruszkowskiPablo MorenoPeter ErtlChristoph Steinbeckchristoph.steinbeck@uni-jena.denanosvNanoSV is a software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.https://github.com/mroosmalen/nanosvnanosvbiotools:nanosvCommand-line toolhttp://edamontology.org/topic_0122Structural genomicshttp://edamontology.org/topic_4056Long-read sequencingMacWindowsLinuxPythonMIThttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_2572BAM10.1038/s41467-017-01343-429109544PMC5673902s3segmenterS3segmenter is a Matlab-based set of functions that generates single cell (nuclei and cytoplasm) label masks.https://github.com/HMS-IDAC/S3segmenters3segmenterbiotools:s3segmenter1.5.7Scripthttp://edamontology.org/topic_3383BioimagingWindowsLinuxMacMATLABNot licensedMatureFree of chargehttp://edamontology.org/operation_2429Mappinghttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3727OME-TIFFhttp://edamontology.org/data_2019Map data10.1038/s41592-021-01308-y34824477PMC8916956CompuCell3DCompuCell3D 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/b978-0-12-388403-9.00013-822482955PMC3612985PrimaryEvoBindDesign of linear and cyclic peptide binders from protein sequence information.https://github.com/patrickbryant1/EvoBindevobindbiotools:evobindCommand-line toolhttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_0082Structure predictionPythonhttp://edamontology.org/operation_3080Structure editinghttp://edamontology.org/operation_4008Protein designhttps://colab.research.google.com/github/patrickbryant1/EvoBind/blob/master/EvoBind.ipynbOther10.1038/S42004-025-01601-340691301PMC12280060Patrick Bryantpatrick.bryant@scilifelab.sehttps://orcid.org/0000-0003-3439-1866PersonCirclatorCirclator 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.ukPersonplantiSMASHPlantiSMASH is a specialized extension of antiSMASH for the identification and analysis of biosynthetic gene clusters (BGCs) in plant genomes. It supports advanced plant-specific detection rules and features for comparative genomics, visualization, and more.https://plantismash.bioinformatics.nl/plantismashbiotools:plantismash2.0-beta4http://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0085Functional genomicsMacWindowsLinuxAGPL-3.0https://github.com/plantismash/plantismash/releasesSoftware package2.0-beta4https://plantismash.github.io/documentation/General10.1093/nar/gkx305PMC55701731.010.1016/j.jmb.2026.16979841962628Primary2.0plantiSMASH 2.0: Improvements to Detection, Annotation, and Prioritization of Plant Biosynthetic Gene ClustersFrameXploreFrameXplore 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.GenErodeWorkflow for whole genome sequencing analysis, including patterns of genome erosion. Written in Snakemake workflow language.https://github.com/NBISweden/GenErodegenerodebiotools:generodeWorkflowhttp://edamontology.org/topic_0622GenomicsOtherGPL-3.0Maturehttp://edamontology.org/operation_0368Sequence maskinghttp://edamontology.org/operation_3211Genome indexinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2572BAMhttps://github.com/NBISweden/GenErodeGeneralhttps://github.com/NBISweden/GenErode/wikiUser manual10.1186/s12859-022-04757-035698034PMC9195343MethodHifiasmHifiasm: a haplotype-resolved assembler for accurate Hifi readshttps://github.com/chhylp123/hifiasmhifiasmbiotools:hifiasm0.16.1Command-line toolhttp://edamontology.org/topic_0196Sequence assemblyCC++MIThttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_0524De-novo assemblyhttps://hifiasm.readthedocs.io/en/latest/General10.1038/s41592-020-01056-533526886PMC7961889Chai-1Structure prediction of DNA, RNA, proteins, and small molecules using a multi-modal foundation model.https://github.com/chaidiscovery/chai-labchai-1biotools:chai-1http://edamontology.org/topic_0082Structure predictionPythonApache-2.0http://edamontology.org/operation_2442DNA structure predictionhttp://edamontology.org/operation_0476Ab initio structure predictionhttp://edamontology.org/operation_2441RNA structure predictionhttps://github.com/chaidiscovery/chai-labRepositoryhttps://github.com/chaidiscovery/chai-lab/blob/main/README.mdGeneral10.1101/2024.10.10.615955Preprint10.1101/2025.07.05.663018Preprint10.1038/s41592-022-01488-135637307PMC9184281PrimaryCite this if automatic MMseqs2 MSA generation is used.VerkkoVerkko is a hybrid genome assembly pipeline for telomere-to-telomere assembly of long reads.https://github.com/marbl/verkkoverkkobiotools:verkko2.3.2Command-line toolhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_4056Long-read sequencingLinuxPerlPythonBashFreewareMatureFree of chargehttp://edamontology.org/operation_3216Scaffoldinghttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1930FASTQ10.1038/s41587-023-01662-636797493PMC10427740Primary10.1101/gr.280383.12440389285PMC12212074Primary2.0.0SCANDAN-DICOM-labellingRegular expression used during the SCANDAN project to label MRI scans based on DICOM tag.https://github.com/SCANDAN-Team/SCANDAN-DICOM-labellingscandan-dicom-labellingbiotools:scandan-dicom-labellingscandanScripthttp://edamontology.org/topic_3473Data miningPythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3778Text annotationMain (only) function of the tools. Take text as input, and output the label derived from the regular expression used.https://github.com/SCANDAN-Team/SCANDAN-DICOM-labellingRepositorygithub repository
main branch is the paper branch, secondary are latest versionhttps://github.com/SCANDAN-Team/SCANDAN-DICOM-labellingSource codescandanhttps://github.com/SCANDAN-Team/SCANDAN-DICOM-labelling/blob/main/README.mdQuick start guide10.1101/2025.10.21.25338469Preprintv2Sub-Saharan Africa Brain Glioma SegmenterThe Sub-Saharan Africa Brain Glioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of intercranial meningiomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of gliomas in brain MRI scans to support clinical decision-making in both diagnosis and prognosis. This tool was trained on a cohort of patients from Sub-Saharan Africa.https://github.com/BIT-UPM/EUCAIM/tree/main/sub_saharan_africa_brain_glioma_segmentersub-saharan_africa_brain_glioma_segmenterbiotools:sub-saharan_africa_brain_glioma_segmenterv1.0Web applicationCommand-line toolWorkflowhttp://edamontology.org/topic_3444MRIhttp://edamontology.org/topic_3474Machine learningWindowsLinuxMacPythonCC-BY-NC-ND-4.0EUCAIMMatureFree of chargeOpen accesshttp://edamontology.org/operation_3553Image annotationhttps://segmenter.hope4kids.io/OtherMain app webpagehttps://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-KidsRepositoryGitHub repositoryhttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ssa-brain-glioma-segmenter/info-tabRepositoryEUCAIM harbor linkhttps://docs.hope4kids.io/HOPE-Segmenter-Kids/API documentationCitation instructionsTerms of useCode of conductRelease notesUser manualGeneralQuick start guide10.1007/978-3-031-76163-8_2010.1109/ISBI56570.2024.1063546910.48550/arXiv.2412.0409410.48550/arXiv.2412.04111Daniel Capellán-Martíndaniel.capellan@upm.eshttps://orcid.org/0000-0002-9743-0845Primary contactDeveloperContributorSupportAbhijeet Paridapabhijeet@childrensnational.orghttps://orcid.org/0000-0002-4978-0576DeveloperContributorSupportMaintainerZhifan Jiangzjiang@childrensnational.orgContributorDeveloperSupportMaría Jesus Ledesma-Carbayomj.ledesma@upm.eshttps://orcid.org/0000-0001-6846-3923Primary contactContributorMarius George Lingurarumlingura@childrensnational.orgPrimary contactContributorIntercranial Meningioma SegmenterThe Intercranial Meningioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of intercranial meningiomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of intercranial meningiomas in brain MRI scans to support clinical decision-making in both diagnosis and prognosis.https://github.com/BIT-UPM/EUCAIM/tree/main/intercranial_meningioma_segmenterintercranial_meningioma_segmenterbiotools:intercranial_meningioma_segmenterv1.0Web applicationCommand-line toolWorkflowhttp://edamontology.org/topic_3444MRIhttp://edamontology.org/topic_3474Machine learningWindowsLinuxMacPythonCC-BY-NC-ND-4.0EUCAIMMatureFree of chargeOpen accesshttp://edamontology.org/operation_3553Image annotationhttps://segmenter.hope4kids.io/OtherMain app webpagehttps://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-KidsRepositoryGitHub repositoryhttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/intracranial-meningioma-segmenter/info-tabRepositoryEUCAIM harbor linkhttps://docs.hope4kids.io/HOPE-Segmenter-Kids/API documentationCitation instructionsTerms of useCode of conductRelease notesUser manualGeneralQuick start guide10.1007/978-3-031-76163-8_2010.1109/ISBI56570.2024.1063546910.48550/arXiv.2412.0409410.48550/arXiv.2412.04111Daniel Capellán-Martíndaniel.capellan@upm.eshttps://orcid.org/0000-0002-9743-0845Primary contactDeveloperContributorSupportAbhijeet Paridapabhijeet@childrensnational.orghttps://orcid.org/0000-0002-4978-0576DeveloperContributorSupportMaintainerZhifan Jiangzjiang@childrensnational.orgContributorDeveloperSupportMaría Jesus Ledesma-Carbayomj.ledesma@upm.eshttps://orcid.org/0000-0001-6846-3923Primary contactContributorMarius George Lingurarumlingura@childrensnational.orgPrimary contactContributorBrain Metastasis SegmenterThe Brain Metastasis Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of brain metastases in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of brain metastases in MRI scans to support clinical decision-making in both diagnosis and prognosis.https://github.com/BIT-UPM/EUCAIM/tree/main/brain_metastasis_segmenterbrain_metastasis_segmenterbiotools:brain_metastasis_segmenterv1.0Web applicationCommand-line toolWorkflowhttp://edamontology.org/topic_3444MRIhttp://edamontology.org/topic_3474Machine learningWindowsLinuxMacPythonCC-BY-NC-ND-4.0EUCAIMMatureFree of chargeOpen accesshttp://edamontology.org/operation_3553Image annotationhttps://segmenter.hope4kids.io/OtherMain app webpagehttps://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-KidsRepositoryGitHub repositoryhttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/brain-metastasis-segmenter/info-tabRepositoryEUCAIM harbor linkhttps://docs.hope4kids.io/HOPE-Segmenter-Kids/API documentationCitation instructionsTerms of useCode of conductRelease notesUser manualGeneralQuick start guide10.1007/978-3-031-76163-8_2010.1109/ISBI56570.2024.1063546910.48550/arXiv.2412.0409410.48550/arXiv.2412.04111Daniel Capellán-Martíndaniel.capellan@upm.eshttps://orcid.org/0000-0002-9743-0845Primary contactDeveloperContributorSupportAbhijeet Paridapabhijeet@childrensnational.orghttps://orcid.org/0000-0002-4978-0576DeveloperContributorSupportMaintainerZhifan Jiangzjiang@childrensnational.orgContributorDeveloperSupportMaría Jesus Ledesma-Carbayomj.ledesma@upm.eshttps://orcid.org/0000-0001-6846-3923Primary contactContributorMarius George Lingurarumlingura@childrensnational.orgPrimary contactContributorBrain Glioma SegmenterThe Brain Glioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of brain gliomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of brain gliomas in MRI scans to support clinical decision-making in both diagnosis and prognosis.https://github.com/BIT-UPM/EUCAIM/tree/main/brain_glioma_segmenterbrain_glioma_segmenterbiotools:brain_glioma_segmenterv1.0Command-line toolWeb applicationWorkflowhttp://edamontology.org/topic_3444MRIhttp://edamontology.org/topic_3474Machine learningMacLinuxWindowsPythonCC-BY-NC-ND-4.0EUCAIMMatureFree of chargeOpen accesshttp://edamontology.org/operation_3553Image annotationhttps://segmenter.hope4kids.io/OtherMain app webpagehttps://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-KidsRepositoryGitHub repositoryhttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/brain-glioma-segmenter/info-tabRepositoryEUCAIM harbor linkhttps://docs.hope4kids.io/HOPE-Segmenter-Kids/API documentationCitation instructionsTerms of useCode of conductRelease notesUser manualGeneralQuick start guide10.1007/978-3-031-76163-8_2010.1109/ISBI56570.2024.1063546910.48550/arXiv.2412.0409410.48550/arXiv.2412.04111Daniel Capellán-Martíndaniel.capellan@upm.eshttps://orcid.org/0000-0002-9743-0845Primary contactContributorDeveloperSupportAbhijeet Paridapabhijeet@childrensnational.orghttps://orcid.org/0000-0002-4978-0576ContributorDeveloperSupportMaintainerZhifan Jiangzjiang@childrensnational.orgContributorDeveloperSupportMaría Jesus Ledesma-Carbayomj.ledesma@upm.eshttps://orcid.org/0000-0001-6846-3923Primary contactContributorMarius George Lingurarumlingura@childrensnational.orgPrimary contactContributorPediatric Brain Tumor SegmenterThe Pediatric Brain Tumor Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of pediatric brain tumors in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of pediatric brain tumors in MRI scans to support clinical decision-making in both diagnosis and prognosis.https://github.com/BIT-UPM/EUCAIM/tree/main/pediatric_brain_tumor_segmenterpediatric_brain_tumor_segmenterbiotools:pediatric_brain_tumor_segmenterv1.0Web applicationCommand-line toolWorkflowhttp://edamontology.org/topic_3444MRIhttp://edamontology.org/topic_3474Machine learningWindowsLinuxMacPythonCC-BY-NC-SA-4.0EUCAIMMatureFree of chargeOpen accesshttp://edamontology.org/operation_3553Image annotationhttps://segmenter.hope4kids.io/OtherMain app webpagehttps://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-KidsRepositoryGitHub repositoryhttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/pediatric-brain-tumor-segmenter/info-tabRepositoryEUCAIM harbor linkhttps://docs.hope4kids.io/HOPE-Segmenter-Kids/API documentationCitation instructionsTerms of useCode of conductRelease notesUser manualGeneralQuick start guide10.1007/978-3-031-76163-8_2010.1109/ISBI56570.2024.1063546910.48550/arXiv.2412.0409410.48550/arXiv.2412.04111Daniel Capellán-Martíndaniel.capellan@upm.eshttps://orcid.org/0000-0002-9743-0845PersonPrimary contactDeveloperContributorSupportAbhijeet Paridapabhijeet@childrensnational.orghttps://orcid.org/0000-0002-4978-0576DeveloperContributorSupportMaintainerZhifan Jiangzjiang@childrensnational.orgContributorDeveloperSupportMaría Jesus Ledesma-Carbayomj.ledesma@upm.eshttps://orcid.org/0000-0001-6846-3923Primary contactContributorMarius George Lingurarumlingura@childrensnational.orgPrimary contactContributorRACLAHERACLAHE (Region-Adaptive Contrast Limited Adaptive Histogram Equalization) is an image enhancement method specifically designed for improving CNN-based segmentation of the prostate and prostatic zones in T2-Weighted MR images.https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/raclahe/info-tabraclahebiotools:raclahe3.0Workflowhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3474Machine learningWindowsLinuxMacPythonEUPL-1.2eucaimhttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/raclahe/info-tabSoftware cataloguehttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/raclahe/info-tabhttps://github.com/dzaridis/RACLAHE_Image_Enhancement_for_CNN_model_segmentation/tree/mainRepositoryOfficial Git Repository of RACLAHEhttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/raclaheContainer fileEUCAIM Harbor RACLAHE Image,
Can be pulled via the following command after successfull login to Harbor
docker pull harbor.eucaim.cancerimage.eu/processing-tools/raclahe@sha256:b3e9d383dfed95b7a6f1cca9dcbd271379946c97188e162d66f0d96b923410473.0https://drive.eucaim.cancerimage.eu/f/2359User manualUser Manual in the EUCAIM Drivehttps://github.com/dzaridis/RACLAHE_Image_Enhancement_for_CNN_model_segmentation/tree/mainQuick start guide10.1038/s41598-023-27671-8MethodFoundation for Research and Technology Hellas (FORTH)https://www.forth.gr/en/home/InstituteProviderDimitrios I. Zaridisdimzaridis@gmail.comhttps://orcid.org/0000-0003-2549-3887PersonDeveloperSenior Researcher@FORTHNikolaos Tachosntachos@gmail.comhttps://orcid.org/0000-0002-8627-6352ContributorSenior Researcher@FORTHDimitrios I. Fotiadisfotiadis@uoi.grhttps://orcid.org/0000-0002-7362-5082PersonContributorProfessor, University of IoanninaBoltzBoltz is the name given to a set of models designed for biomolecular interaction prediction.https://github.com/jwohlwend/boltzboltzbiotools:boltzCommand-line toolhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_2275Molecular modellingPythonMITMaturehttps://github.com/jwohlwend/boltz/blob/main/README.mdOtherGitHub README.10.1101/2025.06.14.65970710.1101/2024.11.19.62416710.1038/s41592-022-01488-135637307PMC9184281Cite if you use automatic MSA generation.pathway-subtypingDisease-agnostic Python framework for discovering molecular subtypes using pathway-level analysis and Gaussian mixture model clustering with built-in validation gateshttps://codeberg.org/pathways/pathway-subtyping-frameworkpathway-subtypingbiotools:pathway-subtyping0.4.00.3.10.5.00.6.20.6.3LibraryCommand-line toolhttp://edamontology.org/topic_3391Omicshttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_4019BiosciencesWindowsMacLinuxPythonMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_2495Expression analysishttp://edamontology.org/operation_3432Clusteringhttp://edamontology.org/operation_2945Data analysishttps://pypi.org/project/pathway-subtyping/Software cataloguePython Library Repositoryhttps://codeberg.org/pathways/pathway-subtyping-framework/src/branch/main/docsOtherDocumentationhttps://codeberg.org/pathways/pathway-subtyping-frameworkOtherSource code repositoryhttps://pypi.org/project/pathway-subtyping/Software packagepip install pathway-subtyping
Or with all extras:
pip install pathway-subtyping[viz,graph]0.3.1https://codeberg.org/pathways/pathway-subtyping-framework/src/branch/main/docsUser manual10.21203/rs.3.rs-8913089/v1PreprintTitle: Pathway-Based Molecular Subtyping Reveals a GABA-Collapsed Autism Subgroup and Cross-Disease Convergence with Schizophrenia in Human Cerebral CortexUM - Automated detection and segmentation NSCLCAutomated detection and segmentation of non-small cell lung cancer computed tomography imageshttps://github.com/precision-medicine-um/EUCAIM/tree/main/DuneAIautomated_detection_and_segmentation_nsclcbiotools:automated_detection_and_segmentation_nsclchttp://edamontology.org/topic_3365Data architecture, analysis and designWindowsMacLinuxPythonEUCAIMFree of chargeOpen access10.1038/s41467-022-30841-3PicoporeReduce the size of Oxford Nanopore Technologies' datasets without losing information.https://github.com/scottgigante/picoporepicoporebiotools:picopore1.2.0Libraryhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0622GenomicsWindowsLinuxMacPythonGPL-3.0BiocondaPython Software Foundationhttps://anaconda.org/bioconda/picoporeRepositoryBioconda packagehttps://pypi.org/project/picopore/RepositoryPython Software Foundation10.12688/f1000research.11022.1PrimaryScott GigantePersonPrimary contactInChI Open Education Resource (OER)The InChI Open Education Resource (OER) provides resources, training materials, and information related to the IUPAC International Chemical Identifier (InChI). It aggregates over 100 resources and offers search and filtering functionalities, aiming to support chemical educators and promote understanding of InChI's role in science.https://www.inchi-trust.org/oer/oerbiotools:oerhttp://edamontology.org/topic_3406Ear, nose and throat medicinehttp://edamontology.org/topic_3314Chemistryhttp://edamontology.org/topic_4044Data protectionhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_2422Data retrieval10.1515/CTI-2023-000938601265PMC1100345610.1007/S00106-024-01465-438625372Robert E. Belfordrebelford@ualr.eduhttps://orcid.org/0000-0002-4933-6379PersonC V Degendegen.chantal@mh-hannover.dePersonSLiMEvolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Includes a graphical modeling environment.https://messerlab.org/slim/SLiM_softwarebiotools:SLiM_software5.2Command-line toolDesktop applicationhttp://edamontology.org/topic_0610Ecologyhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3299Evolutionary biologyWindowsLinuxMacC++GPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0230Sequence generationhttp://edamontology.org/operation_0550DNA substitution modellinghttp://edamontology.org/operation_3946Ecological modellingRun individual-based eco-evolutionary simulations with explicit geneticshttps://messerlab.org/slim/Software catalogueSLiM home page in the Messer Lab websitehttps://github.com/MesserLab/SLiMRepositoryGitHub repository for SLiMhttps://groups.google.com/g/slim-discussDiscussion forumDiscussion forum for SLiM questionshttps://groups.google.com/g/slim-announceMailing listAnnouncements mailing listhttp://benhaller.com/slim/SLiM.zipSource codeA source archive for the command-line `slim` tool only. Complete source code is on GitHub, but most platforms have an installer anyway; see the manual, chapter 2, for installation instructions.https://github.com/MesserLab/SLiM/releases/latestDownloads pageThe GitHub page for the current release version, to obtain full source code.http://benhaller.com/slim/SLiM_Manual.pdfUser manualThe manual for SLiM itselfhttp://benhaller.com/slim/Eidos_Manual.pdfUser manualThe manual for Eidos, the scripting language used by SLiMhttp://benhaller.com/slim/SLiMEidosRefSheets.zipQuick start guideQuick reference sheets for SLiM and Eidos10.1093/molbev/msy22830517680PMC6389312Primary3.0B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond the Wright–Fisher Model. Molecular Biology and Evolution 36(3), 632–637.10.1093/molbev/msy23730590560PMC6501880Method3.0B.C. Haller, P.W. Messer. (2019). Evolutionary modeling in SLiM 3 for beginners. Molecular Biology and Evolution 36(5), 1101–1109.10.1111/1755-0998.1296830565882PMC6393187Primary3.0B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources 19(2), 552–566.10.1101/2025.08.07.66915540832315PMC12363870Primary5.0BC Haller, PL Ralph, PW Messer. (2025). SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes. bioRxiv, 2025.08. 07.66915510.1086/72360137130229PMC10793872Primary4.0B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary modeling. The American Naturalist 201(5), E127–E139.Philipp Messermesser@cornell.eduhttps://messerlab.orghttps://orcid.org/0000-0001-8453-9377PersonPrimary contactBenjamin C. Hallerbhaller@benhaller.comhttp://benhaller.comhttps://orcid.org/0000-0003-1874-8327PersonPrimary contactGromacsVersatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since it is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.http://www.gromacs.org/gromacsbiotools:gromacsCommand-line toolLibrarySuitehttp://edamontology.org/topic_0176Molecular dynamicsLinuxLGPL-2.1BioExcelMatureFree of chargehttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/data_0883Structurehttp://edamontology.org/format_1476PDBhttp://www.gromacs.org/DownloadsSoftware packagehttp://www.gromacs.org/DocumentationGeneral10.1016/j.softx.2015.06.001Benchmarking study10.1002/jcc.2029116211538Benchmarking study10.1063/5.001851633032406Benchmarking study10.1007/978-3-319-15976-8_1Benchmarking study10.1093/bioinformatics/btt05523407358PMC360559910.1021/ct700301q26620784Benchmarking study10.1007/s008940100045Benchmarking study10.1016/0010-4655(95)00042-EBenchmarking study10.1002/jcc.2403026238484PMC5042102Benchmarking study10.1002/jcc.2601131260119Benchmarking studyGROMACS supporthttp://www.gromacs.org/support/mailing_listsPersonPrimary contacthicapIdentify cap locus serotype and structure in your Haemophilus influenzae assemblies.https://github.com/scwatts/hicaphicapbiotools:hicap1.0.4Command-line tool10.1128/jcm.00190-1930944197PMC6535587bio.toolsThe community registry of computational tools and data resources for biosciences.https://bio.toolsbio.toolsbiotools:bio.toolsRRID:SCR_014695rridWeb APIDatabase portalWeb applicationhttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0219Data curation and archivalhttp://edamontology.org/topic_3307Computational biologyJavaScriptPythonGPL-3.0EmergingFree of chargeOpen accessToolsDenmarkhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/data_3671Texthttp://edamontology.org/format_1964plain text format (unformatted)https://biotools.readthedocs.io/en/latest/support.html?highlight=helpHelpdeskhttps://github.com/bio-tools/biotoolsregistry/issuesIssue trackerhttps://biotools.readthedocs.io/en/latest/contributors_guide.html#mailing-listMailing listhttps://github.com/bio-tools/biotoolsregistry/Repositoryhttps://github.com/bio-tools/biotoolsRegistrySource codehttps://biotools.readthedocs.io/en/latest/api_usage_guide.htmlAPI documentationAPI usage guidehttps://biotools.readthedocs.io/en/latest/api_reference.htmlAPI documentationAPI Referencehttps://biotools.readthedocs.io/en/latest/publications.html#citationCitation instructionshttps://biotools.readthedocs.io/en/latest/contributors_guide.htmlContributions policyhttps://biotools.readthedocs.io/en/latest/Generalhttps://biotools.readthedocs.io/en/latest/governance.htmlGovernancehttps://biotools.readthedocs.io/en/latest/curators_guide.htmlUser manualCurators Guide10.1093/nar/gkv1116Primary10.12688/f1000research.12974.1Other10.1093/gigascience/gix022Other10.1007/s10009-015-0392-zOtherContributorshttps://biotools.readthedocs.io/en/latest/contributors.htmlPerson