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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki Resource Report Resource Website 10+ mentions |
Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki (RRID:SCR_008046) | IMAG | group | Special interest group that brings together program officers who have a shared interest in applying modeling and analysis methods to biomedical systems. The meetings are formatted to facilitate an open discussion of what is currently being supported, and for planning future directions in these areas. At each meeting, time is allotted to hear focused presentations from one or two participants to discuss issues relating to modeling and analysis across the government agencies. Discussions also occur online, and participants are informed of talks, conferences and other activities of interest to the group. IMAG recognized that the modeling community is on the forefront of thinking across the biological continuum, rather than just focusing at one scale or level of resolution. In addition IMAG identified a strong desire among modelers to form multi-disciplinary partnerships across varied research communities. Overall Intent of IMAG through the MSM Consortium is: * To develop new methodologies that span across biological scales * To develop multiscale methodologies applicable to biomedical, biological and behavioral research * To develop methodologies within the local multidisciplinary team and within the larger Framework environment * To further promote multiscale modeling through model sharing This wiki contains information relevant to the IMAG (Interagency Modeling and Analysis Group) and the MSM (Multi-scale Modeling Consortium). | environment, analysis, behavioral, biological, biomedical, continuum, modeling, research, scale, system |
is listed by: 3DVC has parent organization: National Institute of Biomedical Imaging and Bioengineering |
NIBIB ; NIH Blueprint for Neuroscience Research |
nif-0000-10261 | SCR_008046 | IMAG wiki, MSM wiki | 2026-07-25 12:06:49 | 15 | |||||||
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Particle Metrix: ZetaView Nanoparticle Tracking Analyzer Resource Report Resource Website 100+ mentions |
Particle Metrix: ZetaView Nanoparticle Tracking Analyzer (RRID:SCR_016647) | ZetaView NTA | instrument resource | Instrument for nanoparticle tracking analysis. A semi-automated method for the characterization of extracellular vesicles with associated analysis software by ParticleMetrix GmbH. | instrument, nanoparticle, tracking, analysis, ParticleMetrix GmbH, extracellular, vesicles, method | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_016647.pdf | https://partoshar.com/administrator/files/UploadFile/DLS/Zeta-View/Catalog/zetaview-en.pdf | SCR_016647 | ZetaView NTA, ZetaView Nanoparticle Tracking Analyzer | 2026-07-25 12:08:26 | 290 | ||||||||
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nanoPOTS Resource Report Resource Website 1+ mentions |
nanoPOTS (RRID:SCR_017129) | instrument resource | Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes. | nanodroplet, processing, platform, quantitative, proteome, profiling, analysis, mammalian, cell, small, volume | has parent organization: Pacific Northwest National Laboratory | NIBIB R21 EB020976; NCI R33 CA225248; NIGMS P41 GM103493; NIDDK UC4 DK104167; NIDDK DP3 DK110844; NIH Office Of The Director S10 OD016350; JDRF |
PMID:29491378 | SCR_017129 | 2026-07-25 12:08:27 | 1 | |||||||||
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Varian Medical Systems, Inc. Resource Report Resource Website 1+ mentions |
Varian Medical Systems, Inc. (RRID:SCR_017372) | commercial organization | Manufacturer located in Palo Alto, California, USA, that has made developments in fields of radiotherapy, radiosurgery, X-ray tube technology, digital image detectors, cargo screening, and non-destructive testing. Varian technology and software for processing diagnostic X-ray images is being used in radiotherapy and analysis. | Manufacturer, commercial, company, component, radiotherapy, spectrometry, software, analysis, therapy, medical, imaging, technology, development | grid.482350.8, ISNI: 0000 0004 0482 3442, Wikidata: Q30343843 | https://ror.org/049tb1q96 | SCR_017372 | Varian | 2026-07-25 12:08:32 | 8 | |||||||||
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Genboree Workbench Resource Report Resource Website |
Genboree Workbench (RRID:SCR_011864) | Genboree | service resource | Service where users are able to upload and store data, access bioinformatics tools, and perform analyses. | metagenome, visualization, genome, transcriptiome, cistrome, epigenome, analysis, rna-seq, chip-seq |
is listed by: OMICtools has parent organization: Baylor University; Texas; USA |
Free for academic use | OMICS_01142 | SCR_011864 | 2026-07-25 12:07:26 | 0 | ||||||||
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LookSeq Resource Report Resource Website 1+ mentions |
LookSeq (RRID:SCR_005625) | LookSeq | software resource | A web-based application for alignment visualization, browsing and analysis of genome sequence data. | alignment, visualization, browsing, analysis, genome, sequence |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00886 | SCR_005625 | 2026-07-25 12:06:07 | 5 | |||||||||
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CGARS Resource Report Resource Website |
CGARS (RRID:SCR_006404) | CGARS | software resource | Software package to dissect random from non-random patterns in copy number data and thereby to assess significantly enriched somatic copy number aberrations (SCNA) across a set of tumor specimens or cell lines. | genome, analysis |
is listed by: OMICtools has parent organization: University of Cologne; Cologne; Germany |
Cancer | PMID:24413525 | GNU General Public License, v3 or later | OMICS_02210 | SCR_006404 | CGARS: Cancer Genome Analysis by Rank Sums, Cancer Genome Analysis by Rank Sums | 2026-07-25 12:06:20 | 0 | |||||
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ChIPMonk Resource Report Resource Website 1+ mentions |
ChIPMonk (RRID:SCR_002975) | ChIPMonk | software resource | Software tool to visualize and analyse ChIP-on-chip array data. Main features: * Import of data from Nimblegen arrays (other formats can be added if people send us examples) * Normalization of data (both per array and per probe) * Various data plotting options to assess data quality and the effectiveness of normalization * Creation of data groups for visualization and analysis * Visualization of data against an annotated genome. * Statistical analysis of data to find probes of interest * Creation of reports containing probes, data and genome annotation Note: This project is no longer being developed, but critical bug fixes will still be provided | java, chip, chip-on-chip, plotting, normalization, visualization, genome, annotation, probe, array, analysis |
is listed by: OMICtools has parent organization: Babraham Institute |
Free, Available for download, Freely available | OMICS_02043, nif-0000-30159 | http://www.bioinformatics.bbsrc.ac.uk/projects/chipmonk/ | SCR_002975 | 2026-07-25 12:05:35 | 4 | |||||||
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SeqMonk Resource Report Resource Website 500+ mentions |
SeqMonk (RRID:SCR_001913) | SeqMonk | software resource | Software tool to visualize and analyse high throughput mapped sequence data. | java, high throughput sequencing, mapped, visualization, analysis |
is listed by: OMICtools has parent organization: Babraham Institute |
Free, Available for download, Freely available | OMICS_01936 | http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ | SCR_001913 | 2026-07-25 12:05:12 | 594 | |||||||
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NeuroMorph Resource Report Resource Website 10+ mentions |
NeuroMorph (RRID:SCR_002091) | NeuroMorph | software resource | A toolset for the morphometric analysis and visualization of 3D models derived from electron microscopy image stacks. It is designed to import, analyze, and visualize mesh models. It has been designed specifically for the morphological analysis of 3D objects derived from serial electron microscopy images of brain tissue, although much of its functionality can be applied to any 3D mesh. These models can be generated by software that allows the images to be segmented so that 3D objects can be built. These objects can be generated by any 3D image segmentation software, such as ilastik or Fiji. The NeuroMorph toolset has been developed as a set of add-ons for Blender, a widely used free and open source 3D modeling software package. | electron microscopic imaging assay, morphometry, analysis, visualization, 3d |
is related to: Blender has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland |
Free | SciRes_000156 | SCR_002091 | NeuroMorph Toolkit | 2026-07-25 12:05:19 | 35 | |||||||
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DMET-Analyzer Resource Report Resource Website 1+ mentions |
DMET-Analyzer (RRID:SCR_002030) | DMET-Analyzer | software resource | Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way. | drug, metabolism, enzyme, transporter, affymetrix, variation, genome, clinical, affymetrix dmet, single nucleotide polymorphism, annotation, analysis, pharmacogenomic, pathway |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23035929 | Free, Available for download, Freely available | OMICS_01920 | SCR_002030 | DMETANALYZER, DMETANALYZER - A tool for supporting pharmacogenomics data analysis | 2026-07-25 12:05:18 | 1 | ||||||
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Jackal Resource Report Resource Website 10+ mentions |
Jackal (RRID:SCR_008665) | software resource | Jackal is a collection of programs designed for the modeling and analysis of protein structures. Its core program is a versatile homology modeling package. It contains twelve individual programs, each with their own function. | software, software repository, modeling, analysis, protein structure |
has parent organization: Columbia University; New York; USA has parent organization: Howard Hughes Medical Institute |
NSF DBI-9904841; NIGMS 5 R37 GM30518 |
Public, Free | nif-0000-33373 | SCR_008665 | 2026-07-25 12:06:54 | 14 | ||||||||
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Ingenuity Pathway Analysis Resource Report Resource Website 5000+ mentions Rating or validation data |
Ingenuity Pathway Analysis (RRID:SCR_008653) | IPA | pathway analysis tool | A web-based software application that enables users to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays, metabolomics, proteomics, and RNA-Seq experiments, and small-scale experiments that generate gene and chemical lists. Users can search for targeted information on genes, proteins, chemicals, and drugs, and build interactive models of experimental systems. IPA allows exploration of molecular, chemical, gene, protein and miRNA interactions, creation of custom molecular pathways, and the ability to view and modify metabolic, signaling, and toxicological canonical pathways. In addition to the networks and pathways that can be created, IPA can provide multiple layering of additional information, such as drugs, disease genes, expression data, cellular functions and processes, or a researchers own genes or chemicals of interest. | software, drug, gene, analysis, chemical, metabolic, model, pathway, protein, signal, molecular signaling, genomic, pathway analysis tool |
uses: Ingenuity Pathways Knowledge Base is listed by: Biositemaps is listed by: OMICtools is listed by: SoftCite |
Commercial license | nif-0000-33144, OMICS_00399 | http://www.ingenuity.com/products/ipa, http://www.ingenuity.com/products/ipa/microrna-research | SCR_008653 | QIAGEN Ingenuity Pathway Analysis | 2026-07-25 12:06:50 | 6581 | ||||||
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Spotfire Resource Report Resource Website 100+ mentions |
Spotfire (RRID:SCR_008858) | Spotfire | software resource | The Spotfire Gene Ontology Advantage Application integrates GO annotations with gene expression analysis in Spotfire DecisionSite for Functional Genomics. Researchers can select a subset of genes in DecisionSite visualizations and display their distribution in the Gene Ontology hierarchy. Similarly, selection of any process, function or cellular location in the Gene Ontology hierarchy automatically marks the corresponding genes in DecisionSite visualizations. Platform: Windows compatible | analysis, predictive analytics, big data, visualization, gene ontology, annotation, gene expression, functional genomics, gene, function, cellular location, statistical analysis, genomics |
is listed by: Gene Ontology Tools is listed by: Metabolomics Workbench is related to: Gene Ontology |
Commercial license. Spotfire is available for purchase (individual license / enterprise use) / Free trial. | nlx_149169 | SCR_008858 | Tibco Spotfire, Spotfire Inc., Spotfire Gene Ontology Advantage Application, Spotfire - TIBCO Software | 2026-07-25 12:06:54 | 474 | |||||||
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CHAoS Resource Report Resource Website 10+ mentions |
CHAoS (RRID:SCR_005174) | CHAoS | software resource | A Perl-based system for annotation of variants identified in high-throughput sequencing experiments. Functionality includes annotation of variants with information relating to population genetics, known transcripts, positional records, and sequence motif-based prediction. In addition, annotated variants can be summarized and extracted to facilitate downstream analysis. There is also basic support for gene-based biological annotation, and eventually will include tools for variant and genotype analysis and visualization. | annotation, analysis, visualization, variant, high-throughput sequencing, perl, population genetic, transcript, positional record, sequence, motif, genotype |
is listed by: OMICtools has parent organization: Wellcome Trust Centre for Human Genetics |
GNU General Public License, v2 | OMICS_00170 | SCR_005174 | chaos - Annotation analysis and visualization of variants from high-throughput sequencing experiments | 2026-07-25 12:06:02 | 26 | |||||||
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HIVCD Resource Report Resource Website |
HIVCD (RRID:SCR_005201) | HIVCD | software resource | Informatics software tool to identify patient sequences that are too similar to happen by chance alone. Highly similar sequences are likely to occur from contamination or other situations like geographic linkage. | java, perl, contamination, sequencing, error, pairwise comparison, testing, analysis, contamination screening |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23583427 | Apache License, v2 | OMICS_00220 | SCR_005201 | HIVCD - Informatics tool for contamination screening in the HIV sequencing lab, HIV Contamination Detection | 2026-07-25 12:06:00 | 0 | ||||||
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Illumina Resource Report Resource Website 1000+ mentions |
Illumina (RRID:SCR_010233) | Illumina, Inc. | commercial organization | American company incorporated that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Provides a line of products and services that serve the sequencing, genotyping and gene expression and proteomics markets. Its headquarters are located in San Diego, California. | Commercial, organization, develope, manufacture, system, analysis, genetic, sequencing, genotyping, gene, expression, proteomic |
is related to: fermi-lite is related to: Illumina: NextSeq 2000 system is parent organization of: Strelka2 is parent organization of: Tk-GO is parent organization of: BaseSpace is parent organization of: Illumina: iSeq 100 Sequencing System |
nlx_156846, grid.185669.5, Wikidata: Q2068984, ISNI: 0000 0004 0507 3954 | https://ror.org/05k34t975 | SCR_010233 | Inc., Illumina | 2026-07-25 12:06:58 | 2340 | |||||||
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TREES toolbox Resource Report Resource Website 10+ mentions |
TREES toolbox (RRID:SCR_010457) | TREES toolbox | software resource | Software package, written in Matlab (Mathworks, Natick, MA), providing tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees. It provides the basic tools to edit, visualize and analyze dendritic and axonal trees, methods for quantitatively comparing branching structures between neurons, and tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distance. | neuronal branching, microscopy, neuron, matlab, visualization, rendering, reconstruction, analysis, modeling, morphology, dendrite, axon, computational neuroanatomy, tree |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
Max Planck Society ; Wellcome Trust ; Gatsby Charitable Foundation ; Alexander von Humboldt-Stiftung ; European Research Council |
PMID:20700495 | GNU General Public License v3, Creative Commons Attribution-NonCommercial-ShareAlike License v3, The community can contribute to this resource | nlx_157723 | http://www.nitrc.org/projects/treestoolbox | SCR_010457 | treestoolbox - A Matlab toolbox to generate edit visualize and analyze neuronal structure | 2026-07-25 12:07:03 | 28 | ||||
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PEAKS Studio Resource Report Resource Website 10+ mentions |
PEAKS Studio (RRID:SCR_022841) | software resource | Software platform with complete solutions for discovery proteomics, including protein identification and quantification, analysis of post translational modifications and sequence variants (mutations), and peptide/protein de novo sequencing. | Bioinformatics Solutions Inc., peptide de novo sequencing, mass spectrometry, discovery proteomics, protein identification and quantification, analysis, post translational modifications, sequence variants, mutations, | PMID:14558135 | Restricted | SCR_022841 | PEAKS Studio Xpro | 2026-07-25 12:10:22 | 13 | |||||||||
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PopTools Resource Report Resource Website 10+ mentions |
PopTools (RRID:SCR_022840) | software resource | Software to allow construction, analysis, and simulation of complex models in spreadsheet format. | construction, analysis, simulation, complex models, spreadsheet format | Free, Available for download, Freely available | https://www.maa.org/press/periodicals/loci/resources/poptools | SCR_022840 | 2026-07-25 12:10:25 | 49 |
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