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http://www.imagwiki.nibib.nih.gov/

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).

Proper citation: Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki (RRID:SCR_008046) Copy   

•   Source: SciCrunch Registry

https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_016647.pdf

Instrument for nanoparticle tracking analysis. A semi-automated method for the characterization of extracellular vesicles with associated analysis software by ParticleMetrix GmbH.

Proper citation: Particle Metrix: ZetaView Nanoparticle Tracking Analyzer (RRID:SCR_016647) Copy   

•   Source: SciCrunch Registry

https://www.nature.com/articles/s41467-018-03367-w

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.

Proper citation: nanoPOTS (RRID:SCR_017129) Copy   

•   Source: SciCrunch Registry

https://www.varian.com/

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.

Proper citation: Varian Medical Systems, Inc. (RRID:SCR_017372) Copy   

•   Source: SciCrunch Registry

http://www.genboree.org/java-bin/EpigenomeAtlas/workbench.jsp?isPublic=yes&context=EpigenomeAtlas

Service where users are able to upload and store data, access bioinformatics tools, and perform analyses.

Proper citation: Genboree Workbench (RRID:SCR_011864) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/lookseq/

A web-based application for alignment visualization, browsing and analysis of genome sequence data.

Proper citation: LookSeq (RRID:SCR_005625) Copy   

•   Source: SciCrunch Registry

http://www.uni-koeln.de/med-fak/cgars/

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.

Proper citation: CGARS (RRID:SCR_006404) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.babraham.ac.uk/projects/chipmonk/

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

Proper citation: ChIPMonk (RRID:SCR_002975) Copy   

•   Source: SciCrunch Registry

https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/

Software tool to visualize and analyse high throughput mapped sequence data.

Proper citation: SeqMonk (RRID:SCR_001913) Copy   

•   Source: SciCrunch Registry

http://cvlab.epfl.ch/NeuroMorph

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.

Proper citation: NeuroMorph (RRID:SCR_002091) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dmetanalyzer/

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.

Proper citation: DMET-Analyzer (RRID:SCR_002030) Copy   

•   Source: SciCrunch Registry

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Jackal

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.

Proper citation: Jackal (RRID:SCR_008665) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.ingenuity.com/products/pathways_analysis.html

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.

Proper citation: Ingenuity Pathway Analysis (RRID:SCR_008653) Copy   

•   Source: SciCrunch Registry

http://spotfire.tibco.com/

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

Proper citation: Spotfire (RRID:SCR_008858) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/~kgaulton/chaos.shtml

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.

Proper citation: CHAoS (RRID:SCR_005174) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hivcd/

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.

Proper citation: HIVCD (RRID:SCR_005201) Copy   

•   Source: SciCrunch Registry

http://www.illumina.com/

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.

Proper citation: Illumina (RRID:SCR_010233) Copy   

•   Source: SciCrunch Registry

http://treestoolbox.org/

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.

Proper citation: TREES toolbox (RRID:SCR_010457) Copy   

•   Source: SciCrunch Registry

https://www.bioinfor.com/peaks-studio/

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.

Proper citation: PEAKS Studio (RRID:SCR_022841) Copy   

•   Source: SciCrunch Registry

http://www.bioquest.org/esteem/esteem_details.php?product_id=248

Software to allow construction, analysis, and simulation of complex models in spreadsheet format.

Proper citation: PopTools (RRID:SCR_022840) Copy   

•   Source: SciCrunch Registry