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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Atlas3D Resource Report Resource Website 10+ mentions |
Atlas3D (RRID:SCR_001808) | software resource, atlas, software application, data processing software, data or information resource, data visualization software | A multi-platform visualization tool which allows import and visualization of 3-D atlas structures in combination with tomographic and histological image data. The tool allows visualization and analysis of the reconstructed atlas framework, surface modeling and rotation of selected structures, user-defined slicing at any chosen angle, and import of data produced by the user for merging with the atlas framework. Tomographic image data in NIfTI (Neuroimaging Informatics Technology Initiative) file format, VRML and PNG files can be imported and visualized within the atlas framework. XYZ coordinate lists are also supported. Atlases that are available with the tool include mouse brain structures (3-D reconstructed from The Mouse Brain in Stereotaxic Coordinates by Paxinos and Franklin (2001)) and rat brain structures (3-D reconstructed from The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (2005)). Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images. | analysis, brain, histological, mouse, rat, slicing, structure, 3d, tomographic, visualization, neuroimaging, image, magnetic resonance, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Oslo; Oslo; Norway |
Research Council of Norway ; NIH ; NIBIB R01-EB00790; NCRR U24-RR021382 |
Free, Freely available | nif-0000-10373 | http://www.nitrc.org/projects/incf_atlas3d | SCR_001808 | Neural Systems and Graphics Computing Laboratory: Atlas3D Software, NeSys Atlas3D | 2026-02-12 09:43:14 | 17 | ||||||
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MEME Suite - Motif-based sequence analysis tools Resource Report Resource Website 1000+ mentions |
MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) | MEME Suite | analysis service resource, source code, software resource, service resource, production service resource, database, software application, data analysis service, data analysis software, data processing software, data or information resource | Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use. | gene ontology, motif, comparative genomics, dna regulatory motif, dna sequence, dna, gene, transcription factor, genome, protein, analysis, function analysis, comparison, cluster, enrichment analysis, sequence analysis, bio.tools, FASEB list |
lists: DREME is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Glam2 is related to: ANNOgesic is related to: memesuite-lite has parent organization: National Biomedical Computation Resource is parent organization of: GOMO - Gene Ontology for Motifs |
NCRR R01 RR021692 | PMID:19458158 DOI:10.1093/nar/gkl198 |
Free, Freely available | nif-0000-10298, biotools:meme_suite, OMICS_08103 | https://bio.tools/meme_suite | http://meme.sdsc.edu/meme4_6_1/intro.html, http://meme.nbcr.net/meme/, https://sources.debian.org/src/meme/ | SCR_001783 | The MEME Suite | 2026-02-12 09:43:14 | 2091 | |||
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Appion Package Resource Report Resource Website 10+ mentions |
Appion Package (RRID:SCR_016734) | Appion | software resource, software application, data processing software, image processing software, image analysis software | Software package for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools. | processing, analysis, electron, microscope, image | NCRR RR17573; NCRR RR023093; ARCS |
PMID:19263523 | Free, Available for download, Freely available | http://www.appion.org | SCR_016734 | 2026-02-12 09:46:24 | 16 | |||||||
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BinPacker Resource Report Resource Website 10+ mentions |
BinPacker (RRID:SCR_017038) | software resource, software application, data analysis software, data processing software | Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcriptome, assembler, RNAseq, data, full, length, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; NSF 1553680; NCRR P20 RR01 6460; NIGMS P20 GM103429 |
PMID:26894997 | Free, Available for download, Freely available | OMICS_11199, biotools:binpacker | http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download https://bio.tools/binpacker |
SCR_017038 | 2026-02-12 09:46:28 | 10 | ||||||
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Montage RTS2000 Resource Report Resource Website |
Montage RTS2000 (RRID:SCR_013439) | software application, image processing software, software resource, data processing software | Software program for creating montages from multiphoton microscopy. | microscopy, mosaic, montage, image |
is listed by: 3DVC has parent organization: National Center for Microscopy and Imaging Research |
NCRR P41 RR04050 | GNU General Public License | nif-0000-10515 | SCR_013439 | 2026-02-12 09:45:40 | 0 | ||||||||
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Northwestern University Schizophrenia Data and Software Tool (NUSDAST) Resource Report Resource Website |
Northwestern University Schizophrenia Data and Software Tool (NUSDAST) (RRID:SCR_014153) | NUSDAT | data or information resource, database, image collection | A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data. | database, neuroimaging, clinical, cognitive, genetic, schizophrenia, longitudinal |
uses: CAWorks is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Northwestern University; Illinois; USA |
Schizophrenia | NIMH 1R01 MH084803; NIMH 1U01 MH097435; NIMH P50 MH071616; NIMH R01 MH056584; NCRR P41 RR15241; NIGMS U24 GM104203; NIH Bio-Informatics Research Network Coordinating Center |
Available to the research community | SCR_014153 | Northwestern University Schizophrenia Data and Software Tool | 2026-02-12 09:46:14 | 0 | ||||||
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oligo Resource Report Resource Website 1000+ mentions |
oligo (RRID:SCR_015729) | source code, software resource, software application, data analysis software, data processing software | Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). | oligonucleotide, microarray gene expression, r, oligonucleotide array, snp, gene expression, probe-level, affymetrix array, cel file, and nimblegen array, xys file, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
CAPES (Coordenação de Aprimoramento Pessoal de Nível Superior) ; NCRR R01RR021967; NHGRI P41HG004059 |
PMID:20688976 | Free, Available for download, Runs on Mac OS, Runs on Windows | biotools:oligo | https://bio.tools/oligo | SCR_015729 | oligo package | 2026-02-12 09:46:18 | 1749 | |||||
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Statistics Online Computational Resource Resource Report Resource Website 10+ mentions |
Statistics Online Computational Resource (RRID:SCR_003378) | SOCR | software toolkit, software resource, training material, narrative resource, software application, data or information resource | A hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications. The tools and resources include a repository of interactive applets, computational and graphing tools, instructional and course materials. The core SOCR educational and computational components include the following suite of web-based Java applets: * Distributions (interactive graphs and calculators) * Experiments (virtual computer-generated games and processes) * Analyses (collection of common web-accessible tools for statistical data analysis) * Games (interfaces and simulations to real-life processes) * Modeler (tools for distribution, polynomial and spectral model-fitting and simulation) * Graphs, Plots and Charts (comprehensive web-based tools for exploratory data analysis), * Additional Tools (other statistical tools and resources) * SOCR Java-based Statistical Computing Libraries * SOCR Wiki (collaborative Wiki resource) * Educational Materials and Hands-on Activities (varieties of SOCR educational materials), * SOCR Statistical Consulting In addition, SOCR provides a suite of tools for volume-based statistical mapping (http://wiki.stat.ucla.edu/socr/index.php/SOCR_EduMaterials_AnalysesCommandLine) via command-line execution and via the LONI Pipeline workflows (http://www.nitrc.org/projects/pipeline). Course instructors and teachers will find the SOCR class notes and interactive tools useful for student motivation, concept demonstrations and for enhancing their technology based pedagogical approaches to any study of variation and uncertainty. Students and trainees may find the SOCR class notes, analyses, computational and graphing tools extremely useful in their learning/practicing pursuits. Model developers, software programmers and other engineering, biomedical and applied researchers may find the light-weight plug-in oriented SOCR computational libraries and infrastructure useful in their algorithm designs and research efforts. The three types of SOCR resources are: * Interactive Java applets: these include a number of different applets, simulations, demonstrations, virtual experiments, tools for data visualization and analysis, etc. All applets require a Java-enabled browser (if you see a blank screen, see the SOCR Feedback to find out how to configure your browser). * Instructional Resources: these include data, electronic textbooks, tutorials, etc. * Learning Activities: these include various interactive hands-on activities. * SOCR Video Tutorials (including general and tool-specific screencasts). | probability, statistics, instruction, statistical computing, applet, computational tool, graphing tool, course material, computation, java, statistical mapping, graphing, computational neuroscience, java, loni pipeline, educator, student, tool developer |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NIH Roadmap for Medical Research ; NSF 0442992; NSF DUE 0716055; NSF 1023115; NCRR U54 RR021813 |
PMID:21451741 PMID:21297884 |
Free, Freely available | nif-0000-32655 | http://www.nitrc.org/projects/socr | SCR_003378 | 2026-02-12 09:43:36 | 13 | |||||
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Mouse Biomedical Informatics Research Network Resource Report Resource Website |
Mouse Biomedical Informatics Research Network (RRID:SCR_003392) | MouseBIRN, mBIRN | data or information resource, atlas, reference atlas, data set | Animal model data primarily focused on mice including high resolution MRI, light and electron microscopic data from normal and genetically modified mice. It also has atlases, and the Mouse BIRN Atlasing Toolkit (MBAT) which provides a 3D visual interface to spatially registered distributed brain data acquired across scales. The goal of the Mouse BIRN is to help scientists utilize model organism databases for analyzing experimental data. Mouse BIRN has ended. The next phase of this project is the Mouse Connectome Project (https://www.nitrc.org/projects/mcp/). The Mouse BIRN testbeds initially focused on mouse models of neurodegenerative diseases. Mouse BIRN testbed partners provide multi-modal, multi-scale reference image data of the mouse brain as well as genetic and genomic information linking genotype and brain phenotype. Researchers across six groups are pooling and analyzing multi-scale structural and functional data and integrating it with genomic and gene expression data acquired from the mouse brain. These correlated multi-scale analyses of data are providing a comprehensive basis upon which to interpret signals from the whole brain relative to the tissue and cellular alterations characteristic of the modeled disorder. BIRN's infrastructure is providing the collaborative tools to enable researchers with unique expertise and knowledge of the mouse an opportunity to work together on research relevant to pre-clinical mouse models of neurological disease. The Mouse BIRN also maintains a collaborative Web Wiki, which contains announcements, an FAQ, and much more. | electron microscopy, expression, functional, gene, 3-dimentional, brain, cellular, disorder, genomic, genotype, mouse, neurodegenerative disease, phenotype, molecular neuroanatomy resource, mri, light microscopy, model organism, gene expression, atlas data, imaging genomics, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Mouse BIRN Atlasing Toolkit is related to: Mouse Connectome Project has parent organization: Biomedical Informatics Research Network |
Normal, Neurodegenerative disease, Multiple Sclerosis, Alzheimer's disease, Parkinson's disease | NIH ; Collaborative Tools Support Network Award ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01 |
Free, Available for download, Freely available | nif-0000-00200 | https://loni.usc.edu/research/software?name=MBATWA | http://www.loni.ucla.edu/BIRN/Projects/Mouse/index.shtml | SCR_003392 | Mouse BIRN | 2026-02-12 09:43:36 | 0 | |||
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MiMI Plugin for Cytoscape Resource Report Resource Website 1+ mentions |
MiMI Plugin for Cytoscape (RRID:SCR_003424) | MiMI Plugin | software application, data processing software, software resource, data visualization software | The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways. | protein interaction, network visualization, xquery, interactive database, information refining, molecular interaction, bioinformatics tool, java, protein-protein interaction, interaction network, biological effect, bimolecular, interaction, molecular, network, pathway, protein, visualization, plugin |
is listed by: Biositemaps is related to: Cytoscape is related to: Michigan Molecular Interactions has parent organization: University of Michigan; Ann Arbor; USA has parent organization: National Center for Integrative Biomedical Informatics |
NIH ; NIDA U54 DA021519; NLM R01 LM008106; NCRR P41 RR018627 |
PMID:18812364 | nif-0000-33090 | http://mimiplugin.ncibi.org/index.html | SCR_003424 | Cytoscape Plugin for MiMI, MiMI Plugin - Cytoscape Plugin for MiMI | 2026-02-12 09:43:35 | 1 | |||||
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caTIES - Cancer Text Information Extraction System Resource Report Resource Website |
caTIES - Cancer Text Information Extraction System (RRID:SCR_003444) | caTIES | software resource, data access protocol, web service, software application, data processing software | The Cancer Text Information Extraction System (caTIES) provides tools for de-identification and automated coding of free-text structured pathology reports. It also has a client that can be used to search these coded reports. The client also supports Tissue Banking and Honest Broker operations. caTIES focuses on two important challenges of bioinformatics * Information extraction (IE) from free text * Access to tissue. Regarding the first challenge, information from free-text pathology documents represents a vital and often underutilized source of data for cancer researchers. Typically, extracting useful data from these documents is a slow and laborious manual process requiring significant domain expertise. Application of automated methods for IE provides a method for radically increasing the speed and scope with which this data can be accessed. Regarding the second challenge, there is a pressing need in the cancer research community to gain access to tissue specific to certain experimental criteria. Presently, there are vast quantities of frozen tissue and paraffin embedded tissue throughout the country, due to lack of annotation or lack of access to annotation these tissues are often unavailable to individual researchers. caTIES has three goals designed to solve these problems: * Extract coded information from free text Surgical Pathology Reports (SPRs), using controlled terminologies to populate caBIG-compliant data structures. * Provide researchers with the ability to query, browse and create orders for annotated tissue data and physical material across a network of federated sources. With caTIES the SPR acts as a locator to tissue resources. * Pioneer research for distributed text information extraction within the context of caBIG. caTIES focuses on IE from SPRs because they represent a high-dividend target for automated analysis. There are millions of SPRs in each major hospital system, and SPRs contain important information for researchers. SPRs act as tissue locators by indicating the presence of tissue blocks, frozen tissue and other resources, and by identifying the relationship of the tissue block to significant landmarks such as tumor margins. At present, nearly all important data within SPRs are embedded within loosely-structured free-text. For these reasons, SPRs were chosen to be coded through caTIES because facilitating access to information contained in SPRs will have a powerful impact on cancer research. Once SPR information has been run through the caTIES Pipeline, the data may be queried and inspected by the researcher. The goal of this search may be to extract and analyze data or to acquire slides of tissue for further study. caTIES provides two query interfaces, a simple query dashboard and an advanced diagram query builder. Both of these interfaces are capable of NCI Metathesaurus, concept-based searching as well as string searching. Additionally, the diagram interface is capable of advanced searching functionalities. An important aspect of the interface is the ability to manage queries and case sets. Users are able to vet query results and save them to case sets which can then be edited at a later time. These can be submitted as tissue orders or used to derive data extracts. Queries can also be saved, and modified at a later time. caTIES provides the following web services by default: MMTx Service, TIES Coder Service | extraction, cancer, code, de-identification, information, paraffin, pathology, research, structure, surgical, system, tissue, tool, text, natural language processing, tissue banking, translational research, data sharing, collaboration, natural language processing, text-processing, text-mining, grid computing, service oriented architecture, query visualization, medical record, bioinformatics, automated coding |
is listed by: Biositemaps is related to: Cancer Biomedical Informatics Grid has parent organization: University of Pittsburgh School of Medicine; Pennsylvania; USA |
Cancer Biomedical Informatics Grid contract 79207CBS10; NCI R01 CA132672; NCI U01 CA 091343; NCRR U54 RR023506-01 |
PMID:20442142 | Open unspecified license | nif-0000-33212 | SCR_003444 | Cancer Text Information Extraction System, Cancer Text Information Extraction System (caTIES) | 2026-02-12 09:43:36 | 0 | |||||
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Karma Resource Report Resource Website 50+ mentions |
Karma (RRID:SCR_003732) | Karma | software application, software resource, data management software | An information integration software tool that enables users to integrate data from a variety of data sources including databases, spreadsheets, delimited text files, XML, JSON, KML and Web APIs. Users integrate information by modeling it according to an ontology of their choice using a graphical user interface that automates much of the process. Karma learns to recognize the mapping of data to ontology classes and then uses the ontology to propose a model that ties together these classes. Users then interact with the system to adjust the automatically generated model. During this process, users can transform the data as needed to normalize data expressed in different formats and to restructure it. Once the model is complete, users can publish the integrated data as RDF or store it in a database. | integration, FASEB list |
is related to: GitHub has parent organization: University of Southern California; Los Angeles; USA |
Air Force Research Laboratory FA8750-14-C-0240; NCRR 1 U24 RR025736-01; NCRR 1 UL1 RR031986-01; NSF IIS-1117913; NSF CMMI-0753124 |
PMID:15215426 | Apache License, v2 | nlx_157923 | https://github.com/InformationIntegrationGroup/Web-Karma | SCR_003732 | Karma A Data Integration Tool, Karma - A Data Integration Tool | 2026-02-12 09:43:39 | 83 | ||||
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Macaque.org Resource Report Resource Website 1+ mentions |
Macaque.org (RRID:SCR_002767) | Macaque.org | organization portal, topical portal, research forum portal, disease-related portal, data or information resource, portal, laboratory portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on June 8, 2020.Macaque genomic and proteomic resources and how they are providing important new dimensions to research using macaque models of infectious disease. The research encompasses a number of viruses that pose global threats to human health, including influenza, HIV, and SARS-associated coronavirus. By combining macaque infection models with gene expression and protein abundance profiling, they are uncovering exciting new insights into the multitude of molecular and cellular events that occur in response to virus infection. A better understanding of these events may provide the basis for innovative antiviral therapies and improvements to vaccine development strategies. | genomic, hiv, infection, proteomic, virus, simian immunodeficiency virus, influenza virus, animal model | has parent organization: University of Washington; Seattle; USA | Viral infection, Infectious disease | NCRR ; NIAID ; NHLBI ; NIDA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24370 | SCR_002767 | Macaque.org | 2026-02-12 09:43:27 | 3 | |||||
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University of Southern California LONI Software Resource Report Resource Website 1+ mentions |
University of Southern California LONI Software (RRID:SCR_002802) | data or information resource, portal, topical portal | Portal provides list of software resources. LONI is leader in development of advanced computational algorithms and software for comprehensive and quantitative mapping of brain structure and function. Aims to encourage communication between users and LONI software engineers in order to improve effectiveness. | visualization, image processing, shape analysis, pre-processing, registration, segmentation, statistical analysis, surface modeling, data management | NIH Roadmap for Medical Research ; NCRR U54 RR021813 |
Free, Freely available, Available for download | nif-0000-00445, nif-0000-00063, SCR_003323 | http://www.loni.ucla.edu/Software/ | SCR_002802 | 2026-02-12 09:43:27 | 2 | ||||||||
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FFT Library Resource Report Resource Website |
FFT Library (RRID:SCR_002698) | FFT Library | software toolkit, software resource, software application, data processing software, software library, image processing software | Java library used for the execution of discrete Fourier transforms in 1-D, 2-D and 3-D through the implementation of Fast Fourier Transform (FFT) algorithms. * The FFT library has been written in Java for portability across different platforms, integrated into a single jar file for easy implementation. * The FFT library provides forward and backward fast Fourier transforms in 1-D, 2-D and 3-D with an easy-to-use manner. * The FFT requires the length equal to a number with an integer power of two. This library automatically examines the input data and detects the length to prevent improper execution. | fourier transform, fast fourier transform, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15; NCRR U54 RR021813 |
PMID:24822428 | Free, Freely available | nif-0000-23324 | http://www.nitrc.org/projects/fft http://www.loni.ucla.edu/Software/FFT | SCR_002698 | Fast Fourier Transform JavaLibrary, FFT Java library, Fast Fourier Transform Library, Fast Fourier Transform (FFT) JavaLibrary | 2026-02-12 09:43:26 | 0 | ||||
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Sal-Site Resource Report Resource Website 50+ mentions |
Sal-Site (RRID:SCR_002850) | Sal-Site | analysis service resource, portal, service resource, production service resource, topical portal, database, data analysis service, organism-related portal, data or information resource, image collection | Portal that supports Ambystoma-related research and educational efforts. It is composed of several resources: Salamander Genome Project, Ambystoma EST Database, Ambystoma Gene Collection, Ambystoma Map and Marker Collection, Ambystoma Genetic Stock Center, and Ambystoma Research Coordination Network. | gene, genomic, expressed sequence tag, blast, model organism, genome, salamander, animal model, genetic map, genetic marker, gene expression, limb regeneration, microarray, quantitative-pcr, rna-seq, nanostring, husbandry, embryo, limb, mutant, strain, neural, olfaction, phentotype, regeneration, renal, retina, sequence, vision, human, chicken, xenopus tropicalis, FASEB list | has parent organization: University of Kentucky; Kentucky; USA | NSF OB0242833; NSF DBI0443496; NCRR R24 RR016344; NIH Office of the Director R24 OD010435 |
PMID:16359543 | Free, Freely available | nif-0000-25309 | https://orip.nih.gov/comparative-medicine/programs/vertebrate-models | SCR_002850 | Ambystoma Resources for Model Amphibians Database | 2026-02-12 09:43:28 | 92 | ||||
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LONI ShapeViewer Resource Report Resource Website |
LONI ShapeViewer (RRID:SCR_002695) | software application, data processing software, software resource, data visualization software | Java-based geometry viewer that supports file formats used by Center for Computational Biology (CCB) researchers and provides necessary viewing functions. ShapeViewer uses ShapeTools library support to read and display LONI Ucf, VTX XML, FreeSurfer, Minc Obj (both binary and ascii), Open Dx, Gifti, and OFF format data files. | ccb license, manifold viewer, computed tomography, magnetic resonance, pet, java |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: LONI ShapeTools has parent organization: Laboratory of Neuro Imaging |
NCRR U54 RR021813 | Free, Available for download, Freely available | nif-0000-23321 | SCR_002695 | ShapeViewer, LONI Shape Viewer | 2026-02-12 09:43:26 | 0 | |||||||
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Synchronized Histological Image Viewing Architecture Resource Report Resource Website |
Synchronized Histological Image Viewing Architecture (RRID:SCR_002690) | SHIVA | software resource, d visualization software, software application, data processing software, image processing software, image analysis software | A Java-based visualization and analysis application that can process 2D and 3D image files and provides convenient methods for users to overlay multiple datasets. * Simultaneous visualization of multiple image volumes. * Tools for labeling and masking of structures. * Framework for the Mouse Atlas Project. | data visualization, image analysis, 3d image, image, microscopy, magnetic resonance, java, manifold viewer |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
Free, Freely available | nif-0000-23318 | http://www.nitrc.org/projects/shiva | SCR_002690 | Synchronized Histological Image View Arc | 2026-02-12 09:43:26 | 0 | |||||
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Mutant Mouse Resource and Research Center Resource Report Resource Website 1000+ mentions |
Mutant Mouse Resource and Research Center (RRID:SCR_002953) | MMRRC | organism supplier, material resource, biomaterial supply resource | National public repository system for mutant mice. Archives and distributes scientifically valuable spontaneous and induced mutant mouse strains and ES cell lines for use by biomedical research community. Includes breeding/distribution facilities and information coordinating center. Mice strains are cryopreserved, unless live colony must be established. Live mice are supplied from production colony, from colony recovered from cryopreservation, or via micro-injection of cell line into host blastocysts. MMRRC member facilities also develop technologies to improve handling of mutant mice, including advances in assisted reproductive techniques, cryobiology, genetic analysis, phenotyping and infectious disease diagnostics. | RIN, Resource Information Network, stem cell, mouse strain, embryonic stem cell, embryonic stem cell line, cryopreserved, mutant mouse strain, mutant, transgenic, database, FASEB list, RRID Community Authority |
is used by: Integrated Animals is listed by: One Mind Biospecimen Bank Listing is listed by: Biositemaps is listed by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NIDDK Research Resources is listed by: NIDDK Information Network (dkNET) is listed by: Resource Information Network is affiliated with: MUGA is affiliated with: MegaMUGA is related to: Federation of International Mouse Resources is related to: Mouse Mutagenesis Center for Developmental Defects is related to: MGI strains has parent organization: Jackson Laboratory has parent organization: University of California at Davis; California; USA has parent organization: University of Missouri; Missouri; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: National Institutes of Health is parent organization of: Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource provides: Knockout Mouse Project Repository has organization facet: University of California at Davis Mutant Mouse Resource and Research Center has organization facet: Mutant Mouse Resource and Research Center - University of North Carolina has organization facet: Mutant Mouse Resource and Research Center - University of Missouri has organization facet: Mutant Mouse Resource and Research Center - Jackson Laboratory |
NIH Office of the Director U42 OD012210; NIH Office of the Director U42 OD010918; NIH Office of the Director U42 OD010924; NIH Office of the Director U42 OD010921; NCRR RR026296; NIH Blueprint for Neuroscience Research |
Restricted | nif-0000-00045 | SCR_002953 | Mutant Mouse Regional Resource Center | 2026-02-12 09:43:29 | 1025 | ||||||
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Special Mouse Strains Resource Resource Report Resource Website |
Special Mouse Strains Resource (RRID:SCR_002885) | SMSR | organism supplier, material resource, biomaterial supply resource | Resource of special strains of mice that are valuable tools for genetic analysis of complex diseases. They include panels of recombinant inbred (RI) and chromosome substitution (CS) strains. | strain panel, frozen, cryopreserved, recombinant inbred mouse, chromosome substitution mouse, consomic strain, gene, disease, strain |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: Mouse Phenome Database (MPD) has parent organization: Jackson Laboratory |
Recombinant inbred mouse, Chromosome substitution mouse, Consomic strain | NCRR P40 RR016049; NIH Office of the Director P40 OD011102 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25593 | SCR_002885 | Special Mouse Strains Resource (SMSR) | 2026-02-12 09:43:28 | 0 |
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