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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
University of Southern California LONI Software
 
Resource Report
Resource Website
10+ 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 2026-09-12 12:55:46 11
FFT Library
 
Resource Report
Resource Website
FFT Library (RRID:SCR_002698) FFT Library data processing software, image processing software, software application, software library, software resource, software toolkit 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 2026-09-12 12:55:44 0
LONI ShapeViewer
 
Resource Report
Resource Website
LONI ShapeViewer (RRID:SCR_002695) data processing software, data visualization software, software application, software resource 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 2026-09-12 12:55:44 0
Synchronized Histological Image Viewing Architecture
 
Resource Report
Resource Website
Synchronized Histological Image Viewing Architecture (RRID:SCR_002690) SHIVA d visualization software, data processing software, image analysis software, image processing software, software application, software resource 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 2026-09-12 12:55:44 0
Mutant Mouse Resource and Research Center
 
Resource Report
Resource Website
1000+ mentions
Mutant Mouse Resource and Research Center (RRID:SCR_002953) MMRRC biomaterial supply resource, material resource, organism supplier 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
NCRR RR026296;
NIH Blueprint for Neuroscience Research ;
NIH Office of the Director U42 OD010918;
NIH Office of the Director U42 OD010921;
NIH Office of the Director U42 OD010924;
NIH Office of the Director U42 OD012210
Restricted nif-0000-00045 SCR_002953 Mutant Mouse Regional Resource Center 2026-09-12 12:55:49 1079
Sal-Site
 
Resource Report
Resource Website
50+ mentions
Sal-Site (RRID:SCR_002850) Sal-Site analysis service resource, data analysis service, data or information resource, database, image collection, organism-related portal, portal, production service resource, service resource, topical portal 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 NCRR R24 RR016344;
NIH Office of the Director R24 OD010435;
NSF DBI0443496;
NSF OB0242833
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 2026-09-12 12:55:47 92
General Clinical Research Centers Program
 
Resource Report
Resource Website
10+ mentions
General Clinical Research Centers Program (RRID:SCR_002847) GCRC funding resource THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Through the General Clinical Research Centers (GCRC) program, NCRR funds a national network that provides settings for medical investigators to conduct safe, controlled, state-of-the-art, in-patient and out-patient studies of both children and adults. GCRCs also provide infrastructure and resources that support several career development opportunities. clinical research program, career development has parent organization: National Center for Research Resources
has parent organization: National Institutes of Health
NCRR THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-25308 SCR_002847 General Clinical Research Centers, General Clinical Research Centers (GCRC) 2026-09-12 12:55:47 35
Special Mouse Strains Resource
 
Resource Report
Resource Website
Special Mouse Strains Resource (RRID:SCR_002885) SMSR biomaterial supply resource, material resource, organism supplier 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) 2026-09-12 12:55:48 0
Development of a Specific-Pathogen-Free Baboon Colony
 
Resource Report
Resource Website
Development of a Specific-Pathogen-Free Baboon Colony (RRID:SCR_002900) Development of a SPF Baboon Colony biomaterial supply resource, material resource, organism supplier THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Program developing a self-sustaining colony of baboons free of all known herpesviruses, four retroviruses, and SV40 for research. When the program is fully developed, they will provide healthy, behaviorally normal, SPF baboons that are free of all known herpes viruses, four retroviruses, and SV40. To accomplish this goal, the center has established in collaboration with co-investigators and consultants serological and PCR tests for each of the 11 target viruses. These baboon viruses include six herpesviruses (analogs of human HSV, VZV, CMV, HHV6, EBV, and HHV8), four retroviruses (simian foamy virus, SRV/D, SIV, and STLV), and SV40. Twenty-four infant baboons are being recruited into the SPF program in each of the first five years, for a final total of at least 66 SPF baboons. All infants will be repeatedly tested for each of the target viruses. At one month of age, larger social groups of 4-6 SPF animals are formed. Beginning at 2-3 years of age, SPF animals will be integrated into larger socially compatible groups. These groups will eventually mature into breeding harems of SPF animals. This approach provides infants with age-matched companions for socialization during their early period of development, minimizes opportunities for transmission of viruses to the infants from adult animals, and allows for the simultaneous elimination of many different viruses from SPF animals. baboon, herpes virus, human, macaque, pathogen, primate, retrovirus, virus has parent organization: University of Oklahoma; Oklahoma; USA NCRR R24 RR016556 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-25871 http://www.ncrr.nih.gov/comparative_medicine/resource_directory/primates.asp SCR_002900 2026-09-12 12:55:48 0
Montage RTS2000
 
Resource Report
Resource Website
Montage RTS2000 (RRID:SCR_013439) data processing software, image processing software, software application, software resource 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 2026-09-12 12:58:03 0
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 2026-09-12 12:58:13 0
ROSIE
 
Resource Report
Resource Website
10+ mentions
ROSIE (RRID:SCR_018764) ROSIE application programming interface, data access protocol, software resource, web application Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community. Web interface for Rosetta, Rosetta online server, Rosetta application serverification, Rosetta user interface works with: Rosetta Howard Hughes Medical and Institute International Student Research Fellowship ;
NCI U54 CA143907;
NCRR R00 RR024107;
NEI PN2 EY016586;
NIGMS R01 GM073151;
NIGMS R01 GM07822;
NIGMS R21 GM102716;
NIGMS T32 GM 88118;
NSF ;
Taiwan Governmental Scholarship for Study Abroad
PMID:23717507 Restricted https://rosie.rosettacommons.org/ SCR_018764 Rosetta Online Server that Includes Everyone 2026-09-12 12:59:05 10
oligo
 
Resource Report
Resource Website
1000+ mentions
oligo (RRID:SCR_015729) data analysis software, data processing software, software application, software resource, source code 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 2026-09-12 12:58:29 1808
SerialEM
 
Resource Report
Resource Website
100+ mentions
SerialEM (RRID:SCR_017293) data acquisition software, data processing software, software application, software resource Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function. automated, data, acquisition, tilt, image, capture, display, storage, microscope NCRR RR00592;
NIGMS P01 GM61306
PMID:16182563 Restricted SCR_017293 2026-09-12 12:58:51 228
UltraScan
 
Resource Report
Resource Website
10+ mentions
UltraScan (RRID:SCR_018126) data analysis software, data processing software, software application, software resource Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis. Hydrodynamic data, analytical ultracentrifugation experiment, data editing, analysis, sedimentation velocity experiment, spectrum analysis, genetic algorithm, Monte Carlo analysis Howard Hughes Medical Institute ;
NCRR RR 022200 03S1;
NCRR RR022200;
NIGMS GM120600;
NSF ACI 1339649;
NSF ANI 228927;
NSF DBI 9724273;
NSF DBI 9974819;
NSF OCI 1032742;
NSF TG-MCB 060019T;
NSF TG-MCB 070038;
NSF TG-MCB 070039;
NSF TG-MCB 070040;
Robert J. Kleberg Jr. and Helen C. Kleberg Foundation ;
San Antonio Life Science Institute
Free, Available for download, Freely available SCR_018126 2026-09-12 12:58:58 20
Database of Immune Cell Epigenomes
 
Resource Report
Resource Website
50+ mentions
Database of Immune Cell Epigenomes (RRID:SCR_018259) DICE data access protocol, data or information resource, database, software resource, web service Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis. Data set, immune cell expression, expression quantitative trait loci, epigenomics, data, cis-eQLC, gene, protein coding gene, human cell type, genetic polymorphism disease, immune cell, pathogenesis has parent organization: La Jolla Institute for Immunology NCRR S10 RR027366;
NIAID R24 AI108564;
NIH Office of the Director S10 OD016262;
William K. Bowes Jr Foundation
PMID:30449622 Free, Freely available SCR_018259 Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics 2026-09-12 12:58:59 73
Appion Package
 
Resource Report
Resource Website
10+ mentions
Appion Package (RRID:SCR_016734) Appion data processing software, image analysis software, image processing software, software application, software resource 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 ARCS ;
NCRR RR023093;
NCRR RR17573
PMID:19263523 Free, Available for download, Freely available http://www.appion.org SCR_016734 2026-09-12 12:58:44 16
BinPacker
 
Resource Report
Resource Website
10+ mentions
BinPacker (RRID:SCR_017038) data analysis software, data processing software, software application, software resource 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 ;
NCRR P20 RR01 6460;
NIGMS P20 GM103429;
NSF 1553680
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 2026-09-12 12:58:47 10
BrainInfo
 
Resource Report
Resource Website
10+ mentions
BrainInfo (RRID:SCR_003142) atlas, data or information resource, database, narrative resource, portal, standard specification, topical portal Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures. brain, neuroanatomy is used by: NIF Data Federation
is listed by: Biositemaps
is related to: INIA19 Primate Brain Atlas
has parent organization: University of Washington; Seattle; USA
has parent organization: University of California at San Diego; California; USA
The Human Brain Project ;
NIBIB ;
NLM LM/OD-06243;
NIH Office of the Director LM/OD-06243;
NIMH MHO69259;
NCRR RR-00166
PMID:21789500
PMID:21163300
PMID:18368361
PMID:15055392
Free, Freely available nif-0000-00019 SCR_003142 Brain Info 2026-09-12 12:55:52 16
Statistics Online Computational Resource
 
Resource Report
Resource Website
10+ mentions
Statistics Online Computational Resource (RRID:SCR_003378) SOCR data or information resource, narrative resource, software application, software resource, software toolkit, training material 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 2026-09-12 12:55:57 13

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