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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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North American Conditional Mouse Mutagenesis Project Resource Report Resource Website 1+ mentions |
North American Conditional Mouse Mutagenesis Project (RRID:SCR_001614) | NorCOMM | production service resource, material service resource, service resource, biomaterial manufacture | Large-scale research initiative focused on developing and distributing a library of mouse embryonic stem (ES) cell lines carrying single gene trapped or targeted mutations across the mouse genome. NorCOMM's large and growing archive of ES cells is publicly available on a cost-recovery basis from the Canadian Mouse Mutant Repository. As an international public resource, access to clones is unrestricted and nonexclusive. Through NorCOMM's affiliation with the Canadian Mouse Consortium (CMC), NorCOMM also provides clients with a single point of access to regional mouse derivation, phenotyping, genetic and archiving services across Canada. These value-added services can help your company harness NorCOMM's resources for drug discovery, target discovery and preclinical validation. | gene, target, embryonic stem cell line, gene trap, targeted mutation, mouse genome, mutation, genome, derivation, phenotype, genetic, archive, phenotyping, archiving, gene target, clone |
is related to: CMMR - Canadian Mouse Mutant Repository is related to: CMMR - Canadian Mouse Mutant Repository has parent organization: International Knockout Mouse Consortium |
Genome Canada | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153880 | SCR_001614 | 2026-08-10 09:31:31 | 4 | |||||||
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Texas A and M Institute for Genomic Medicine Resource Report Resource Website 10+ mentions |
Texas A and M Institute for Genomic Medicine (RRID:SCR_001615) | TIGM | cell repository, material resource, organism supplier, biomaterial supply resource | Resource for any researcher looking to obtain knockout mice and embryonic stem (ES) cells quickly and with favorable intellectual property (IP) terms. Our resources include the world’s largest gene trap library of ES cells in the C57BL/6N mouse strain and a constantly expanding repository of cryopreserved germplasm of knockout lines. TIGM provides both ES cell clones and mice as well as other transgenic core services including CRISPR/Cas9-based genome modifications within the Texas A&M system and to the public and private international research community. | RIN, Resource Information Network, embryonic stem cell, knockout mouse, transgenic, phenotyping, phenotype, c57bl/6, 129/svevbrd, gene trap, clone, knockout mouse line, 129, database, gene, mutation, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: International Knockout Mouse Consortium has parent organization: Texas A and M University; Texas; USA works with: International Mouse Strain Resource |
Free, Freely available | nlx_153881 | SCR_001615 | Texas A&M Institute for Genomic Medicine | 2026-08-10 09:31:28 | 20 | |||||||
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Sequencher Resource Report Resource Website 5000+ mentions |
Sequencher (RRID:SCR_001528) | Sequencher sequence analysis software | data analysis software, software application, software resource, sequence analysis software, data processing software | Software for Next-Generation DNA sequencing, Sanger DNA analysis, and RNA sequencing. It contains sequence analysis tools which include reference-guided alignments, de novo assembly, variant calling, and SNP analyses. It has integrated the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data. | dna, sequencing, sequence analysis software, NGS, sanger, data visualization |
is listed by: OMICtools is listed by: SoftCite |
Available for download | OMICS_01817 | http://genecodes.com/sequencher-features | SCR_001528 | Sequencher sequence analysis software | 2026-08-10 09:31:27 | 5032 | ||||||
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International Mouse Strain Resource Resource Report Resource Website 10+ mentions |
International Mouse Strain Resource (RRID:SCR_001526) | IMSR | material resource, organism supplier, biomaterial supply resource | Database of mouse strains and stocks available worldwide, that will assist international research community in finding mouse resources they need, including inbred, mutant, and genetically engineered mice. IMSR is multi institutional international collaboration supporting use of mouse as model system for studying human biology and disease. IMSR began with initial collaboration between Mouse Genome Informatics (MGI) group at Jackson Laboratory and Medical Research Council Mammalian Genetics Unit at Harwell. Additional institutions and collaborators are now contributing mouse resource information to IMSR. Data content found in IMSR is as it was supplied by data provider sites. You are encouraged to participate in making this database as complete as possible for all worldwide mouse strain resources. If you or your institution hold mice, cryopreserved gametes or embryos, or ES cell lines that you distribute to other researchers, contributing information about them to IMSR catalog will make them more widely known. | RIN, Resource Information Network, mouse, strain, stock, inbred, mutant, genetically engineered, embryo, embryonic stem cell line, database, knockout mouse, mutant mouse strain, transgenic mouse, embryonic mouse, live mouse, gamete, ovary, sperm, germplasm, model organism, RRID Community Authority |
uses: Vanderbilt Cryopreserved Mouse Repository uses: Janvier Labs uses: Korea Mouse Phenotyping Center uses: CLEA Japan, Inc. uses: genOway uses: Inotiv uses: Cyagen Biosciences uses: Cam-Su Genomic Resource Center is used by: BioSample Database at EBI is used by: Integrated Animals lists: Oak Ridge Collection at JAX lists: National Resource Center for Mutant Mice lists: JAX Mice and Services lists: National Applied Research Laboratories lists: Oriental BioService Inc. is listed by: Resource Information Network is related to: NIF Data Federation is related to: Recombinase (cre) Activity is related to: One Mind Biospecimen Bank Listing is related to: Integrated Cell Lines is related to: Mouse Genome Informatics (MGI) has parent organization: MRC Mammalian Genetics Unit works with: Shanghai Model Organisms Center works with: European Mouse Mutant Archive works with: Texas A and M Institute for Genomic Medicine works with: JAX Mice and Services works with: CMMR - Canadian Mouse Mutant Repository works with: RIKEN BioResource Center works with: Center for Animal Resources and Development works with: National Institute of Genetics; Shizuoka; Japan works with: NHMRC Australian PhenomeBank works with: Taconic Biosciences works with: Charles River Laboratories works with: Medical Research Council Harwell: An International Centre for Mouse Genetics |
NLM LM009693 | PMID:10098412 PMID:26373861 |
Restricted | nif-0000-09876 | http://www.findmice.org/ | SCR_001526 | IMSR, International Mouse Strain Resource | 2026-08-10 09:31:28 | 14 | ||||
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DTI and Fibertools Software Package Resource Report Resource Website 1+ mentions |
DTI and Fibertools Software Package (RRID:SCR_001641) | DTI and Fibertools, DTI&FiberTools | software application, software toolkit, software resource, image processing software, data processing software | Implemented under MATLAB, this DTI image processing toolbox provides import-filters for several MR file standards, a processing unit to calculate the diffusion tensors; several GUI based tools to calculate fiber tracks and to evaluate the DTI dataset. The results can be filed as images with 3D impression or can be logged in formatted ASCII files. Tools and features: * DTI Processing Unit: Calculates the diffusion tensors and their eigenvalues and eigenvectors. Different file formats are supported (like DICOM, Bruker, binary files, Matlab structures). The standard SIEMENS and GE diffusion encoding schemes are supported; other schemes have to be defined in a separate text, .m or .mat file. * FiberTracking: ** Fiber tracking is realized by using the FACT algorithm (Mori et al., Annal. Neurol 1999). ** Probabilistic tracking realized by using the PiCo (Parker et al., JMRI 2003) approach but with DTI data as basis. It is possible to extract pathways between two seeds by combining two maps (Kreher et al., NeuroImage 2008). ** Global Fiber Tracking on basis of HARDI or DTI data. The method is based on the approach reported in (Marco Reisert et al: Global fiber reconstruction becomes practical. NeuroImage 54(2):955-62) * FiberViewer: ** Visualization and Navigation through different data modalities like DTI maps, fiber tracks, diffusion main directions. ** Supports different kinds of DTI maps (e.g. FA, Trace, lambda images ) ** Creation and manipulation of mask based ROIs. ** Selection of streamline fibers ** Visualization of probabilistic fiber tracking results ** Documentation by logging statistics of ROIs and fiber tracks into text files. ** Import/Export from/to ANALYZE or Nifti * 3D Visualizer: Visualization of map slices, ROIs, and fiber tracks with 3D impression. * Batch Editor: Automatic processing of high amounts of data. Possibility to link processing with SPM8 easily. | diffusion, dti, fiber tracking, diffusion tensor, visualization, navigation |
is related to: Diffusion MRI of Traumatic Brain Injury has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
Free, Available for download, Freely available | nlx_153913 | SCR_001641 | DTI & Fibertools | 2026-08-10 09:31:29 | 5 | |||||||
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Globin Gene Server Resource Report Resource Website 10+ mentions |
Globin Gene Server (RRID:SCR_001480) | Globin Gene Server | data or information resource, training material, analysis service resource, source code, resource, production service resource, database, narrative resource, service resource, software resource, data analysis service | Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles. | dna sequence, hemoglobin, mutation, globin gene cluster, sequence comparison, functional genomics, gene, alignment, genetic analysis, variant, gene expression, protein, thalassemia, globin gene, genome, pairwise alignment, multiple alignment, annotation, sequence analysis, dna |
is listed by: NIDDK Information Network (dkNET) has parent organization: Pennsylvania State University |
NLM R01LM05773; NLM R01LM05110; NIDDK DK27635 |
PMID:11857738 PMID:11480780 PMID:9799599 PMID:9576329 PMID:8088828 |
Free, Freely available | nlx_152723 | SCR_001480 | 2026-08-10 09:31:26 | 30 | ||||||
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Nonalcoholic Steatohepatitis Clinical Research Network Resource Report Resource Website 10+ mentions |
Nonalcoholic Steatohepatitis Clinical Research Network (RRID:SCR_001519) | NASH CRN | data or information resource, resource, portal, clinical trial, topical portal, research forum portal, disease-related portal | Clinical research network to focus on the etiology, contributing factors, natural history, complications, and therapy of nonalcoholic steatohepatitis. They research the nature and underlying cause of Nonalcoholic Steatohepatitis (NASH) and conduct clinical studies on prevention and treatment. Approximately 1,500 pediatric and adult participants throughout the United States and Canada with nonalcoholic fatty liver disease (NAFLD) have enrolled into a database. The NASH CRN has recently reopened the database to enroll additional pediatric and adult participants with NAFLD. Serum, liver tissue, and genomic DNA samples are being collected and stored in the NIDDKrepository for ongoing as well as future studies. A three-arm randomized, placebo-controlled clinical trial of pioglitazone versus vitamin E completed enrollment in 2009. In addition to this adult trial, a similar trial in pediatric NASH patients randomized 180 children to receive treatment with vitamin E, metformin, or placebo. | prevention, treatment, pediatric, child, adult human, serum, liver tissue, dna, placebo, pioglitazone, vitamin e, metformin, etiology, contributing factor, natural history, complication, therapy, young human, database, clinical trial, bibliography, patient registry |
is listed by: One Mind Biospecimen Bank Listing is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Central Repository has parent organization: Johns Hopkins University; Maryland; USA |
Nonalcoholic steatohepatitis, Nonalcoholic fatty liver disease | NIDDK 1ZIADK075013 | Free, Freely available | nlx_152845 | https://www.nashcrn.com | SCR_001519 | Nonalcoholic Steatohepatitis Clinical Research Network (NASH CRN), Clinical Research Network in Nonalcoholic Steatohepatitis | 2026-08-10 09:31:27 | 21 | ||||
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Brain Gene Expression Map Resource Report Resource Website 10+ mentions |
Brain Gene Expression Map (RRID:SCR_001517) | BGEM | data or information resource, atlas, expression atlas, database | This database contains gene expression patterns assembled from mouse nervous tissues at 4 time points throughout brain development including embryonic (e) day 11.5, e15.5, postnatal (p) day 7 and adult p42. Using a high throughput in situ hybridization approach we are assembling expression patterns from selected genes and presenting them in a searchable database. The database includes darkfield images obtained using radioactive probes, reference cresyl violet stained sections, the complete nucleotide sequence of the probes used to generate the data and all the information required to allow users to repeat and extend the analyses. The database is directly linked to Pubmed, LocusLink, Unigene and Gene Ontology Consortium housed at the National Center for Biotechnology Information (NCBI) in the National Library of Medicine. These data are provided freely to promote communication and cooperation among research groups throughout the world. | embryonic, expression pattern, gene expression, gene, adult, brain, brain development, in situ hybridization, mouse, nervous tissue, postnatal, molecular neuroanatomy resource, image | NINDS 5R37NS036558; NINDS N01-NS-0-2331 |
PMID:16602821 | nif-0000-09579 | SCR_001517 | BGEM - Brain Gene Expression Map, Mousebrain Gene Expression Map | 2026-08-10 09:31:27 | 10 | |||||||
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GenitoUrinary Development Molecular Anatomy Project Resource Report Resource Website 100+ mentions |
GenitoUrinary Development Molecular Anatomy Project (RRID:SCR_001554) | GUDMAP | material resource, organism supplier, biomaterial supply resource | Project aggregates and provides experimental gene expression data from genito-urinary system. International consortium providing molecular atlas of gene expression for developing organs of GenitoUrinary (GU) tract. Mouse strains to facilitate developmental and functional studies within GU system. Experimental protocols and standard specifications. Tutorials describing GU organogenesis and primary data via database. Data are from large-scale in situ hybridization screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of developing mouse genitourinary (GU) system. | gene expression, genitourinary tract, molecular anatomy, genitourinary system, organogenesis, genitourinary, in situ hybridization, immunohistochemistry, microarray, mutant mouse strain, development, rna, protein, theiler stage, gene, anatomy, male, female, embryonic mouse, kidney, urogenital tract, urinary, reproductive, disease, molecule, cell, gene, phenotype, functional annotation, protein interaction, transgenic transgene, image, rna extraction, sample preparation, fluorescent immunohistochemistry, rna isolation, rna amplification, labeling, fluorescent in situ-hybridization, riboprobe synthesis, cellular localization, tissue isolation, embedding, cryostat sectioning, laser capture microdissection, paraffin, whole mount, optimal cutting temperature, riboprobe synthesis, target amplification, sectioning, FASEB list |
is used by: NIDDK Information Network (dkNET) is listed by: One Mind Biospecimen Bank Listing is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology is related to: ToppCluster is related to: One Mind Biospecimen Bank Listing is parent organization of: GUDMAP Ontology is parent organization of: GATACA GUDMAP Gene Explorer |
NIDDK DK070136; NIDDK DK070200; NIDDK DK070181 |
PMID:21652655 PMID:18287559 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152871, nif-0000-33426 | SCR_001554 | Murine Atlas for Genitourinary Development | 2026-08-10 09:31:27 | 289 | |||||
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SISTEr Resource Report Resource Website 100+ mentions |
SISTEr (RRID:SCR_001542) | SISTEr | data or information resource, data set, resource, clinical trial | Clinical trial under the Urinary Incontinence Treatment Network to compare the treatment success for two surgical procedures that are frequently used and have similar cure rates, yet have not been compared directly to each other in a large, rigorously conducted randomized trial. The secondary aims of the trial are to compare other outcomes for the two surgical procedures, including quality of life, sexual function, satisfaction with treatment outcomes, complications, and need for other treatment(s) after surgery. Follow-up will be a minimum of two years and up to four years. | urinary, incontinence, dataset, surgical procedure, outcome, quality of life, sexual function, satisfaction, treatment, complication, burch procedure, sling procedure, female, surgery |
is listed by: NIDDK Information Network (dkNET) has parent organization: Urinary Incontinence Treatment Network |
Urinary incontinence, Stress, Stress urinary incontinence | NIDDK ; NICHD |
Free, Freely available | nlx_152852 | http://www.uitn.net/sister.asp | SCR_001542 | Stress Incontinence Surgical Treatment Efficacy Trial | 2026-08-10 09:31:27 | 151 | ||||
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Immune Tolerance Network (ITN) Resource Report Resource Website 10+ mentions |
Immune Tolerance Network (ITN) (RRID:SCR_001535) | ITN | data or information resource, funding resource, clinical trial, portal, topical portal | International clinical research consortium dedicated to the clinical evaluation of novel tolerogenic approaches for the treatment of autoimmune diseases, asthma and allergic diseases, and the prevention of graft rejection. They aim to advance the clinical application of immune tolerance by performing high quality clinical trials of emerging therapeutics integrated with mechanism-based research. In particular, they aim to: * Establish new tolerance therapeutics * Develop a better understanding of the mechanisms of immune function and disease pathogenesis * Identify new biomarkers of tolerance and disease Their goals are to identify and develop treatment game changers for tolerance modulating therapies for the treatment of immune mediated diseases and disabling conditions, and to conduct high quality, innovative clinical trials and mechanistic studies not likely to be funded by other sources or to be conducted by private industry that advance our understanding of immunological disorders. In the Immune Tolerance Network's (ITN) unique hybrid academic/industry model, the areas of academia, government and industry are integral to planning and conducting clinical studies. They develop and fund clinical trials and mechanistic studies in partnership. Their development model is a unique, interactive process. It capitalizes on their wide-ranging, multidisciplinary expertise provided by an advisory board of highly respected faculty from institutions worldwide. This model gives investigators special insight into developing high quality research studies. The ITN is comprised of leading scientific and medical faculty from more than 50 institutions in nine countries worldwide and employs over 80 full-time staff at the University of California San Francisco (UCSF), Bethesda, Maryland and Benaroya Research Institute in Seattle, Washington. | immune tolerance, prevent, cure, disease, multiple sclerosis, therapy, biomarker, transplant |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is related to: Immune Tolerance Network TrialShare has parent organization: Benaroya Research Institute |
Type 1 diabetes, Diabetes, Allergy, Asthma, Autoimmune disease, Transplantation, Immunological disorder | NIAID N01AI15416 | nlx_152838 | SCR_001535 | 2026-08-10 09:31:27 | 15 | |||||||
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National Center for Integrative Biomedical Informatics Resource Report Resource Website 1+ mentions |
National Center for Integrative Biomedical Informatics (RRID:SCR_001538) | data or information resource, organization portal, portal | The Center develops conceptual models, computational infrastructure, an integrated knowledge repository, and query and analysis tools that enable scientists to effectively access and integrate the wealth of biological data. The National Center for Integrative Biomedical Informatics (NCIBI) was founded in October 2005 and is one of seven National Centers for Biomedical Computing (NCBC) in the NIH Roadmap. NCIBI is based at the University of Michigan as a part of the Center for Computational Medicine and Biology (CCMB). NCIBI is composed of biomedical researchers, computational biologists, computer scientists, developers and human-computer interaction specialists organized into seven major core functions. They work in interdisciplinary teams to collectively develop tools that are not only computationally powerful but also biologically relevant and meaningful. The four initial Driving Biological Projects (prostate cancer progression, Type 1 and type 2 diabetes and bipolar disorder) provide the nucleation point from which tool development is informed, launched, and tested. In addition to testing tools for function, a separate team is dedicated to testing usability and user interaction that is a unique feature of this Center. Once tools are developed and validated the goal of the Center is to share and disseminate data and software throughout the research community both internally and externally. This is achieved through various mechanisms such as training videos, tutorials, and demonstrations and presentations at national and international scientific conferences. NCIBI is supported by NIH Grant # U54-DA021519. | analysis tools, bipolar disorder, code, computational infrastructure, conceptual models, data, diabetes, knowledge repository, presentations, prostate cancer, query tools, seminar material, tool development, tutorials, videos, model |
is listed by: 3DVC is related to: Biological Concept Diagram Editor is related to: Gene Interaction Extraction from the Literature is related to: National Centers for Biomedical Computing has parent organization: University of Michigan; Ann Arbor; USA is parent organization of: Substructure Index-based Approximate Graph Alignment is parent organization of: miniTUBA is parent organization of: Michigan Molecular Interactions is parent organization of: Cell Line Knowledge Base is parent organization of: HubMed is parent organization of: MiMI Plugin for Cytoscape |
Type 1 diabetes, Type 2 diabetes, Diabetes, Cancer, Bipolar disorder | PMID:22101971 | Free, Freely available | nif-0000-09660 | http://portal.ncibi.org/gateway/ | SCR_001538 | NCIBI | 2026-08-10 09:31:28 | 1 | |||||
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Farsight Toolkit Resource Report Resource Website 1+ mentions |
Farsight Toolkit (RRID:SCR_001728) | FARSIGHT | software application, software toolkit, software resource, image analysis software, image processing software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A collection of software modules for image data handling, pre-processing, segmentation, inspection, editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks. All of the modules are written in accordance with software practices of the Insight Toolkit Community. Importantly, all modules are accessible through the Python scripting language which allows users to create scripts to accomplish sophisticated associative image analysis tasks over multi-dimensional microscopy image data. This language works on most computing platforms, providing a high degree of platform independence. Another important design principle is the use of standardized XML file formats for data interchange between modules. | editing, 2d, 3d, algorithm, analysis, bio-format, computational, data, graphical, inspection, metadata, microscopy, morphological, morphology, pixel, processing, segmentation, taxonomy, image | has parent organization: University of Houston; Texas; USA | NIBIB R01-EB005157; NSF EEC-9986821; NIBIB R01EB005157 |
PMID:24808857 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10227 | SCR_001728 | FARSIGHTWiki | 2026-08-10 09:31:33 | 2 | |||||
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GenABEL Resource Report Resource Website 500+ mentions |
GenABEL (RRID:SCR_001842) | software library, software toolkit, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits. | r, genome-wide association, single nucleotide polymorphism |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: SoftCite |
Centre for Medical Systems Biology; Netherlands ; Netherlands Genomics Initiative ; Netherlands Organisation for Scientific Research ; Russian Foundation for Basic Research |
PMID:17384015 DOI:10.1186/1471-2105-11-134 DOI:10.1093/bioinformatics/btm108 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154328, OMICS_00234 | http://mga.bionet.nsc.ru/~yurii/ABEL/GenABEL/, https://cran.r-project.org/web/packages/GenABEL/index.html, https://sources.debian.org/src/probabel/ | SCR_001842 | GenABEL package, R/GENABEL | 2026-08-10 09:31:32 | 506 | |||||
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TaLasso Resource Report Resource Website 1+ mentions |
TaLasso (RRID:SCR_001726) | TaLasso | analysis service resource, production service resource, service resource, software resource, data analysis service | Tool for quantification of human miRNA-mRNA Interactions. TaLasso is also available as Matlab or R code. | mirna, mrna, matlab, r, gene expression, gene |
is listed by: OMICtools has parent organization: Autonomous University of Madrid; Madrid; Spain |
PMID:22348024 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00417 | SCR_001726 | 2026-08-10 09:31:30 | 1 | |||||||
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FreeSurfer Resource Report Resource Website 10000+ mentions |
FreeSurfer (RRID:SCR_001847) | FreeSurfer | software application, data visualization software, software resource, image analysis software, data processing software | Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS. | processing, analysis, human, brain, MRI, image, reconstruction, cortical, surface, fMRI, data |
is used by: Wisconsin Cortical Thickness Analysis (CTA) Toolbox is used by: freesurfR is used by: Automatic Analysis is used by: NHP Freesurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: Debian is listed by: SoftCite is related to: PySurfer is related to: RFT FDR is related to: FMRLAB is related to: TRACULA is related to: BASH4RfMRI has parent organization: Harvard University; Cambridge; United States has plug in: JOSA works with: NIAG Addiction Data |
NCRR U24 RR021382; NINDS R01 NS052585; NCRR RR014075 |
PMID:22248573 | Free, Available for download, Freely available | nif-0000-00304 | https://sources.debian.org/src/freesurfer/, http://www.nitrc.org/projects/freesurfer, http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall | SCR_001847 | 2026-08-10 09:31:32 | 12664 | |||||
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Duke University Medical Center: Duke Image Analysis Laboratory Resource Report Resource Website 10+ mentions |
Duke University Medical Center: Duke Image Analysis Laboratory (RRID:SCR_001716) | data or information resource, topical portal, portal, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Duke Image Analysis Laboratory (DIAL) is committed to providing comprehensive imaging support in research studies and clinical trials to various agencies. The capabilities of the lab include protocol development, site training and certification, and image archival and analysis for a variety of modalities including magnetic resonance imaging, magnetic resonance spectroscopy, computed tomography and nuclear medicine. DIAL uses the latest technologies to analyze Magnetic Resonance Imaging (MRI) data sets of the brain. Currently the lab is engaged in measurement of the hippocampus, amygdala, caudate, ventricular system, and other brain regional volumes. Each of these techniques have undergone a rigorous validation process. The measurements of brain structures provide a useful means of non-invasively testing for changes in the brain of the patient. Changes over time in the brain can be detected, and evaluated with respect to the treatment that the patient is receiving. Magnetic Resonance Spectroscopy (MRS) allows DIAL to obtain an accurate profile of the chemical content of the brain. This sensitive technique can detect small changes in the metabolic state of the brain; changes that vary in response to administration of therapeutic agents. The ability to detect these subtle shifts in brain chemistry allows DIAL to identify changes in the brain with more sensitivity than allowed by image analysis. In this respect, NMR spectroscopy can provide early detection of changes in the brain, and serves to compliment the data obtained from image analysis. Additionally, DIAL also contains SQUID (Scalable Query Utility and Image Database). It is an image management system developed to facilitate image management in research and clinical trials: SQUID offers secure, redundant image storage and organizational functions for sorting and searching digital images for a variety of modalities including MRI, MRS, CAT Scan, X-Ray and Nuclear Medicine. SQUID can access images directly from DUMC scanners. Data can also be loaded via DICOM CDs, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | academic, amygdala, analysis, biotechnology, brain, cat scan, caudate, chemical, clinical, computed, development, digital, hippocampus, imaging, lab, laboratory, magnetic resonance imaging, magnetic resonance spectroscopy, medical, medicine, metabolic, mri, mrs, nmr, nuclear, nuclear medicine, pharmaceutical, research, spectroscopy, structure, technology, therapeutic, tomography, treatment, trial, ventricular, ventricular system, volume, x-ray, FASEB list | has parent organization: Duke University; North Carolina; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10213 | SCR_001716 | DMC DIAL | 2026-08-10 09:31:30 | 33 | ||||||||
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Stable Isotope Labeling with Amino Acids in Cell Culture Resource Report Resource Website 500+ mentions |
Stable Isotope Labeling with Amino Acids in Cell Culture (RRID:SCR_001873) | data or information resource, topical portal, portal | Stable isotope labeling with amino acids in cell culture (SILAC) is a simple and straightforward approach for in vivo incorporation of a label into proteins for mass spectrometry (MS)-based quantitative proteomics. SILAC relies on metabolic incorporation of a given "light" or "heavy" form of the amino acid into the proteins. The method relies on the incorporation of amino acids with substituted stable isotopic nuclei (e.g. deuterium, 13C, 15N). In an experiment, two cell populations are grown in culture media that are identical except that one of them contains a "light" and the other a "heavy" form of a particular amino acid (e.g. 12C and 13C labeled L-lysine, respectively). When the labeled analog of an amino acid is supplied to cells in culture instead of the natural amino acid, it is incorporated into all newly synthesized proteins. After a number of cell divisions, each instance of this particular amino acid will be replaced by its isotope labeled analog. Since there is hardly any chemical difference between the labeled amino acid and the natural amino acid isotopes, the cells behave exactly like the control cell population grown in the presence of normal amino acid. It is efficient and reproducible as the incorporation of the isotope label is 100%. SILAC Applications: - Differential expression of proteins and identification of disease biomarkers - Cell signaling dynamics - Analysis of yeast pheromone signaling pathway - Identification of methylation sites - Identification of protease substrates - Study of protein complexes/protein interactions - Analysis of signaling pathways and effect of pharmacological inhibitors - Subcellular proteomics Sponsors: Supported in part by an NIH Roadmap grant Technology Center for Networks & Pathways of Lysine Modification. | amino acid, analog, biomarker, cell culture, cell division, cell signal, chemical, deuterium, disease, inhibitor, in vivo, isotope, labeling, lysine, mass spectrometry, media, metabolic, methylation site, nucleus, pharmacological, protease, protein, protein complex, protein interaction, proteomics, signaling pathway, subcellular, substrate, yeast pheromone | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10435 | SCR_001873 | SILAC | 2026-08-10 09:31:34 | 673 | |||||||||
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Animal QTLdb Resource Report Resource Website 50+ mentions |
Animal QTLdb (RRID:SCR_001748) | Animal QTLdb | data or information resource, data repository, database, service resource, storage service resource | Database of trait mapping data, i.e. QTL (phenotype / expression, eQTL), candidate gene and association data (GWAS) and copy number variations (CNV) mapped to livestock animal genomes, to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features, such as annotated genes. QTLdb is open to house QTL/association date from other animal species where feasible. Most scientific journals require that any original QTL/association data be deposited into public databases before paper may be accepted for publication. User curator accounts are provided for direct data deposit. Users can download QTLdb data from each species or individual chromosome. | chromosome, comparative genomics, dna sequence, genome, livestock, quantitative trait locus, non-human animal, structural genomics, single-nucleotide polymorphism, gene association, genomics, trait, copy number variation, trait, phenotype, expression, eqtl, genome wide association study, candidate gene, genotype |
uses: Entrez Gene uses: Ensembl is used by: NIF Data Federation is used by: MONARCH Initiative is listed by: re3data.org is related to: Ensembl Variation is related to: Vertebrate Trait Ontology has parent organization: Iowa State University; Iowa; USA has parent organization: NAGRP Bioinformatics Coordination Program |
USDA NRSP-8; USDA 2007-04187 |
PMID:23180796 PMID:17245610 |
Free, Freely available | nif-0000-02550, r3d100010744 | http://www.animalgenome.org/QTLdb/ | SCR_001748 | Animal QTL database, Animal Quantitative Trait Loci database, AnimalQTLdb, Animal Quantitative Trait Loci (QTL) database | 2026-08-10 09:31:33 | 56 | ||||
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SPRUSTON / KATH LAB: Neuraling Modeling Database NEURAL MODELING DATABASE Resource Report Resource Website 1+ mentions |
SPRUSTON / KATH LAB: Neuraling Modeling Database NEURAL MODELING DATABASE (RRID:SCR_001869) | data or information resource, software application, database, simulation software, software resource | This database contains morphologies of hippocampal pyramidal cells and interneurons (in Neurolucida, NEURON, and pdf formats) as well as data recorded from those cells. Sponsors:This work was supported by grants from the NIH (T32-GM-08061 to T.J.M., F32-NS-10532 to N.L.G., and R01-NS35180 and R01-NS 46064 to N.S. and W.L.K.) and NSF (IGERT fellowship to Y.K.). NS46064 is part of the NSF/NIH Collaborative Research in Computational Neuroscience Program | cell, hippocampal, interneuron, morphology, neurolucida, neuron, pyramidal cell | Free, Freely available | nif-0000-10434 | http://www.northwestern.edu/neurobiology/faculty/spruston/sk_models/ | SCR_001869 | SPRUSTON / KATH LAB | 2026-08-10 09:31:33 | 5 |
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