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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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University of Virginia School of Medicine Molecular Electron Microscopy Core Facility Resource Report Resource Website 10+ mentions |
University of Virginia School of Medicine Molecular Electron Microscopy Core Facility (RRID:SCR_019031) | MEMC | access service resource, core facility, service resource | Facility dedicated to high resolution electron cryomicroscopy and electron cryotomography. It houses three electron microscopes,120kV Spirit, 200kV F20, and 300kV Titan Krios. These microscopes are available to researchers either for direct use, or aided by MEMC personnel, to collect data aimed at high resolution structural biology projects. | USEDit, electron microscopy, electron cryotomography, microscope, data collection, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: University of Virginia School of Medicine; Virginia; USA |
NCRR G20 RR31199 | ABRF_1048 | https://coremarketplace.org/?FacilityID=1048 | SCR_019031 | University of Virginia Molecular Electron Microscopy Core, UVa-Molecular Electron Microscopy Core, Molecular Electron Microscopy Core | 2026-08-04 09:44:28 | 36 | ||||||
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Vermont University Larner College of Medicine Microscopy Imaging Center Core Facility Resource Report Resource Website 50+ mentions |
Vermont University Larner College of Medicine Microscopy Imaging Center Core Facility (RRID:SCR_018821) | MIC | access service resource, core facility, service resource | Core provides imaging equipment including JEOL 1400 transmission electron microscope with AMT 11 megapixel digital camera,JEOL JSM 6060 scanning electron microscope with attached Oxford INCA energy dispersive spectroscopy detector for element analysis,Nikon Air HD confocal scanning laser microscope, Nikon C2 confocal scanning laser microscope, Andor Spinning Disk confocal microscope, Zeiss LSM 7 Multiphoton confocal microscope, Nikon STORM super-resolution light microscope, Olympus BX50 research microscope for transmitted light, phase contrast, and epi-fluorescence microscopy, Asylum Research MFP-3D BIO atomic force microscope, Asylum Research Cypher Environmental atomic force microscope,Arcturus XT-Ti Laser Capture Microdissector system, Olympus IX70 inverted microscope with associated Applied BioPhysics Electri Cell-Substrate Impedance Sensing (ECIS Ztheta) system, Leica VERSA 8 whole slide imager, Dell workstations containing Molecular Devices MetaMorph image analysis software for complex quantitative image analysis, Indica Labs HALO software, Improvision Volocity, MBR StereoInvestigator. | USEDit, microscopy imaging, transmission electron microscope, microscope, image analysis service, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Vermont; Vermont; USA |
NCRR S10RR025498; NIH Office of the Director 1S10OD025030 |
Open | ABRF_22 | https://coremarketplace.org/?FacilityID=22 | SCR_018821 | , UVM - Microscopy Imaging Center, Vermont University Larner College of Medicine Microscopy Imaging Center, University of Vermont Larner College of Medicine Microscopy Imaging Center | 2026-08-04 09:44:24 | 50 | |||||
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Nemours Biomolecular Core Facility Resource Report Resource Website |
Nemours Biomolecular Core Facility (RRID:SCR_018265) | access service resource, core facility, service resource | Develops research projects in pediatric genetics and provides essential services in molecular biology and genetics to Nemours clinicians and research staff and to affiliates researchers of University of Delaware and Thomas Jefferson University. Resource for staff of Alfred I. duPont Hospital for Children, Nemours affiliates, COBRE / INBRE investigators and outside customers. Offers expertise in molecular genetics and genomics. Operates according to policies set forth by federal CLIA standards.Services provided include Ion Torrent PGM Next Generation Sequencing, QuantStudio (QS) 3D Digital PCR, Cell Line Authentication, Nucleic Acid Quality Number (AATI Fragment Analyzer),Genotyping including Allelic Discrimination Probes (SNP Real-Time PCR), Affymetrix Microarray (CNV CytoScan, SNP arrays), Fragment Analysis (Capillary Electrophoresis up to 1200 bp), DNA Sequencing (Sanger Sequencing), Expression Analysis including Affymetrix Microarray (global gene expression, transcriptome assays), Pathway-focused Real-Time qPCR (mRNA and miRNA). Shared Instrumentation including Beckman Biomek 3000 Liquid Handler, NanoDrop 2000c, ABI7900 384-well Real-Time Genetic Analyzer, PCR Tamer, Thermocyclers. | Pediatric genetics, molecular biology service, genetics, Next Generation Sequencing, PCR, qPCR, microarray, Cell Line Authentication, Genotyping, Alfred I. duPont Hospital for Children, federal CLIA standards, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit |
NCRR 4P20 RR020173 | Open | ABRF_117 | https://coremarketplace.org/?FacilityID=117, https://my.ilabsolutions.com/account/signup/299?sc_id=3122, | SCR_018265 | , Nemours Biomolecular Core Laboratory | 2026-08-04 09:44:18 | 0 | ||||||
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OpenSlide Resource Report Resource Website |
OpenSlide (RRID:SCR_028483) | software toolkit, software resource, software library | Software C library that provides a simple interface to read whole-slide images (also known as virtual slides). | read whole-slide images, virtual slides, | NCRR UL1RR024153; NCATS UL1TR000005 |
PMID:24244884 | Free, Available for download, Freely available | SCR_028483 | 2026-08-04 09:46:26 | 0 | |||||||||
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Resource Center for Medical Ultrasonic Transducer Technology Resource Report Resource Website 1+ mentions |
Resource Center for Medical Ultrasonic Transducer Technology (RRID:SCR_001404) | UTRC | training resource | Biomedical technology research center focusing on the development of very high frequency (above 20 MHz) ultrasonic transducers/arrays for applications in medicine and biology that include ophthalmology, dermatology, vascular surgery, and small animal imaging. The research is pursued simultaneously in three directions: novel piezoelectric materials, very high frequency single element transducers and linear arrays, and finite element modeling and material property measurements. The Center also serves the community through collaborative efforts with investigators having a research interest in high-frequency ultrasound imaging. In addition, it performs the function of training and information dissemination by offering conferences, seminars and specialized courses at the University of Southern California. The Center has set forth a number of goals which define its mission: * Conduct novel research and development of very high frequency (>20MHz) ultrasonic transducers, arrays and imaging applications * Collaborate with other academic institutions, non-profit organizations, and small businesses supported by the NIH to further the development of these high-frequency applications and provide the expertise in transducers necessary for project success * Serve as an educational center for training scientists and engineers interested in ultrasonic transducer technology One of the primary goals of the Center is to provide service to outside investigators and small business. Often an investigator or company has a specific application in mind but is without the expertise to develop the necessary ultrasonic device. Investigators at academic institutions, research institutes, or small businesses supported by NIH grants who have a need for medical ultrasound transducers and are interested in a collaborative effort should contact Dr. Hyung Ham Kim or Dr. K. Kirk Shung. Ultrasound transducers and components can be fabricated either completely by center personnel or in a joint effort with other investigators. In addition, collaborators are encouraged to visit the facility for additional training in fabrication and assembly. | ultrasonic transducer, array, ultrasound, imaging | has parent organization: University of Southern California; Los Angeles; USA | NCRR 1S10RR023653-01 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152627 | SCR_001404 | Ultrasonic Transducer Resource Center, USC Resource Center for Medical Ultrasonic Transducer Technology, Resource on Medical Ultrasonic Transducer Technology | 2026-08-01 12:01:41 | 3 | ||||||
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MS-GF+ Resource Report Resource Website 100+ mentions |
MS-GF+ (RRID:SCR_015646) | software resource | Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. | protein idenitification, peptide sequence, ms, ms spectrum, proteomic, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Pacific Northwest National Laboratory |
NCRR RR018522; NCRR 1-P41-RR024851; NIAID ; W.R. Wiley Environmental Molecular Science Laboratory |
PMID:25358478 | Free, Available for download, Acknowledgment requested | biotools:ms-gf | https://github.com/sangtaekim/msgfplus, https://bio.tools/ms-gf | SCR_015646 | MSGF+, MSGFPlus | 2026-08-01 12:05:26 | 155 | |||||
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University of Michigan Biorepository Resource Report Resource Website |
University of Michigan Biorepository (RRID:SCR_004643) | MICHER Biorepository | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 24,2025. In 2009, the Medical School and the Michigan Institute for Clinical & Health Research (MICHR) unveiled a new biorepository for U-M researchers in need of a controlled storage environment for biological samples. MICHR is pleased to be able to add to its many services for the research community a centralized biological repository for controlled storage of biological samples, and related services (including DNA, RNA, and other downstream preparation) within the U-M campus. The biorepository, located in the CAP/CLIA-certified Michigan Center for Translational Pathology (MCTP) laboratory at the U-M Traverwood facility on Huron Parkway, will store biologic material, including blood and urine. Sample accessioning and tracking will be accomplished using the caTISSUE suite of programs, and samples will be processed and stored in compliance with CAP/CLIA guidelines. Initially, all samples will be used only with the authorization of the individual investigator who directed the project under which the samples were obtained. Samples will be used in accordance with the relevant informed consent. Long-term plans include federating the database in order to facilitate sharing of data and samples between research teams. | biologic material, blood, urine |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Michigan Medical School; Michigan; USA |
NCRR UL1RR024986 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_63960 | http://www.michr.umich.edu/biorepository/index.html | SCR_004643 | 2026-08-01 12:10:47 | 0 | ||||||
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New Iberia Research Center Resource Report Resource Website 10+ mentions |
New Iberia Research Center (RRID:SCR_008279) | biomaterial supply resource, material resource, organism supplier | NIRC maintains and provides available research facilities accredited by the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) International; a ready source of chimpanzees of mixed ages and sex for use in biomedical and behavioral sciences, and also provides professional staff necessary to support investigators with their research needs. Current Research: Vaccine development and testing; pharmacokinetic, pharmacodynamic, preclinical safety, and efficacy studies. Services Provided: The University of Louisiana at Lafayette-New Iberia Research Center (UL Lafayette-NIRC) is an AAALAC-International-accredited nonhuman primate research facility dedicated to the support of basic and applied biomedical and behavioral research. All proposed programs must be approved by the presenting institution and the UL Lafayette-NIRC animal care and use committees. State-of-the-art biomedical support facilities are available that include access to ultrasound, radiography with automatic processor and computer imagery for diagnostic enhancement, and endoscopy and laparoscopy with video monitors, camera and color photo imagery. Diagnostic Laboratory: A 12,000-square-foot laboratory is available for investigators'' research support requirements. Capabilities within the laboratory include but are not limited to hematology, chemistry, microbiology, urinalysis, parasitology, and histology. Among the investigator support procedures are Ficoll gradient isolation of peripheral blood mononuclear cells, platelet aggregation profiles, nonhuman primate lymphocyte proliferation assay, and flow cytometry (lymphocyte enumeration). Emergency generator power is accessible in each laboratory unit and for all major instrumentation and critical freezers. Animals: The center cares for approximately 360 chimpanzees and 5,500 New and Old World species of nonhuman primates. In addition to chimpanzees, the following species of nonhuman primates are being bred at the center: Vervet monkey (Chlorocebus aethiops), cynomolgus macaque (Macaca fascicularis), pigtailed macaque (M. nemestrina), rhesus macaque (M. mulatta). | endoscopy, animal, assay, behavioral, biomedical, blood, cell, chemistry, chimpanzee, chlorocebus aethiops, cynomolgus, cytometry, development, hematology, histology, imagery, laboratory, laparoscopy, lymphocyte, macaca fascicularis, macaca mulatta, macaca nemestrina, macaque, microbiology, monkey, mononuclear, nonhuman, parasitology, peripheral, pharmacodynamic, pharmacokinetic, photo, pigtailed, platelet, primate, radiography, research, rhesus, science, testing, ultrasound, urinalysis, vaccine, vervet | has parent organization: University of Louisiana; Louisiana; USA | NIH Office of the Director R24 OD010947; NCRR U42 RR01 5087 |
nif-0000-24364 | SCR_008279 | NIRC | 2026-08-03 09:33:58 | 41 | ||||||||
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Alamogordo Primate Facility Resource Report Resource Website |
Alamogordo Primate Facility (RRID:SCR_008376) | APF | biomaterial supply resource, material resource, organism supplier | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It houses chimpanzees that have been used in biomedical research, but no active, invasive research is conducted on the site. The APF provides for the long-term care and husbandry of chimpanzees that have been used in biomedical research. Charles River Laboratories Inc. operates the facility under contract with the National Institutes of Health. To be used in continuing virological research, the animals must be transferred to active chimpanzee research settings. All chimpanzees at the APF have been exposed to various microorganisms, such as hepatitis C virus and HIV. For this reason, they may be candidates for studies related to these diseases. The National Center for Research Resources (NCRR) may remove infected animals from the APF to other accredited chimpanzee facilities for research purposes. Investigators interested in the chimpanzees at the APF should contact Dr. Harold Watson in NCRR''s Division of Comparative Medicine to discuss research requirements. | animal, biomedical, chimpanzee, comparative medicine, disease, hepatitis c, hiv, husbandry, infection, microorganism, primate, research, virological, virus | NCRR | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25894 | SCR_008376 | Alamogordo Primate Facility | 2026-08-03 09:34:05 | 0 | |||||||
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National Center for Research Resources - Primate Resources Resource Report Resource Website 1+ mentions |
National Center for Research Resources - Primate Resources (RRID:SCR_006863) | NCRR Primate Resources | biomaterial supply resource, material resource, organism supplier | THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 16, 2013. NCRR has been absorbed into other parts of the National Institutes of Health. This organizational structure is no longer available. Provides laboratory scientists and clinical researchers with the resources and tools they need to understand, detect, treat and prevent a wide range of diseases. Animal models, such as nonhuman primates, are a critical component of biomedical research, having profound implications for public health. Scientists depend on laboratory animals and other nonhuman models for investigating biological processes, studying the causes of diseases and testing promising new therapies. Nonhuman primates, in particular, are important for translational research because of their close physiological similarities to humans. They enable discoveries that have direct application to human studies, bridging the gap between basic science and human medicine. Discoveries in animal models are helping scientists test treatments for human conditions such as drug addiction, obesity, malaria, HIV/AIDS and neurodegenerative diseases, accelerating the pace at which these research advances can be translated into treatments for patients. Through its Division of Comparative Medicine, NCRR offers a wide variety of primate resources for NIH-funded scientists across the nation. Additionally, funding opportunities are available to National Primate Research Centers. Eight National Primate Research Centers (NPRCs) located throughout the country provide animals, facilities and expertise in all aspects of nonhuman primate biology and husbandry. These facilities and resources enable collaborative research among NPRC staff scientists, investigators from the NPRC host institution and other NIH-funded researchers. Major areas of research benefiting from the primate centers include AIDS, avian flu, Alzheimer''s disease, Parkinson''s disease, diabetes, asthma and endo-metriosis. The centers????????????????? specialized resources are intended to support investigators who receive their primary research project funding from NIH, but they also may be used by investigators who are funded by other federal, state and local agencies, as well as by research foundations and the private sector. Together the primate centers have more than 28,000 nonhuman primates of 20 different species. This portal covers the following topics: * National Primate Research Centers * Monkey Research Resources * Chimpanzee Research Resources * Chimpanzee Management Program * Specific-Pathogen-Free Macaque Resources * Nonhuman Primate Research Reagents | grant, animal model, non-human primate, monkey, chimpanzee, reagent |
is listed by: One Mind Biospecimen Bank Listing is parent organization of: Yerkes National Primate Research Center is parent organization of: Washington National Primate Research Center |
NCRR ; NIH Blueprint for Neuroscience Research |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00495 | http://www.ncrr.nih.gov/comparative_medicine/resource_directory/primates.aspcenters, http://www.ncrr.nih.gov/primates | SCR_006863 | Nonhuman Primate Research Resources | 2026-08-03 09:33:11 | 1 | |||||
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JAX Cre Repository Resource Report Resource Website 1+ mentions |
JAX Cre Repository (RRID:SCR_005566) | Cre Repository | biomaterial supply resource, material resource, organism supplier | Repository of Cre Driver lines and related information resources. Their services include analysis of Cre line excision function in both target and non-target tissues using Cre reporter lines and presenting the annotated data in the expression data portion of this website, http://cre.jax.org/data.html. | cre, cre reporter, organism, cre driver line, cryopreserved, live, cre, cre expression, cre reporter strain, cre strain with floxed allele, image, strain, expression data, neurobiology |
is listed by: One Mind Biospecimen Bank Listing is related to: CRE Driver Network is related to: Allen Institute for Brain Science Transgenic Mouse Study is related to: Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders is related to: Recombinase (cre) Activity has parent organization: Jackson Laboratory |
Cre, Cre expression, Cre reporter strain, Cre strain with floxed allele | NIH Blueprint for Neuroscience Research ; NIDCR ; NCRR RR03 2656; NCRR RR026117; NCRR RR001183; NIH Office of the Director OD011190; NIH Office of the Director OD010972; NIH Office of the Director DE020052 |
Public | nlx_144662 | SCR_005566 | Jackson Laboratory Cre Repository, Cre Driver Strain Resources, The Jackson Laboratory Cre Repository | 2026-08-03 09:32:52 | 5 | |||||
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Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software toolkit, software resource | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG006399; NIMH R01 MH101244; NHGRI F32HG007805; Wellcome Trust WT098051; Austrian Science Fund J-3401; NHGRI HG007022; NHLBI HL117626; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NWO 480-05-003; Dutch Brain Foundation |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/, https://github.com/poruloh/Eagle, https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ | SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-08-02 09:07:16 | 51 | |||||
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SAINTexpress Resource Report Resource Website 10+ mentions |
SAINTexpress (RRID:SCR_018562) | software toolkit, software resource | Software tool for upgraded implementation of probabilistic scoring of affinity purification mass spectrometry data. Used for filtering high confidence interaction data from affinity purification mass spectrometry experiments. Used for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments. | Probabilistic scoring, affinity purification, mass spectrometry data, mass spectrometry experiment data, assigning confidence score, protein-protein interaction, quantitative proteomic data | NCRR R01 RR024031; NIGMS R01 GM094231; NCI R01 CA126239 |
PMID:24513533 | Free, Freely available | SCR_018562 | Significance Analysis of INTeractome Express | 2026-08-02 09:07:59 | 13 | ||||||||
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New England National Primate Research Center Resource Report Resource Website |
New England National Primate Research Center (RRID:SCR_002887) | NERPRC | biomaterial supply resource, material resource, organism supplier | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. A U.S. Regional Primate Research Center that focuses on AIDS, cancer, neuropsychiatric disorders, drug addiction, and neurodegenerative disease. The Division of Primate Resources provides researchers with the services and facilities to support biomedical research. It offers a broad spectrum of services ranging from analysis of tissue specimens to partnership investigations with leading biomedical research institutions. Outside investigators have access to tissue specimens, organs, blood, skeletal structures, and viral specimens. Services include veterinary services, animals and animal care, surgical and radiographic services, timed mating, biocontainment, pathology services, and professional and technical expertise. Additional diagnostic and research services at NEPRC include testing for antiviral antibodies, DNA cloning, and DNA sequencing. The colony of nine species includes rhesus macaques and other Old World monkeys and New World species including the common marmoset and squirrel monkey. Other species can be obtained. Animals with exceptional characteristics (specific-pathogen-free, timed pregnancy, surgically altered, etc.) can be made available if needed. Scientists wishing to conduct research at the center must have projects reviewed and approved by the center animal allocation committee. | non human primate, flow cytometry, aids, behavioral, brain imaging, callithrix, macaque, parkinsons disease, herpesvirus, marmoset, monkey, neurobiology, neurodegenerative, neuropharmacology, oncogene, pathogenesis, pharmacology, primate, rhesus, rhesus macaque, squirrel monkey, tissue, vaccine |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Harvard Medical School; Massachusetts; USA |
Human immunodeficiency virus, Simian immunodeficiency virus, AIDS, Oncogenic herpesviruses, Infectious disease, Neurodegenerative disease, Cocaine abuse, Cancer, Neuropsychiatric disorder, Drug addiction, Parkinson's disease | NCRR P51 RR000168 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25596 | SCR_002887 | 2026-08-03 09:32:04 | 0 | ||||||
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Washington National Primate Research Center Resource Report Resource Website 1+ mentions |
Washington National Primate Research Center (RRID:SCR_002761) | WaNPRC | biomaterial supply resource, material resource, organism supplier | Center that aims to provide an environment to support biomedical research directed towards human health issues and nonhuman primate health and biology. To meet this mission, the WaNPRC supports biomedical research activities, professional research staff, specifically bred and maintained nonhuman primate colonies, and dedicated facilities and equipment required for nonhuman primate research protocols. | aids, clinical, disease, monkey, developmental biology, functional genomics, immunology, reproduction, biology, neurophysiology, infectious disease, transplantation, stem cell, biology, virology, disease model, animal model, neurobiology, neuroscience, systems biology, baboon, long-tailed macaque, rhesus monkey, live animal, macaca nemestrina, macaca fascicularis, macaca mulatta, papio cynocephalus, papio anubis |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Washington; Seattle; USA has parent organization: National Center for Research Resources - Primate Resources is parent organization of: WaNPRC Pathology and Tissue Program |
NCRR ; NIH Office of the Director P51 OD010425; NIH Office of the Director U42 OD011123 |
Free | nif-0000-24361 | https://orip.nih.gov/comparative-medicine/programs/vertebrate-models | http://www.wanprc.org/WaNPRC/index.php | SCR_002761 | 2026-08-03 09:32:08 | 4 | |||||
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IMOD Resource Report Resource Website 1000+ mentions |
IMOD (RRID:SCR_003297) | IMOD | data processing software, source code, software resource, software application, image processing software, image analysis software | A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X | electron microscopy, magnetic resonance, tomographic reconstruction, reconstruction, segmentation, 3d volume |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite has parent organization: University of Colorado Boulder; Colorado; USA |
NCRR ; NIGMS ; NIBIB |
PMID:27444392 | Free, Available for download, Freely available | nif-0000-31686 | http://www.nitrc.org/projects/imod | SCR_003297 | IMOD - 3D Reconstruction and Analysis | 2026-08-04 09:40:52 | 1585 | ||||
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i2b2 Cross-Institutional Clinical Translational Research project Resource Report Resource Website |
i2b2 Cross-Institutional Clinical Translational Research project (RRID:SCR_003367) | i2b2CICTR, i2b2-CICTR | topical portal, portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A two year Clinical and Translational Science Award (CTSA) supplement that set up a SHRINE (Shared Health Research Informatics NEtwork) network to create an information exchange environment that successfully shared 4.2M deidentified patient records. The network successfully linked i2b2 sites at UW, UCSF, UC Davis and Harvard Catalyst. Recombinant Data Corporation was actively involved in this implementation. This is a collaborative information exchange pilot project to adapt and extend data discovery tools and processes to enhance research design and retrospective data study capabilities for clinical translational investigators. The novel approach of this project will be to incrementally build a common technical, semantic and appropriately secure and governed distributed system in close partnership with active researchers at three large and geographically distributed academic medical centers. This collaboration will extend the Informatics for Integrating Biology and the Bedside (i2b2) software architecture developed by the Harvard based National Center for Biomedical Computing (NCBC) to support multi-institution data query capabilities. The anticipated outcome of this two-year project is to make high-level anonymized descriptive characteristics of population-level data discoverable for research design, hypothesis generation and retrospective data studies. | exchange, biomedical, clinical, medical, pilot, retrospective, translational, integration, interoperability, information exchange environment, software network, data sharing, network, federation |
is listed by: Biositemaps is related to: SHRINE has parent organization: Informatics for Integrating Biology and the Bedside has parent organization: University of Washington; Seattle; USA |
NCRR Contract HHSN268200700031C | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33108 | SCR_003367 | 2026-08-04 09:40:53 | 0 | |||||||
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UCSF Chimera Resource Report Resource Website 1000+ mentions |
UCSF Chimera (RRID:SCR_004097) | Chimera | software application, data processing software, software resource, d visualization software | Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials. | molecular modeling, electron microscopy, interactive visualization and analysis, molecular structures |
is used by: Structure-function linkage database is listed by: 3DVC is listed by: SoftCite is related to: Integrative Modeling Platform is related to: UCSF ChimeraX is related to: UCSF ChimeraX has parent organization: Resource for Biocomputing Visualization and Informatics |
NIGMS P41 GM103311; NCRR P41 RR001081 |
PMID:15264254 | Restricted | nlx_143560 | http://plato.cgl.ucsf.edu/chimera/ | SCR_004097 | Chimera - an Extensible Molecular Modeling System, UCSF Chimera - an Extensible Molecular Modeling System | 2026-08-04 09:41:03 | 2078 | ||||
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Velvet-SC Resource Report Resource Website 1+ mentions |
Velvet-SC (RRID:SCR_004377) | Velvet SC | data processing software, data analysis software, software resource, sequence analysis software, software application | Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria. | genome, single, cell, short, read, assembly |
is listed by: OMICtools is related to: Velvet has parent organization: University of California at San Diego; California; USA |
NHGRI R01 HG003647; Sloan Foundation ; NCRR P41 RR024851 |
PMID:21926975 | Free, Available for download, Freely available | OMICS_01504 | SCR_004377 | Velvet Single Cell | 2026-08-04 09:41:07 | 5 | |||||
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Pharmabase - an open content cheminformatics resource linking physiology with pharmacology Resource Report Resource Website |
Pharmabase - an open content cheminformatics resource linking physiology with pharmacology (RRID:SCR_002462) | Pharmabase | database, data or information resource, image collection | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2015. Open content cheminformatics database linking physiology with pharmacology, it targets the action and use of pharmacological compounds in modifying protein function, while revealing molecular relationships and linking out to related databases and sites. Pharmabase has been developed as a research tool, a resource for students, and an ongoing interactive forum on the use of pharmacological compounds in cellular research. It has several navigational routes, including a graphics browser (shows graphics of cell types and pathways) and membrane transport, which also illustrates the diversity of mechanisms that are covered. Users have access to detailed compound records with interactive features, and a form to send comments to the editor. Investigators are encouraged to alert the editors to mistakes, omissions or new compound information available from their reading and research. | function, cell, compound, graphic, illustration, membrane, molecular, pharmacological, pharmacology, protein, transport, metabolism, intracellular messenger, cell signaling, disease, tissue, cell type, pathway, pharmacology, channel, pump, carriers, protein transporter, membrane transport | has parent organization: BioCurrents Research Center | NCRR P41 RR001395 | PMID:18428760 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21324 | SCR_002462 | 2026-08-04 09:40:39 | 0 |
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