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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Colorado University at Boulder EM Services Core Facility Resource Report Resource Website 10+ mentions |
Colorado University at Boulder EM Services Core Facility (RRID:SCR_001432) | access service resource, core facility, service resource, training resource | Core provides access to instruments including:FEI Tecnai 12 Spirit TEM, FEI Tecnai F20 (200kV) FEG-TEM 200kV FEG-TEM,Gatan US4000 4k x 4k CCD, bottom-mount,CryoTEM and electron tomography,High-resolution TEM;FEI Tecnai F20 (200kV) FEG-TEM,300kV FEG-TEM,Gatan US4000 4k x 4k CCD, bottom-mount,CryoTEM and electron tomography,High-resolution TEM,FEI/Phillips CM100 (100kV) TEM,100kV, tungsten TEM,2k x 2k AMT CCD, bottom-mount. | USEDit, electron microscopy, electron tomography, high resolution | has parent organization: University of Colorado; Colorado; USA | NCRR P41 RR000592 | Free, Freely Available | nlx_152656, SCR_018991 | http://bio3d.colorado.edu/, http://mcdb.colorado.edu/facilities/ems/index.shtml, https://www.colorado.edu/sharedinstrumentation/core-facilities/boulder-em-services-core-facility | SCR_001432 | Boulder Lab for 3D Electron Microscopy, Boulder Electron Microscopy Laboratory Core, Colorado University Boulder Electron Microscopy Core Facility, Boulder EM Services Core Facility | 2026-09-12 01:03:11 | 12 | ||||||
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Wellcome-CTC Mouse Strain SNP Genotype Set Resource Report Resource Website 1+ mentions |
Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) | Wellcome-CTC Mouse Strain SNP Genotype Set | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34. | genome, genotype, snp, chromosome, haplotype, haplotype structure, recombinant inbred mouse strain | has parent organization: Wellcome Trust Centre for Human Genetics | Wellcome Trust ; NCRR R24RR015116; NIGMS R01GM072863; NIAAA U01AA014425; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156947 | SCR_003216 | 2026-09-12 01:03:13 | 3 | |||||||
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Ultrafast Optical Processes Laboratory Resource Report Resource Website 1+ mentions |
Ultrafast Optical Processes Laboratory (RRID:SCR_006582) | Ultrafast Optical Processes Laboratory | access service resource, biomedical technology research center, service resource, training resource | Biomedical technology research center and training resource that develops time-resolved laser technologies and instrumentation, with a focus on 2-D IR spectroscopy. The technologies enable atomic-level measurements of the fastest steps in biological processes to elucidate structure and dynamics in biological macromolecules, assemblies and cells. The Center makes most of its instrumentation available for service research projects to outside users nation-wide. | spectroscopy, structure, dynamics, macromolecule, assembly, cell, optical and laser technology center, laser spectroscopy, biochemical, biophysical, biomedical, laser, biological process | has parent organization: University of Pittsburgh; Pennsylvania; USA | NIGMS 9P41GM104605; NCRR P41RR001348 |
nlx_152664 | SCR_006582 | Laser and Biomedical Technology Laboratories | 2026-09-12 01:03:16 | 1 | |||||||
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NRCAM Resource Report Resource Website 50+ mentions |
NRCAM (RRID:SCR_006134) | NRCAM | access service resource, biomedical technology research center, service resource, training resource | Biomedical technology research center that develops new technologies for modeling cell biological processes. The technologies are integrated through Virtual Cell, a problem-solving environment built on a central database and disseminated as a Web application for the analysis, modeling and simulation of cell biological processes. NRCAM resides at the Center for Cell Analysis and Modeling, CCAM, and provides a vast array of laboratory equipment that can be used for obtaining experimental data needed to create and enhance Virtual Cell models. Microscopy instrumentation includes three confocal laser scanning microscopes including UV excitation, nonlinear optical microscopy utilizing a titanium sapphire pulsed laser, confocal-based fluorescence correlation spectroscopy, wide-field imaging workstation with cooled CCD and rapid excitation filter wheel, and dual-wavelength spectrofluorometer. Access to the facilities and technical staff is open to all researchers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | modeling, simulation, cell, microscopy, software, biological process, model, cell model, informatics, computing and informatics technology center, FASEB list |
is listed by: 3DVC has parent organization: University of Connecticut; Connecticut; USA is parent organization of: Virtual Cell at the National Resource for Cell Analysis and Modeling |
NIGMS ; NCRR ; NIH Blueprint for Neuroscience Research |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03953 | SCR_006134 | The National Resource for Cell Analysis and Modeling, National Resource of Cell Analysis and Modeling, National Resource of Cell Analysis and Modeling (NRCAM), National Resource for Cell Analysis and Modeling, National Resource of Cell Analysis & Modeling (NRCAM) | 2026-09-12 01:03:16 | 76 | ||||||
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National Resource for Quantitative Functional MRI Resource Report Resource Website 1+ mentions |
National Resource for Quantitative Functional MRI (RRID:SCR_006716) | Resource for Quantitative Functional MRI | biomedical technology research center, training resource | Biomedical technology research center that provides expertise for the design of quantitative magnetic resonance imaging (MRI) and spectroscopy (MRS) data acquisition and processing technologies that facilitate the biomedical research of a large community of clinicians and neuroscientists in Maryland and throughout the USA. These methods allow noninvasive assessment of changes in brain anatomy as well as in tissue metabolite levels, physiology, and brain functioning while the brain is changing size during early development and during neurodegeneration, i.e. the changing brain throughout the life span. The Kirby Center has 3 Tesla and 7 Tesla state of the art scanners equipped with parallel imaging (8, 16, and 32-channel receive coils) and multi-transmit capabilities. CIS has an IBM supercomputer that is part of a national supercomputing infrastructure. Resources fall into the following categories: * MRI facilities, image acquisition, and processing * Computing facilities and image analysis * Novel statistical methods for functional brain imaging * Translating laboratory discoveries to patient treatment | quantitative magnetic resonance imaging, magnetic resonance spectroscopy, mri, fmri, function, metabolism, physiology, brain, neurodevelopment, neurodegeneration, image acquisition, image processing, computing, image analysis, statistical method, neuroimaging, development |
has parent organization: Kennedy Krieger Institute has parent organization: Johns Hopkins University; Maryland; USA |
NIBIB P41 EB015909; NCRR P41 RR015241 |
nlx_152634 | http://mri.kennedykrieger.org/nationalresource/index.html | SCR_006716 | Resource for Quantitative Functional Magnetic Resonance Imaging | 2026-09-12 01:03:16 | 1 | ||||||
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National Bio-Organic Biomedical Mass Spectrometry Resource Center Resource Report Resource Website 1+ mentions |
National Bio-Organic Biomedical Mass Spectrometry Resource Center (RRID:SCR_009004) | Mass Spectrometry Facility | biomedical technology research center, training resource | Provides high-performance tandem mass spectrometry and proteomics, including multiplexed quantitative comparative analysis of protein and post-translational modifications, and a suite of tools for the analysis of mass spectrometry proteomics data. It provides both scientific and technical expertise and state-of-the-art high-performance, tandem mass spectrometric instrumentation. The facility also provides a service for small molecule analysis. Significant instrumentation in the facility includes three QSTAR quadrupole orthogonal time of flight instruments, and both an LTQ-Orbitrap platform with electron transfer dissociation (ETD) and an LTQ-FT linear ion trap FT-ICR instrument equipped with the ability to perform electron capture dissociation (ECD). The Center also has a 4700 Proteomic Analyzer MALDI tandem time of flight instrument; as well as a QTRAP 5500 hybrid triple quadrupole linear ion trap instrument; and a Thermo Fisher LTQ Orbitrap Velos. Major research focuses within the Center are the analysis of post-translational modifications, including phosphorylation and O-GlcNAcylation and development of methods for quantitative comparative analysis of protein and post-translational modification levels. The program also continues to develop one of the leading suites of tools for analysis of mass spectrometry proteomics data, Protein Prospector. The current web-based release allows unrestricted searching of MS and MSMS data, as well as the ability to perform comparative quantitative analysis of samples using isotopic-labeling reagents. It is the only freely-available web-based resource that allows this type of analysis. | systems biology technology center, mass spectrometry, proteomics | has parent organization: University of California at San Francisco; California; USA | NCRR ; NIGMS P41GM103481 |
nlx_152680 | SCR_009004 | UCSF Mass Spectrometry Facility | 2026-09-12 01:03:18 | 2 | |||||||
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SAINTexpress Resource Report Resource Website 10+ mentions |
SAINTexpress (RRID:SCR_018562) | software resource, software toolkit | 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 | NCI R01 CA126239; NCRR R01 RR024031; NIGMS R01 GM094231 |
PMID:24513533 | Free, Freely available | SCR_018562 | Significance Analysis of INTeractome Express | 2026-09-12 01:02:56 | 16 | ||||||||
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LONI De-identification Debablet Resource Report Resource Website |
LONI De-identification Debablet (RRID:SCR_009593) | LONI De-identification Debablet | software application, software resource | Software application for removing patient-identifying information from medical image files. Removing this information is often necessary for enabling investigators to share image files in a HIPAA compliant manner. | analyze, console (text based), dicom, java, minc, magnetic resonance, nifti, os independent, win32 (ms windows), workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
LONI Software License | nlx_155784 | http://www.nitrc.org/projects/did | http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=23 | SCR_009593 | 2026-09-12 01:02:47 | 0 | |||||
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BioMesh3D Resource Report Resource Website 1+ mentions |
BioMesh3D (RRID:SCR_009534) | BioMesh3D | software application, software resource | A free, easy to use program for generating quality meshes for use in biological simulations. It is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh. | mesh, simulation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SCIRun is related to: SCIRun has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
PMID:23367171 | MIT License | nlx_155708 | http://www.nitrc.org/projects/biomesh3d | SCR_009534 | 2026-09-12 01:02:46 | 3 | |||||
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ResearchIQ Resource Report Resource Website |
ResearchIQ (RRID:SCR_014304) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented March 14, 2016. Research Integrative Query (ResearchIQ) tool, a semantically anchored resource discovery platform that facilitates semantic discovery of local and publicly available data through a single web portal designed for researchers in the biomedical informatics domain within The Ohio State University. | Platform, Semantic information | has parent organization: Ohio State University; Ohio; USA | NCRR UL1-RR025755 | PMID:26306248 | THIS RESOURCE IS NO LONGER IN SERVICE | http://researchiq.bmi.osumc.edu:8080/#riqview | SCR_014304 | 2026-09-12 01:02:50 | 0 | |||||||
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eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software application, software resource | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCRR KL2 RR029885; NIDDK P01 DK056492; NIDDK R01 DK088541; NIDDK RC4DK090860; NIGMS P50 GM071558; NLM RC2 LM010994 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k, http://www.maayanlab.net/X2K/ | SCR_016307 | eXpression2Kinases, X2K | 2026-09-12 01:02:53 | 6 | ||||
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Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software resource, software toolkit | 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 |
Austrian Science Fund J-3401; Dutch Brain Foundation ; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NHGRI F32HG007805; NHGRI HG007022; NHGRI R01 HG006399; NHLBI HL117626; NIMH R01 MH101244; NWO 480-05-003; Wellcome Trust WT098051 |
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 | 2026-09-12 01:02:53 | 57 | |||||
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Layton Alzheimers Disease Center Biomarkers and Genetics Core Lab Resource Report Resource Website |
Layton Alzheimers Disease Center Biomarkers and Genetics Core Lab (RRID:SCR_009911) | access service resource, core facility, service resource | In cooperation with the Data and Clinical Cores at the Layton Center, the Biomarkers and Genetics Core generates and maintains biomarker data for select biomarkers which have established roles in the characterization of subjects with or at risk of dementia. Biological markers of brain aging, dementia risk, and neurodegeneration have the potential to accelerate the identification of disease mechanisms and treatment strategies. Biomarkers may include genes, proteins, or other metabolites, and may be identified in DNA, cerebrospinal fluid (CSF), or plasma. Apolipoprotein E (APOE) genotype is generated for all research subjects. Sub-groups of subjects have other types of biomarker data. Many subjects have had genome-wide SNP data generated. In order to foster collaborative research as well as expand resources and expertise, samples (DNA, CSF, and plasma) and data are distributed to qualified investigators worldwide. Most of these researchers are pursuing the causes and modifiers of dementia. Data and samples are collected from well characterized research subjects including the healthy elderly and dementia patients. |
is listed by: Eagle I has parent organization: OHSU Layton Aging and Alzheimer's Disease Center |
Aging | NCRR 5U24RR029825-02 | nlx_156376 | SCR_009911 | Layton Alzheimer''s Disease Center Biomarkers & Genetics Core Lab | 2026-09-12 01:03:24 | 0 | ||||||||
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Layton Alzheimers Disease Center Clinical Core Resource Report Resource Website |
Layton Alzheimers Disease Center Clinical Core (RRID:SCR_009912) | access service resource, core facility, service resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on December 6th,2022. The Oregon Alzheimer?s Disease Center?s (OADC) Clinical Core program, directed by Dr. Jeffrey Kaye, performs longitudinal studies of the natural history of brain aging and Alzheimer''s disease in patients and healthy control volunteers. These studies which are performed through standardized neurological, neuro-psychological, and brain-imaging assessments are carried out in the Alzheimer''s Disease and Memory Assessment Clinics as well as through community-based assessments conducted in the homes of study volunteers. The Layton Center Neuroimaging Lab conducts brain-imaging MRI brain scans to assist in diagnosis of brain disease. Typically, MRI images are taken from three different planes. These planes are known as the coronal plane, sagittal plane and the axial plane. Each series of MRI images is named after the plane from which they were obtained. The Clinical Core?s research is focused on preclinical and early Alzheimer?s disease (AD) yet is also poised to participate in other relevant new research as it arises. The OADC Clinical Core recruits, assesses and follows individuals from population groups at high risk for dementia such as: the healthy ?oldest old?, subjects with family history of AD, and subjects with Mild Cognitive Impairment (MCI). Research with underserved populations The Oregon Alzheimer?s Disease Center also maintains two Satellite programs to enhance understanding of underserved populations: The Klamath Exceptional Aging Project (KEAP) is a community-based study of brain aging being conducted in Klamath Falls. The African American Dementia and Aging Project (AADAPt) s a Portland-based cohort of 100 African American seniors. |
is listed by: Eagle I has parent organization: OHSU Layton Aging and Alzheimer's Disease Center |
Aging | NCRR 5U24RR029825-02 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156377 | SCR_009912 | Layton Alzheimer''s Disease Center Clinical Core | 2026-09-12 01:03:24 | 0 | |||||||
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FMRIB’s Integrated Registration and Segmentation Tool Resource Report Resource Website 1+ mentions |
FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) | FIRST | data analysis software, data processing software, image analysis software, registration software, segmentation software, software application, software resource | Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences. | Functional Magnetic Resonance Imaging of the Brain, segmentation, registration, volumetric segmentation, performing vertex analysis, |
is related to: Multimodal Image Segmentation Tool is a plug in for: FSL |
NCRR P41 RR14075; NCRR R01 RR16594; NIDA R01 DA017905; NIMH K01 MH01798; NIMH K08 MH01573; NINDS R01 NS052585 |
PMID:21352927 | Free, Freely available | SCR_024921 | , Functional Magnetic Resonance Imaging of the Brain's Integrated Registration and Segmentation Tool | 2026-09-12 01:04:34 | 7 | ||||||
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MARIA Resource Report Resource Website |
MARIA (RRID:SCR_028673) | software resource, web application | Web multimodal recurrent neural network tool designed to predict HLA-II (Human Leukocyte Antigen class II) peptide ligand presentation. It uses cell HLA alleles, peptide sequences, and source genes to evaluate antigen presentation. Used for predicting the likelihood of antigen presentation from a gene of interest in the context of specific HLA class II alleles. | multimodal recurrent neural network, predicting likelihood of antigen presentation, gene of interest, specific HLA class II alleles, | is organization facet of: Stanford University; Stanford; California | NCI K08 CA207882; NCI U01 CA194389; NCRR S10RR027431; NIGMS GM 102365 |
PMID:31611695 | Free, Freely available | SCR_028673 | MARIA:Major Histocompatibility Complex Analysis with Recurrent Integrated Architecture | 2026-09-12 01:05:57 | 0 | |||||||
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West Virginia University Flow Cytometry and Single Cell Core Facility Resource Report Resource Website 10+ mentions |
West Virginia University Flow Cytometry and Single Cell Core Facility (RRID:SCR_017738) | access service resource, core facility, service resource | Facility provides instrumentation and scientific support for single cell analysis and sorting. Routinely performs analysis of both eukaryotic and prokaryotic cells for expression of intracellular and extracellular proteins, cell cycle, cell proliferation, cytokine production, and cell sorting based on expression of cell surface antigen(s) and/or expression of genetically engineered intercellular fluorescent proteins. | Single, cell, analysis, sorting, flow, cytometry, West Virginia, service, core | NCRR RR020866; NIGMS P20 GM103434; NIGMS P20 GM109098; NIGMS P30 GM103488; NIGMS U51 GM104942; NIGMS U54 GM104942; NIH Office of the Director S10 OD016165 |
Open | ABRF_221 | SCR_017738 | FCSCCF, WVU Flow Cytometry and Single Cell Core Facility | 2026-09-12 01:04:01 | 15 | ||||||||
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Yale University DNA Analysis on Science Hill Core Facility Resource Report Resource Website 1+ mentions |
Yale University DNA Analysis on Science Hill Core Facility (RRID:SCR_017689) | access service resource, core facility, service resource | Core supports DNA Sequencing of PCR, Plasmid, BAC and Fosmid templates, Fragment Analysis of Microsatellites, AFLP, t-RFLP, SHAPE Experiments and Human Cell Line Authentication. | DNA, sequencing, PCR, plasmid, BAC, Fosmid, template, fragment, analysis, micosatellites, AFLP, tRFLP, human, cell, line, authentication, service, core | NCRR S10 RR025478; NSF Instrumentation Development Grant |
Open | SCR_017711, ABRF_71 | SCR_017689 | DNA Analysis Facility on Science Hill | 2026-09-12 01:04:00 | 2 | ||||||||
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Stanford University Shared FACS Core Facility Resource Report Resource Website 10+ mentions |
Stanford University Shared FACS Core Facility (RRID:SCR_017788) | access service resource, core facility, service resource | Provides flow cytometry instrumentation and expertise. Provides operator assisted analyzer and sorter use, as well as training and support for user instrument operation. | Flow, cytometry, instrumentation, analysis, cell, sorting, training, service, core | NCRR S10 RR025518; NCRR S10 RR027431; NIH Office of the Director S10 OD016318; Parker Institute for Cancer Immunotherapy |
Open | ABRF_398 | SCR_017788 | Stanford Shared FACS Facility | 2026-09-12 01:04:02 | 26 | ||||||||
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University of Wisconsin-Madison Chemistry Instrumentation Center - Mass Spectrometry Core Facility Resource Report Resource Website |
University of Wisconsin-Madison Chemistry Instrumentation Center - Mass Spectrometry Core Facility (RRID:SCR_017931) | access service resource, core facility, service resource | Core provides mass spectrometers including Thermo Q Exactive Plus,Bruker impact II ,Bruker microflex LRF,Bruker ULTRAFLEX III,Shimadzu GCMS-QP2010S,Waters Acquity LCMS. | Instrumentation, mass, spectrometry, service, core, ABRF | is listed by: ABRF CoreMarketplace | NCRR S10 RR024601; NIH Office of the Director S10 OD020022; NSF |
Restricted | ABRF_809 | SCR_017931 | Mass Spectrometry Facility | 2026-09-12 01:04:05 | 0 |
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