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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Conservation Resource Report Resource Website 1000+ mentions |
Conservation (RRID:SCR_016064) | software application, software resource, software toolkit | Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands. | scoring, protein, sequence, conservation, Jensen-Shannon, divergence, predict, catalytic, site, bound, ligands, clustal, fasta, concave | is related to: Princeton University; New Jersey; USA | NIGMS GM076275; NIH P50 GM071508; NIH T32 HG003284; NSF IIS-0612231; NSF PECASE MCB-0093399 |
PMID:17519246 | Free, Available for download | SCR_016064 | Conservation-code | 2026-09-12 01:02:53 | 1606 | |||||||
|
Predictomes Resource Report Resource Website 1+ mentions |
Predictomes (RRID:SCR_026691) | data or information resource, database | Interactive database of protein protein interactions modeled by AlphaFold multimer. Classifier-curated database of AlphaFold-modeled protein-protein interactions. | Classifier-curated database, AlphaFold-modeled protein-protein interactions, interactive database, protein protein interactions, | NHLBI HL098316; NSF |
PMID:38645019 | Free, Freely available | SCR_026691 | 2026-09-12 01:05:10 | 5 | |||||||||
|
RFMix Resource Report Resource Website 1+ mentions |
RFMix (RRID:SCR_027030) | software application, software resource | Software tool for local ancestry and admixture inference. Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference. | Discriminative Modeling, local ancestry and admixture inference, | NHGRI 2R01HG003229; NLM LM007033; NSF |
PMID:23910464 | Restricted | SCR_027030 | 2026-09-12 01:05:17 | 9 | |||||||||
|
University of New Hampshire University Instrumentation Center Core Facility Resource Report Resource Website |
University of New Hampshire University Instrumentation Center Core Facility (RRID:SCR_021101) | UIC | access service resource, core facility, service resource | University wide core facility offers NMR,SEM including FIB, EBS, EBSD, Tensile Stage,Confocal,X-Ray Photoelectron Spectroscopy,X-Ray Microscope aka Micro CT, Expert analysis of research and industrial samples,Training in scientific instrument operation and data analysis, Maintenance, repair, and calibration of instruments,Specialty instrument engineering design and application services,Facilitation of access to scientific instruments throughout the university. | USEDit, ABRF, ABRF | is listed by: ABRF CoreMarketplace | NIGMS GM113131; NSF 1337897; NSF 1429282; NSF 1828319; NSF OIA 1757371 |
open | ABRF_640 | https://coremarketplace.org/?FacilityID=640 | SCR_021101 | University Instrumentation Center, University of New Hampshire University Instrumentation Center | 2026-09-12 01:04:10 | 0 | |||||
|
Cornell University BRC Epigenomics Core Facility Resource Report Resource Website 10+ mentions |
Cornell University BRC Epigenomics Core Facility (RRID:SCR_021287) | access service resource, core facility, service resource | Provides service that maps protein DNA interactions genome wide, tracks experimental metadata, and implements quality controlled data processing and research based analysis pipelines. Provides epigenomic and bioinformatic research resources and services that include sample preparation services and data generation. Open source platforms enable and reinforce FAIR data practices. Core is able to receive and process cell and tissue samples for various diagnostic epigenetic assays. | USEDit, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: Cornell University; New York; USA |
NIH ; NSF |
ABRF_1185 | https://coremarketplace.org/?FacilityID=1185 | SCR_021287 | CU Epigenomics Core Facility, Cornell University Epigenomics Core Facility | 2026-09-12 01:04:11 | 12 | |||||||
|
Boise State University Biomolecular Research Center Core Facility Resource Report Resource Website 50+ mentions |
Boise State University Biomolecular Research Center Core Facility (RRID:SCR_019174) | BRC | access service resource, core facility, service resource | Designed to provide supportive environment for interdisciplinary research and education with opportunities for students and faculty members alike with focus on biomolecules study with emphasis on proteins and protein interactions. Provides instrumentation and facilities for characterization of biomolecules and their role in variety of biomedical and environmental processes. Partnerships between Center and Idaho-BRIN/INBRE, UI, ISU, Boise VA Medical Center, College of Idaho, and Northwest Nazarene University. BRC provides seminars, training workshops, and other networking opportunities. | USEDit, protein study, protein interactions, biomolecule, biomedical and environmental processes, ABRF, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: Boise State University; Idaho; USA |
NSF 0619793; NSF 0923535 |
PMID:34121933 | ABRF_664 | https://coremarketplace.org/?FacilityID=664 | SCR_019174 | The Biomolecular Research Center | 2026-09-12 01:04:09 | 54 | |||||
|
University of California at Santa Cruz Stable Isotope Laboratory Core Facility Resource Report Resource Website 1+ mentions |
University of California at Santa Cruz Stable Isotope Laboratory Core Facility (RRID:SCR_022947) | SiL | access service resource, core facility, service resource | Provides light stable isotope ratio analysis services to scientists from UCSC and from around the world. | ABRF, USEDit, light stable isotope ratio analysis services, |
is related to: USEDit has parent organization: University of California at Santa Cruz; California; USA |
NSF | Open | SCR_022947 | UC Santa Cruz Stable Isotope Laboratory | 2026-09-12 01:04:22 | 8 | |||||||
|
University of Michigan Statistics Online Computational Resource Core Facility Resource Report Resource Website |
University of Michigan Statistics Online Computational Resource Core Facility (RRID:SCR_022917) | SOCR | access service resource, core facility, service resource | SOCR designs, validates and freely disseminates knowledge. The Resource develops AI/ML tools, mathematical models, and end-to-end data analytic protocols for biomedical and health studies. It provides portable online aids for probability, statistics and health science education, promotes technology enhanced instruction, supports efficient statistical computing, supports AI-services, and advances predictive big data analytics. The SOCR platform includes repository of interactive apps, datasets and case-studies, computational tools, visualization approaches, instructional resources, learning materials, and curricular components. SOCR faculty, staff, and students support data and information science collaborations and analytic partnerships involving biomedical, healthcare, and biostatistical investigations. | ABRF, probability, statistics and health science education, statistical computing, predictive big data analytics |
is listed by: ABRF CoreMarketplace has parent organization: University of Michigan; Ann Arbor; USA |
NIH ; NSF |
ABRF_1602 | https://coremarketplace.org/?FacilityID=1602&citation=1 | SCR_022917 | Statistics Online Computational Resource (SOCR), University of Michigan Ann Arbor Statistics Online Computational Resource (SOCR) | 2026-09-12 01:04:21 | 0 | ||||||
|
University of California BioPACIFIC MIP Core Facility Resource Report Resource Website |
University of California BioPACIFIC MIP Core Facility (RRID:SCR_023540) | NSF BioPACIFIC MIP | access service resource, core facility, service resource | BioPolymers, Automated Cellular Infrastructure, Flow, and Integrated Chemistry Materials Innovation Platform is platform dedicated to scalable production of bio-derived building blocks and polymers from yeast, fungi, and bacteria. Automated high-throughput synthesis and characterization of bio-derived polymers aims to accelerate discovery and speed development of new high-performance materials. | USEDit, ABRF, Bio-derived building blocks and polymers production, yeast polymers, fungi polymers, bacteria polymers, |
is listed by: ABRF CoreMarketplace is related to: USEDit is related to: University of California at Los Angeles; Los Angeles; United States is related to: University of California at Santa Barbara; California; USA |
NSF DMR-1933487 | ABRF_1758 | https://coremarketplace.org/?FacilityID=1758&citation=1 | SCR_023540 | BioPACIFIC MIP, Flow, and Integrated Chemistry Materials Innovation Platform Core Facility, BioPACIFIC MIP Core Facility, Automated Cellular Infrastructure, BioPolymers | 2026-09-12 01:04:26 | 0 | ||||||
|
Emory University Robert P. Apkarian Integrated Electron Microscopy Core Facility Resource Report Resource Website 10+ mentions |
Emory University Robert P. Apkarian Integrated Electron Microscopy Core Facility (RRID:SCR_023537) | IEMC | access service resource, core facility, service resource | Core helps investigators use the latest technologies on structural research in their projects. Provides expertise in experimental needs. | USEDit, ABRF, electron microscopy, |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Emory University; Georgia; USA |
Emory University School of Medicine ; Georgia Clinical and Translational Science Alliance ; NIH ; NSF |
ABRF_1753 | https://coremarketplace.org/?FacilityID=1753&citation=1 | SCR_023537 | Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University Robert P. Apkarian Integrated Electron Microscopy Core (IEMC) | 2026-09-12 01:04:26 | 31 | ||||||
|
PaleoClim database Resource Report Resource Website 10+ mentions |
PaleoClim database (RRID:SCR_025657) | data or information resource, database | Database of downscaled paleoclimate outputs at 2.5 minute resolution (~5 km at equator) that includes surface temperature and precipitation estimates from snapshot-style climate model simulations using HadCM3, a version of the UK Met Office Hadley Centre General Circulation Model. Database contains climatic data for three key time periods spanning from 3.3 to 0.787 million years ago: the Marine Isotope Stage 19 (MIS19) in the Pleistocene (~787 ka), the mid-Pliocene Warm Period (~3.264–3.025 Ma), and MIS M2 in the Late Pliocene (~3.3 Ma). Set of historical climate layers (climate grids) with spatial resolution of about 2.5 min. These data can be used for mapping and spatial modelling in Geographic Information Systems (GIS) or other computer programs. | historical climate layers, climate grids, paleoclimate outputs, 2.5 minute resolution, surface temperature, precipitation estimates, climate model simulations, climatic data, | European Research Council ; National Aeronautics and Space Administration ; NSF ; São Paulo State Research Foundation ; Southern Illinois University ; University of Leeds International Research Collaboration Award |
PMID:30422125 | Free, Freely available | SCR_025657 | Paleoclim | 2026-09-12 01:04:49 | 28 | ||||||||
|
tTFtarget Resource Report Resource Website 1+ mentions |
tTFtarget (RRID:SCR_025631) | data or information resource, database | Transcription factor target database. Platform consolidating both computationally predicted and experimentally validated binding sites between transfer RNA-derived fragments and target genes or transcripts across multiple organisms. | Transcription factor target, validated binding sites, transfer RNA-derived fragments, target genes, multiple organisms, | NLM R01LM014087; NSF |
DOI:10.1093/nar/gkad815 | Free, Freely available | SCR_025631 | tRFtarget 2.0, tRFtarget 1.0 | 2026-09-12 01:04:48 | 4 | ||||||||
|
SIMS Resource Report Resource Website 1+ mentions |
SIMS (RRID:SCR_025787) | software application, software resource | Software label transfer tool for single-cell RNA sequencing analysis. Scalable, Interpretable Modeling for Single-cell RNA-seq data classification. | label transfer, single-cell RNA sequencing analysis, single-cell RNA-seq data classification, | NHGRI 1RM1HG011543; NIMH 1U24MH132628; NSF ; QualcommInstitute ; Schmidt Futures ; University of California Office of the President |
PMID:38823397 | Free, Available for download, Freely available | SCR_025787 | scalable, interpretable machine learning for single cell | 2026-09-12 01:04:52 | 2 | ||||||||
|
NSF Network for Advanced NMR Resource Report Resource Website |
NSF Network for Advanced NMR (RRID:SCR_025092) | NAN | data or information resource, organization portal, portal, service resource | Provides distributed services from Universities of Connecticut, Georgia, and Wisconsin to democratize application of high-field NMR spectroscopy for applications in biomedicine, materials science, and chemistry. Multi-institution collaboration creating distributed research infrastructure for NMR applications including resource discovery, access to NMR spectrometers, ranging from bench top to ultra-high field, knowledgebases on best practices, and data archiving and sharing. | Multi-institution collaboration, NMR, spectroscopy, NMR spectroscopy, NMR applications research infrastructure, | NSF | Free, Freely available, | SCR_025092 | Network for Advanced Nuclear Magnetic Resonance | 2026-09-12 01:04:37 | 0 | ||||||||
|
ReDU Resource Report Resource Website 1+ mentions |
ReDU (RRID:SCR_025105) | data access protocol, software resource, web service | Software framework to find and re-analyze public Mass Spectrometry data. Used to find uniformly formatted public MS/MS data in the Global Natural Product Social Molecular Networking Platform (GNPS) via formatted metadata. New or previously collected data can be added provided they adhere to the ReDU metadata standards (the implemented drag-and-drop validator is applicable to any scientific data) and data are available in GNPS/MassIVE. | Mass Spectrometry data, find uniformly formatted public MS/MS data, formatted metadata, Global Natural Product Social Molecular Networking Platform, GNPS, find and re-analyze public Mass Spectrometry data, ReDU metadata standards, data validator, | has parent organization: University of California at San Diego; California; USA | American Society for Mass Spectrometry ; FAPESP ; Gordon and Betty Moore Foundation ; Krupp Endowed Fund ; NCI R03 CA211211; Netherlands eScience Center ; NIGMS P41 GM103484; NIGMS R01 GM107550; NSF ; Sloan Foundation ; University of California ; San Diego Center for Microbiome Innovation SEED grants ; US Office of Naval Research |
PMID:32807955 | Free, Freely available | SCR_025105 | Reanalysis of Data User | 2026-09-12 01:04:37 | 2 | |||||||
|
MassQL Resource Report Resource Website 1+ mentions |
MassQL (RRID:SCR_025106) | software resource, source code | Software application for universal searching of Mass Spectrometry data. Open source MS query language for flexible and mass spectrometer manufacturer-independent mining of MS data. Implements common MS terminology to build consensus vocabulary to search for MS patterns in single mass spectrometry run. Enables set of mass spectrometry patterns to be queried directly from raw data. | Mass Spectrometry data searching, mass spectrometry data, mining of MS data, common MS terminology, mass spectrometry patterns, raw data query, | AMED Japan Program for Infectious Diseases Research and Infrastructure ; Betty and Gordon Moore Foundation ; Burroughs Wellcome Fund ; Czech Science Foundation ; German Ministry for Education and Research ; German Research Foundation ; Horizon 2020 programme of the European Union ; Ministry of Innovative Development of the Republic of Uzbekistan ; National Cancer Center Research and Development Fund ; National Research Foundation of Korea ; NIAID R15 AI137996; NIAID R21 AI156669; NIGMS R01 GM107550; NIGMS R01 GM125943; NIGMS R35 GM128690; Novo Nordisk Foundation ; Denmark ; NSF ; Swedish Research Council ; U.S. Department of Energy Joint Genome Institute ; University of Michigan |
DOI:10.1101/2022.08.06.503000 | Free, Available for download, Freely available | https://pypi.org/project/massql/ | SCR_025106 | Mass Spec Query Language | 2026-09-12 01:04:37 | 1 | |||||||
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Find My Understudied Genes Resource Report Resource Website 1+ mentions |
Find My Understudied Genes (RRID:SCR_025047) | FMUG | software application, software resource, source code | Software data-driven tool to identify understudied genes and characterize their tractability. Users submit list of human genes and can filter these genes down based on list of factors. Code to generate Find My Understudied Genes app for Windows, iOS and macOS platforms. | has parent organization: Northwestern University; Illinois; USA | Moderna Inc ; NAIAD U19AI135964; NIA K99AG068544; NIGMS T32GM008449; Northwestern University ; NSF ; Simons Foundation |
DOI:10.7554/eLife.93429 | Free, Available for download, Freely available | https://github.com/amarallab/fmug | SCR_025047 | 2026-09-12 01:04:36 | 3 | |||||||
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WASP Resource Report Resource Website 1+ mentions |
WASP (RRID:SCR_025497) | software resource, software toolkit, source code | Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery. | molecular QTLs discovery, unbiased allele-specific read mapping and discovery, molecular QTLs, unbiased allele-specific read, mapping and discovery, | Howard Hughes Medical Institute ; NHGRI HG006123; NHGRI HG007036; NIGMS GM007197; NIMH MH101825; NSF |
PMID:26366987 | Free, Available for download, Freely available, | SCR_025497 | 2026-09-12 01:04:45 | 3 | |||||||||
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Bruker: Avance Neo 1.2 GHz NMR Spectrometer Resource Report Resource Website |
Bruker: Avance Neo 1.2 GHz NMR Spectrometer (RRID:SCR_028512) | instrument resource | Spectrometer represents the pinnacle of commercial nuclear magnetic resonance technology. Operating at 28.2 Tesla, this ultra-high-field system is primarily used for advanced structural biology, pharmaceutical research, and materials science. Delivers the highest commercially available spectral resolution, crucial for investigating complex protein dynamics, functional molecular disorders, and viral structures. Console:Avance Neo; Magnet:Gateway; Field Strength: 1.2 GHz; Software:TopSpin 4.4.1 on CentOS 7; Probes:3mm TCI cryoprobe; 3mm BBI room-temperature; 3.2mm HX low-gamma MAS; 1.9mm HX high-gamma MAS; 1.3mm HCN fast MAS; 0.7mm HCN ultra-fast MAS; Chilled SampleCase (up to 24 samples); Automated Tuning and Matching (ATM); Nitrogen Liquefier. | NMR, spectrometer, Gateway 1.2 GHz NMR, | is used by: Ohio State University Campus Chemical Instrument Center NMR Core Facility | NSF RI-1 1935913 | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_028512.pdf | Model_Number_Bruker_Avance_Neo_Gateway_1.2 GHz | https://people.ohioinnovationexchange.org/equipment/1696125, https://www.bruker.com/en/products-and-solutions/mr/nmr/avance-nmr-spectrometer.html | SCR_028512 | , Avance Neo 1.2 GHz NMR Spectrometer system, Bruker: Avance Neo Gateway 1.2 GHz NMR Spectrometer system | 2026-09-12 01:05:53 | 0 | |||||
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CytoVerse Resource Report Resource Website |
CytoVerse (RRID:SCR_028854) | data access protocol, data analysis software, data processing software, data visualization software, software application, software resource, web service | Web application to map single-cell RNA data into AI foundation model spaces. Lets search millions of reference cells and view cell types locally without uploading private data or needing powerful cloud servers. Using ONNX model deployment and compressed IVFPQ indexing, it annotates local datasets against a 23-million-cell reference without server computation, installation, or data upload, and shares embeddings as lightweight files, enabling private, interactive, and collaborative single-cell analysis. | single-cell RNA-seq, foundation models, browser based analysis, WebAssembly, ONNX, scFM, approximate nearest neighbors, latent space collaboration, data privacy, | Brain and Behavior Research Foundation ; California Institute for Regenerative Medicine ; NHGRI RM1HG011543; NIMH U24MH132628; NINDS U24NS146314; NSF ; University of California Office of the President |
PMID:41659670 | Free, Available for download, Freely available | https://github.com/braingeneers/cytoverse | SCR_028854 | 2026-09-12 01:06:01 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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