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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PTNet Resource Report Resource Website |
PTNet (RRID:SCR_022975) | software resource, source code | Graph based learning model for protein expression estimation by considering miRNA-mRNA interactions. Estimates protein levels by considering miRNA-mRNA interaction network, mRNA expression and miRNA expression. | protein level, protein expression estimation, miRNA-mRNA interactions, mRNA expression, miRNA expression, | NIDDK DK097771; NIGMS R01GM113952; NSF III1755761 |
DOI:10.1093/bib/bbab264 | Free, Available for download, Freely available | SCR_022975 | 2026-09-05 06:34:31 | 0 | |||||||||
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Protofilament Bending Models Resource Report Resource Website 1+ mentions |
Protofilament Bending Models (RRID:SCR_023062) | software resource, source code | Code is written to be run with Matlab version r2020b or higher. Model accepts wave assay pulse amplitude data, and simultaneously solves and fits protofilament deflection models to deduce fundamental biophysical properties of microtubule protofilaments. | Matlab, protofilament, microtubule, strain energy, GTP hydrolysis | uses: MATLAB | NIGMS R35GM134842 | DOI:10.7554/eLife.83225 | Free, Available for download, Freely available | SCR_023062 | 2026-09-05 06:34:31 | 1 | ||||||||
|
abSENSE Resource Report Resource Website 1+ mentions |
abSENSE (RRID:SCR_023223) | software resource, source code | Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally. | undetected homolog, gene homolog detection failure, homology search, lineage-specific genes, homology detection failure | Harvard University ; Howard Hughes Medical Institute ; NHGRI R01-HG009116; NIGMS RO1-GM43987; NSF 1764269; Simons Center for the Mathematical and Statistical Analysis of Biology 594596 |
PMID:33137085 | Free, Available for download, Freely available | http://www.eddylab.org/abSENSE/ | SCR_023223 | 2026-09-05 06:34:32 | 1 | ||||||||
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University of Nevada Reno School of Medicine High Spatial and Temporal Resolution Imaging Core Facility Resource Report Resource Website 1+ mentions |
University of Nevada Reno School of Medicine High Spatial and Temporal Resolution Imaging Core Facility (RRID:SCR_024793) | HSTRI Core | access service resource, core facility, service resource | Core provides high spatial and temporal resolution imaging methodologies and instrumentation for studying cellular structure, signaling pathways, and function in health and disease. Offers education, training and expertise in advising investigators in the use of the new technologies. | ABRF, Image acquisition and analysis, high spatial and temporal resolution imaging, |
is listed by: ABRF CoreMarketplace has parent organization: University of Nevada at Reno; Nevada; USA |
NIGMS P20GM130459 | Open | ABRF_2596 | https://coremarketplace.org/?FacilityID=2596&citation=1 | SCR_024793 | , University of Nevada High Spatial and Temporal Resolution Imaging Core | 2026-09-05 06:34:41 | 2 | |||||
|
SomaticSeq Resource Report Resource Website 1+ mentions |
SomaticSeq (RRID:SCR_024891) | software resource, software toolkit | Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification. | NGS variant calling and classification, somatic mutation detection, somatic mutation calls, single nucleotide variants, detect somatic mutations, | NHGRI R01 HG007834; NIGMS R01 GM109836 |
PMID:26381235 | SCR_024891 | 2026-09-05 06:34:44 | 6 | ||||||||||
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PEPhub Resource Report Resource Website 1+ mentions |
PEPhub (RRID:SCR_024892) | data access protocol, data or information resource, database, software resource, web service | Web biological metadata server to view, store, and share your sample metadata in form of Portable Encapsulated Projects. PEPhub takes advantage of PEP biological metadata standard to store, edit, and access your PEPs in one place. Components include database where PEPs are stored; API to programmatically read and write PEPs in database; web based user interface to view and manage these PEPs via front end. | Portable Encapsulated Projects, biological metadata server, sharing, retrieving, validating, sample metadata, | NHGRI R01 HG012558; NIGMS R35 GM128636 |
PMID:37645717 | Free, Available for download, Freely available | https://github.com/pepkit/pephub | SCR_024892 | Portable Encapsulated Projects hub | 2026-09-05 06:34:44 | 2 | |||||||
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PLAAC Resource Report Resource Website 10+ mentions |
PLAAC (RRID:SCR_024973) | data access protocol, software resource, web service | Web and command-line application to identify proteins with prion-like amino acid composition. Searches protein sequences to identify probable prion subsequences using hidden-Markov model algorithm. | protein sequences search, identify proteins with prion-like amino acid composition, identify proteins, identify probable prion subsequences, | G. Harold and Leila Y. Mathers Foundation ; Howard Hughes Medical Institute ; NIGMS GM025874 |
PMID:24825614 | Free, Freely available | SCR_024973 | Prion Like Amino Acid Composition | 2026-09-05 06:34:46 | 49 | ||||||||
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Guided Sparse Factor Analysis Resource Report Resource Website 1+ mentions |
Guided Sparse Factor Analysis (RRID:SCR_025023) | GSFA | software resource, software toolkit | Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data. | sparse factor analysis, differential gene expression, discovery simultaneously, single cell CRISPR screening data, | NHGRI R01 HG011883; NHGRI R01HG010773; NIGMS R01 GM126553; NIMH R01MH110531; NIMH R01MH116281; NSF ; Sloan Research Fellowship |
PMID:37770710 | Free, Available for download, Freely available | SCR_025023 | 2026-09-05 06:34:48 | 1 | ||||||||
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PyContact Resource Report Resource Website 1+ mentions |
PyContact (RRID:SCR_025066) | data analysis software, data processing software, software application, software resource | Software tool for analysis of non-covalent interactions in molecular dynamics trajectories. Implemented in Python and is universally applicable to any kind of MD trajectory supported by MDAnalysis package. | non-covalent interactions, molecular dynamics trajectories, | is related to: MDAnalysis | German Research Foundation ; NIGMS P41 GM104601; NSF |
PMID:29414703 | Free, Available for download, Freely available, | https://github.com/maxscheurer/pycontact | SCR_025066 | 2026-09-05 06:34:49 | 3 | |||||||
|
Natural Products Atlas Resource Report Resource Website 10+ mentions |
Natural Products Atlas (RRID:SCR_025107) | NP Atlas | atlas, data or information resource, knowledge base | Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles. | FAIR principles, microbial natural products discovery, natural product structures, bacterial and fungal natural products, visualize chemical diversity, | has parent organization: Simon Fraser University; British Columbia; Canada | BBSRC ; Carnegie Trust for the Universities of Scotland ; Ministry of Science ; Technology and Telecommunications of Costa Rica ; Natural Sciences and Engineering Research Council of Canada ; NCCIH AT008718; NCCIH F31 AT010098; NCCIH T32 AT007533; NCCIH U41 AT008718; NCI F31 CA236237; Netherlands eScience Center ; NIGMS GM124461; NIGMS R01 GM125943; NIH D43 TW010530; NSERC Discovery ; NSF ; Sao Paulo Research Foundation |
PMID:31807684 DOI:10.1093/nar/gkab941 |
Free, Freely available, | SCR_025107 | , The Natural Products Atlas, The Natural Products Atlas 2.0 | 2026-09-05 06:34:50 | 36 | ||||||
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FusionGDB2 Resource Report Resource Website 1+ mentions |
FusionGDB2 (RRID:SCR_025299) | data or information resource, database | Functional annotation database of human fusion genes.FusionGDB 2.0 has updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with human genomic features across cellular role's categories, transcribed chimeric sequence and following open reading frame analysis with coding potential based on deep learning approach with Ribo-seq read features, and rigorous investigation of protein feature retention of individual fusion partner genes in protein level. | Functional annotation database, human fusion genes, fusion gene breakage tendency score, | NIGMS R35GM138184; University of Texas |
PMID:34755868 | Free, Freely available | SCR_025299 | FusionGDB 2.0 | 2026-09-05 06:34:55 | 4 | ||||||||
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Rhode Island INBRE Molecular Informatics Core Facility Resource Report Resource Website 10+ mentions |
Rhode Island INBRE Molecular Informatics Core Facility (RRID:SCR_017685) | access service resource, core facility, service resource | Core provides sequencing and bioinformatics support for INBRE and non-INBRE researchers. Provides data science services adjacent to traditional bioinformatics; access to computational and software resources for INBRE network institutions, particularly primarily undergraduate institutions; training for students and faculty in data science methods. Maintains professional network with other core and user facilities in Rhode Island and beyond to maximize resources available to our users.Utilizes novel technologies such as virtual/augmented reality for use in teaching and research. | Analysis, interpretation, nucleotide, amino acid, sequence, protein, domain, structure, service, 3D visualization, modeling, USEDit |
has parent organization: University of Rhode Island; Rhode Island; USA has parent organization: USEDit |
NIGMS P20 GM103430 | Open | ABRF_3 | SCR_017685 | Rhode Island INBRE Molecular Informatics, RI-INBRE Bioinformatics Core; RI Genomics and Sequencing Center | 2026-09-05 06:34:10 | 16 | |||||||
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University of Delaware CBCB Bioinformatics Data Science Core Facility Resource Report Resource Website 10+ mentions |
University of Delaware CBCB Bioinformatics Data Science Core Facility (RRID:SCR_017696) | access service resource, core facility, service resource | CBCB Bioinformatics Data Science Core builds upon infrastructure of the Center for Bioinformatics and Computational Biology. Delaware Biotechnology Institute , Delaware Data Science Institute, and Protein Information Resource. Core helps with planning your research or analyzing your current data. Services:Consultation and Collaboration, Proposal Assistance,Training, Bioinformatics Software, Computational Hardware, Database and Web Services, Next Gen Analysis, Custom Analysis. | ABRF, USEDit, CBCB, Bioinformatics, core, Delaware, Biotechnology, Institute, data, analyzing, service, data science |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Delaware; Delaware; USA |
NIGMS P20GM103446; NIH Office of the Director S10OD028725 |
Open | SCR_017712, ABRF_82 | SCR_017696 | Center for Bioinformatics and Computational Biology Bioinformatics Core, CBCB Bioinformatics Core | 2026-09-05 06:34:10 | 46 | |||||||
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University of North Dakota School of Medicine and Health Sciences Imaging Core Facility Resource Report Resource Website 1+ mentions |
University of North Dakota School of Medicine and Health Sciences Imaging Core Facility (RRID:SCR_017733) | access service resource, core facility, service resource | Provides advanced instrumentation for researchers interested in investigating biological processes at cellular, sub cellular and molecular level.Instrumentation include Confocal Microscope Systems :Zeiss LSM-510 Meta Confocal Microscope, Olympus FV1000 MPE Basic Multiphoton Microscope;Brightfield/Fluorescence: Nikon Eclipse TE300 (inverted) Fluorescent Microscope, Nikon Eclipse 80i (upright) Fluorescent Microscope, Leica Thunder Imager; TIRF Systems:Olympus TIRF Microscope; Transmission Electron Microscopy:Hitachi 7500 TEM, RCM MTX Ultramicrotomes;Scanning Electron Microscopy:Hitachi 4700 Field Emission SEM, Denton Desk II Sputter and Turbo-sputter Coaters.Light and electron microscopic facilities, complete with ancillary support equipment, are located in close proximity to each other within suite of rooms housed in medical school. | Light, electron, microscopy, imaging | NIGMS P20 GM113123; NIGMS U54 GM128729; UNDSMHS fund |
Open | ABRF_184 | SCR_017733 | Imaging Core | 2026-09-05 06:34:11 | 1 | ||||||||
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Wyoming University Jenkins Microscopy Core Facility Resource Report Resource Website |
Wyoming University Jenkins Microscopy Core Facility (RRID:SCR_017758) | access service resource, core facility, service resource | Core to assist researchers and students in their imaging needs of fluorescence and electron microscopy and to increase use of microscopes in science education. Consultation, training or touring facility is also available by appointment. | Microscopy, imaging, fluorescence, electron, consultation, training, service, core | NIGMS P20 GM121310; University of Wyoming Neuroscience COBRE and Neuroscience Core Center grant ; UW Sensory Biology COBRE grant |
Restricted | ABRF_268 | SCR_017758 | Jenkins Microscopy Facility | 2026-09-05 06:34:11 | 0 | ||||||||
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University of Nevada at Reno Nevada Proteomics Center Core Facility Resource Report Resource Website 1+ mentions |
University of Nevada at Reno Nevada Proteomics Center Core Facility (RRID:SCR_017761) | access service resource, core facility, service resource | Core offers mass spectral proteomic analysis. Assists with qualitative and quantitative characterization of proteins in biological matrices such as plasma/serum, tissue, cell lines and other biological material to gain understanding of physiological pathways, molecular interactions and regulatory signaling. | Mass, spectral, proteomic, analysis, qualitative, quantitative, protein, plasma, serum, tissue, cell, line, physiological, pathway, interaction, signaling, stury, service, core |
is listed by: ABRF CoreMarketplace has parent organization: University of Nevada at Reno; Nevada; USA |
NIGMS P20 GM103440 | Open | SCR_011043, SciEx_9701, ABRF_281 | https://coremarketplace.org/?FacilityID=281&citation=1 | SCR_017761 | Mick Hitchcock, Ph.D. Nevada Proteomics Center | 2026-09-05 06:34:11 | 6 | ||||||
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Kansas University at Lawrence Protein Production Group Core Facility Resource Report Resource Website |
Kansas University at Lawrence Protein Production Group Core Facility (RRID:SCR_017749) | PPG | access service resource, core facility, service resource | Core focuses on cloning, expression and purification of prokaryotic and eukaryotic proteins for COBRE and other investigators in Kansas and region. Laboratory maintains equipment to support production of properly folded proteins in quantities suitable for structural studies (X-ray and NMR), functional studies (catalytic or biological), label-free binding studies (SPR) and/or high throughput (HTP) screening studies. | Protein, production, purification, expression, cloning, service, core | NCRR P20 RR017708; NIGMS P20 GM103420; NIGMS P30 GM110761 |
Open | ABRF_249 | SCR_017749 | KU COBRE Protein Production Group | 2026-09-05 06:34:11 | 0 | |||||||
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University of Delaware BioImaging Center Core Facility Resource Report Resource Website 1+ mentions |
University of Delaware BioImaging Center Core Facility (RRID:SCR_017814) | access service resource, core facility, service resource | Microscopy facility that houses equipment including confocal microscopes: LSM780 confocal microscope (Located at CBBI),LSM880 confocal microscope (Located at DBI 117),electron microscopes and their accessory instrumentation:Thermo Scientific Apreo VS SEM microscope,Hitachi S-4700, Leica EM ACE600 and Tousimis Autosamdri-815B,CX7 high content analysis system. Our staff has technical expertise across different microscopy platforms and methodologies. | Microscopy, bioimaging, confocal, electron, microscope, analysis, service, core |
is listed by: ABRF CoreMarketplace has parent organization: University of Delaware; Delaware; USA |
NCRR S10 RR027273; NIGMS P20 GM103446; NIGMS P20 GM113125; NIH Office of the Director S10 OD016361; NIH Office of the Director S10 OD025165; NSF IIA 1301765; State of Delaware |
Open | ABRF_537 | https://coremarketplace.org/?FacilityID=537&citation=1 | SCR_017814 | Delaware University BioImaging Center Core Facility, University of Delaware Bio-Imaging Center | 2026-09-05 06:34:13 | 1 | ||||||
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University of New England COBRE Histology and Imaging Core Facility Resource Report Resource Website 1+ mentions |
University of New England COBRE Histology and Imaging Core Facility (RRID:SCR_017885) | access service resource, core facility, service resource | Core provides access to expertise, training and specialized instrumentation related to tissue processing, sectioning, staining, immunohistochemistry and microscopy. Offers services and training related to image analysis and image analysis software to guide investigators in choosing best methods for presenting their data.Services include Trimming of wet tissues,Tissue processing into paraffin, OCT and paraffin embedding, Sectioning of paraffin-embedded/frozen tissues, Routine and special histochemical staining, Immunohistochemistry/Immunofluorescence, Antibody optimization, Brightfield/ widefield/ confocal microscopy, Image capture and image analysis.Core has cryostats, microtomes and microscopes available for reservation. | Instrumentation, tissue, processing, sectioning, staining, immunochemistry, microscopy, training, expertise, image, analysis, data, trimming, wet, tissue, processing, paraffin, embedding, immunofluorescence, antibody, optimization, microscopy, cryostat, microtome, service, core | is listed by: ABRF CoreMarketplace | NIGMS P20 GM103643 | Open | ABRF_748 | https://coremarketplace.org/?FacilityID=748&citation=1 | SCR_017885 | Histology and Imaging Core | 2026-09-05 06:34:14 | 1 | ||||||
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Northwestern University Proteomics Core Facility Resource Report Resource Website 10+ mentions |
Northwestern University Proteomics Core Facility (RRID:SCR_017945) | access service resource, core facility, service resource | Core offers multiple types of experiments from simple protein identification to protein quantitation. Performs traditional bottom-up proteomics, where proteins are digested with enzyme prior to analysis and intact, top-down proteomics analyses. Services include proteins identification after in-gel or in-solution digestion, top-down mass spectrometry to preserve post-translationally modified forms of proteins present in vivo by measuring them intact, IP-MS Pulldown,BioID service to identify target of biotin ligase that has been tagged onto their protein via traditional cloning methods,Untargeted Quantitative Peptide Proteomics,Targeted Quantitative Peptide Proteomics,Epiproteomic Histone Modification Panel A,Epiproteomic Histone Modification Panel B,Untargeted Metabolomics,Phosphoproteomics,PTM Scan,ChIP-MS. | Protein, indentification, quantitation, proteomics, analysis, enzyme, digestion, mass, spectrometry, peptide, targeted, epiproteomic, histone, modification, untargeted, phosphoproteomics, PTM Scan, ChIP-MS, service, core, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Northwestern University; Illinois; USA |
NCI P30 CA060553; NIGMS P41 GM108569; NIH Office of the Director S10 OD025194 |
Open | SCR_017880, ABRF_944 | https://coremarketplace.org/?FacilityID=944 | https://coremarketplace.org/?FacilityID=738 | SCR_017945 | Northwestern Proteomics, Northwestern University Proteomics Center of Excellence Core Facility | 2026-09-05 06:34:16 | 10 |
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