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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GenePattern Notebook Resource Report Resource Website 1+ mentions |
GenePattern Notebook (RRID:SCR_015699) | web application, software application, systems interoperability software, software resource, electronic laboratory notebook | Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code. | gene, genomics research, research narrative, notebook system, analysis notebook, bio.tools |
is listed by: bio.tools is listed by: Debian is affiliated with: GenePattern |
NIGMS R01-GM074024; NCI U24-CA194107 |
PMID:28822753 | Open Source, Free, Available for download, Account required | biotools:GenePattern_notebook | https://bio.tools/GenePattern_notebook | SCR_015699 | GenePattern Notebook environment | 2026-02-14 02:02:53 | 3 | |||||
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TISSUES Resource Report Resource Website 10+ mentions |
TISSUES (RRID:SCR_015665) | data or information resource, software resource, database, web application | Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. | tissue expression, proteomic, transcriptomic, text-mining, brenda tissue ontology, protein identifier, bio.tools |
uses: BRENDA Tissue and Enzyme Source Ontology is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation NNF14CC0001; NCI U54 CA189205-01; CSIRO’s OCE Science Leader program |
PMID:26157623 | Freely available, Free, Available for download | biotools:tissues | https://bio.tools/tissues | SCR_015665 | TISSUES: Tissue Expression Database, Tissue Expression Database | 2026-02-14 02:03:07 | 42 | |||||
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LINCS Joint Project - Breast Cancer Network Browser Resource Report Resource Website 1+ mentions |
LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) | LJP-BCNB, LJP, BCNB | data access protocol, software resource, web service, service resource | Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations. | breast, cancer, tissue, cluster, drug, perturbation, cell, line, gene, expression |
is related to: L1000 Characteristic Direction Signature Search Engine is related to: LINCS Project |
Breast cancer | NHLBI U54 HL127624; NHLBI U54 HL127365; NHGRI U54 HG006093; NCI U54 CA189201 |
PMID:29084964 | Free, Freely available | https://github.com/MaayanLab/LJP | SCR_016181 | LINCS Joint Project, Breast Cancer Network Browser | 2026-02-14 02:03:10 | 1 | ||||
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SV-plaudit Resource Report Resource Website 1+ mentions |
SV-plaudit (RRID:SCR_016285) | data processing software, data analysis software, software application, software resource, image analysis software | Software for rapidly curating structural variant (SVs) predictions. SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis. | genomics, structural, variants, visualization, manual, curation, prediction, image, alignment | NHGRI K99 HG009532; NHGRI R01 HG006693; NIGMS R01 GM124355; NCI U24 CA209999 |
Free, Available for download | SCR_016285 | 2026-02-14 02:03:01 | 2 | ||||||||||
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UniProt Resource Report Resource Website 10000+ mentions |
UniProt (RRID:SCR_002380) | UniProt | data or information resource, database | Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB. | collection, protein, sequence, annotation, data, functional, information |
is used by: LIPID MAPS Proteome Database is used by: ChannelPedia is used by: Open PHACTS is used by: DisGeNET is used by: Smart Dictionary Lookup is used by: MitoMiner is used by: Cytokine Registry is used by: MobiDB is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: Phospho.ELM is used by: GEROprotectors is used by: SwissLipids is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: LabWorm is related to: Clustal W2 is related to: UniProt DAS is related to: UniParc at the EBI is related to: ProDom is related to: LegumeIP is related to: Pathway Commons is related to: NIH Data Sharing Repositories is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: 3D-Interologs is related to: Biomine is related to: EBIMed is related to: STOP is related to: Coremine Medical is related to: BioExtract is related to: STRAP is related to: GOTaxExplorer is related to: GoAnnotator is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: Whatizit is related to: MOPED - Model Organism Protein Expression Database is related to: Polbase is related to: PredictSNP is related to: PSICQUIC Registry is related to: IntAct is related to: p300db is related to: UniProt Proteomes is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation has parent organization: European Bioinformatics Institute has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: Protein Information Resource is parent organization of: UniProtKB is parent organization of: NEWT is parent organization of: UniParc is parent organization of: UniProt Chordata protein annotation program is parent organization of: UniRef works with: Genotate works with: CellPhoneDB works with: MOLEonline works with: MiMeDB |
NHGRI U41 HG006104; NHGRI P41 HG02273; NIGMS 5R01GM080646; NIGMS R01 GM080646; NLM G08 LM010720; NCRR P20 RR016472; NSF DBI-0850319; British Heart Foundation ; NEI ; NHLBI ; NIA ; NIAID ; NIDDK ; NIMH ; NCI ; EMBL ; PDUK ; ARUK ; NHGRI U24 HG007722 |
PMID:19843607 PMID:18836194 PMID:18045787 PMID:17142230 PMID:16381842 PMID:15608167 PMID:14681372 |
nif-0000-00377, SCR_018750, r3d100010357 | http://www.ebi.uniprot.org http://www.uniprot.org/uniprot/ http://www.pir.uniprot.org ftp://ftp.uniprot.org https://doi.org/10.17616/R3BW2M |
SCR_002380 | , The Universal Protein Resource, Universal Protein Resource, UNIPROT Universal Protein Resource | 2026-02-14 02:05:47 | 17565 | |||||
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University of Minnesota Tissue Procurement Facility Resource Report Resource Website |
University of Minnesota Tissue Procurement Facility (RRID:SCR_004270) | TPF | biomaterial supply resource, tissue bank, material resource | Procure and distribute human tissue and other biological samples in support of basic, translational, and clinical cancer research at the University of Minnesota. The TPF is a centralized resource with standardized patient consent, sample collection, processing, storage, quality control, distribution, and electronic record maintenance. Since the 1996 inception of the TPF, over 61,000 tissue samples including well-preserved samples of malignant and benign tumors, organ-matched normal tissue, and other types of diseased tissues, have been collected from surgical specimens obtained at the University of Minnesota Medical Center-Fairview (UMMC-F) University Campus. Surgical pathologists are intellectually engaged in TPF functions, providing researchers with specimen-oriented medical consultation to facilitate research productivity. Prior to surgery, TPF personnel identify and consent patients for procurement of tissue, blood, urine, saliva, and ascites fluid. Within the integrated working environment of the surgical pathology laboratory, freshly obtained tissues not needed for diagnosis are selected and provided by pathologists to TPF personnel. Tissue samples are then assigned an independent code and processed. TPF staff can also work with researchers to individualize the procurement of tissues to fit specific research needs. | human, tissue, biological sample, basic research, translational research, clinical research, cancer research, cancer, malignant tumor, benign tumor, organ-matched normal tissue, normal tissue, diseased tissue, blood, urine, saliva, ascites fluid |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
Cancer, Malignant tumor, Benign tumor, Organ-matched normal tissue, Normal tissue, Diseased tissue | UMN Academic Health Center ; NCI P30 CA77598; NCI P50 CA101955 |
In support of basic, Translational, And clinical cancer research at the University of Minnesota | nlx_28712 | SCR_004270 | Tissue Procurement Facility, UMN TPF, University of Minnesota Tissue Bank | 2026-02-14 02:06:15 | 0 | |||||
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AIDS and Cancer Specimen Resource Resource Report Resource Website 10+ mentions |
AIDS and Cancer Specimen Resource (RRID:SCR_004216) | ACSR | biomaterial supply resource, tissue bank, material resource | A biorepository for HIV-infected human biospecimens from a wide spectrum of HIV-related or associated diseases, including cancer, and from appropriate HIV-negative controls. The ACSR has formalin-fixed paraffin embedded biospecimens, fresh frozen biospecimens, malignant cell suspensions, fine needle aspirates, and cell lines from patients with HIV-related malignancies. It also contains serum, plasma, urine, bone marrow, cervical and anal specimens, saliva, semen, and multi-site autopsy speicmens from patients with HIV-related malignancies including those who have participated in clinical trials. The ACSR has an associated databank that contains prognostic, staging, outcome and treatment data on patients from whom tissues were obtained. The ACSR database contains more than 300,000 individual biospecimens with associated clinical information. Biospecimens are entered into the ACSR database by processing type, disease category, and number of cases defined by disease category. | aids, hiv, cancer, virology, immunology, pathology, epidemiology, tumor, assay development, clinical data, clinical, tumor tissue, biological fluid, bodily fluid, malignant cell suspension, fine needle aspirate, cell line, serum, plasma, urine, bone marrow, cervical specimen, anal specimen, saliva, semen |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of California at San Francisco; California; USA |
AIDS, Cancer, HIV-associated malignancy, HIV | NCI | nlx_23946 | http://acsr.ucsf.edu/Home/tabid/37/Default.aspx | SCR_004216 | ACSR - AIDS and Cancer Specimen Resource | 2026-02-14 02:05:46 | 15 | |||||
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National Surgical Adjuvant Breast and Bowel Project Tissue Bank Resource Report Resource Website |
National Surgical Adjuvant Breast and Bowel Project Tissue Bank (RRID:SCR_004506) | NSABP Tissue Bank | biomaterial supply resource, tissue bank, material resource | The NSABP (National Surgical Adjuvant Breast and Bowel Project) Tissue Bank is the central repository of tissue samples (stained and unstained slides, tissue blocks, and frozen tissue specimens) collected from clinical trials conducted by the NSABP. The main scientific aim of the NSABP Division of Pathology is to develop clinical context-specific prognostic markers and predictive markers that predict response to or benefit from specific therapeutic modality. To achieve this aim, the laboratory collects the tumor and adjacent normal tissues from cancer patients enrolled into the NSABP trials through its membership institutions, and maintain these valuable materials with clinical follow-up information and distribute them to qualified approved investigators. Currently, specimens from more than 90,000 cases of breast and colon cancer are stored and maintained at the bank. Paraffin embedded tumor specimens are available from NSABP trials. We currently do not bank frozen tissues. All blocks are from patients enrolled in prospective NSABP treatment protocols and complete clinical follow up information as well as demographic information is available. Depending on the project, unstained tissue sections of 4-micrometer thickness, tissue microarrays, or stained slides are provided to the investigators in a blinded study format. Any investigators with novel projects that conform to the research goals of NSABP may apply for the tissue. Please refer to the NSABP Tissue Bank Policy to determine if your project conforms to these goals. Priority is given to NSABP membership institutions who regularly submit tissue blocks. | clinical, clinical data, demographic data, tumor, specimen, breast tissue, bowel tissue, tumor tissue, adjacent normal tissue, tissue, stained slide, unstained slide, tissue block, paraffin embedded, tissue microarray, cancer, breast cancer, colon cancer, normal |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Pittsburgh; Pennsylvania; USA |
Cancer, Breast cancer, Colon cancer | NCI | Public: Any investigators with novel projects that conform to the research goals of NSABP may apply for the tissue. Priority is given to NSABP membership institutions who regularly submit tissue blocks. | nlx_48875 | http://www.nsabp.pitt.edu/NSABP_Pathology.asp#2.%20Tissue%20Bank | SCR_004506 | National Surgical Adjuvant Breast Bowel Project Tissue Bank | 2026-02-14 02:06:19 | 0 | ||||
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DeepNeuro Resource Report Resource Website 1+ mentions |
DeepNeuro (RRID:SCR_016911) | software resource, software toolkit | Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners. | Design and train neural network architectures, medical imaging, neuroimaging data, neuroimaging |
uses: Python Programming Language is related to: Massachusetts General Hospital has parent organization: Harvard University; Cambridge; United States |
NIDA T90 DA022759; NIDA R90 DA023427; NIH Blueprint for Neuroscience Research ; NIBI ; NIBIB T32 EB1680; NCI U01 CA154601; NCI U24 CA180927; NCI U24 CA180918; NIBIB P41 EB015896 |
PMID:32578020 | Free, Available for download, Freely available | SCR_016911 | 2026-02-14 02:07:18 | 2 | ||||||||
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SYGNAL Resource Report Resource Website 1+ mentions |
SYGNAL (RRID:SCR_023080) | software resource, software toolkit | Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts. | Integrating genomic and transcriptomic measurements, human cohorts, transcriptional regulatory networks, integrate correlative, causal and mechanistic inference, unified framework, infers causal flow of information, mutations to TFs, miRNAs to perturbed gene expression patterns across patients, | NIGMS P50GM076547; NIGMS R01GM077398; NSF ABI NSF-1262637; NSF DBI-0640950; NCI U24CA143835; American Cancer Society Research Scholar Grant |
PMID:27426982 | Free, Available for download, Freely available | SCR_023080 | SYstems Genetic Network AnaLysis | 2026-02-14 02:07:38 | 1 | ||||||||
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mtradeR Resource Report Resource Website |
mtradeR (RRID:SCR_022977) | software resource, software toolkit | Software R package implements Joint model with Matching and Regularization and simulation pipeline. Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually. | test association between taxa and disease risk, correlated taxa screening, taxa and disease risk | NIDDK U24DK097771; NCI CA21765; American Lebanese Syrian Associated Charities |
PMID:36123651 | Free, Available for download, Freely available | SCR_022977 | Metagenomic TRajectory Analysis with Disease Endpoint and Risk factors | 2026-02-14 02:07:22 | 0 | ||||||||
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SCRuB Resource Report Resource Website 1+ mentions |
SCRuB (RRID:SCR_023518) | software resource, software toolkit | Software R package to help researchers address common issue of contamination in microbial studies. Well aware MiSeq decontamination program. | Source tracking, contamination removal, microBiomes, MiSeq decontamination, contamination in microbial studies, | Rockefeller University ; Columbia University ; CIFAR Azrieli Global Scholarship ; NICHD R01HD106017; NCI R01CA245894 |
PMID:36928429 | Free, Available for download, Freely available | SCR_023518 | Source-tracking for Contamination Removal in microBiomes, Source tracking for Contamination Removal in microBiomes | 2026-02-14 02:07:23 | 1 | ||||||||
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bam readcount Resource Report Resource Website 10+ mentions |
bam readcount (RRID:SCR_023653) | software resource, software application | Software tool that runs on BAM or CRAM file and generates low level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads. | BAM file, CRAM file, sequencing data, nucleotide positions, | NCI R50CA211782; NCI P01CA101937; NCI K22CA188163; NCI 1U01CA209936; NCI U24CA237719; Edward P. Evans Foundation ; NHGRI R00 HG007940 |
PMID:34341766 | Free, Available for download, Freely available | SCR_023653 | bam-readcount | 2026-02-14 02:07:36 | 22 | ||||||||
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Sanford Burnham Prebys Medical Discovery Institute Cancer Metabolism Core Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Cancer Metabolism Core Facility (RRID:SCR_014873) | core facility, access service resource, service resource | Facility that aims to investigate role of metabolism in cancer on cellular and organismal level, combining in vitro and in vivo analysis. Comprehensive metabolic facility, including stable isotope tracing and flux analysis. Provides analysis of metabolism using specialist instruments and methodologies, together with advice on planning experiments and analyzing data. All instruments and approaches are available on fee-for-service basis to Cancer Center scientists, but alsoto outside users. Samples for most services can be shipped, but Seahorse analyzer users need to be local so they can bring live cells for analysis. | Cancer metabolism, cellular metabolism, metabolism analysis, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Sanford Burnham Prebys Medical Discovery Institute |
NCI P30CA030199 | Open | ABRF_565 | https://coremarketplace.org/?FacilityID=565 | http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_CancerMetabolism.aspx | SCR_014873 | SBP Cancer Metabolism Core, Sanford Burnham Prebys Medical Discovery Institute Cancer Metabolism Core, SBP Medical Discovery Institute Cancer Metabolism Core | 2026-02-14 02:08:34 | 0 | |||||
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Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) Resource Report Resource Website 500+ mentions |
Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842) | SALK IGC, IGC | core facility, access service resource, service resource | Core facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications. | core facility, gene, genomic, genomic data, analysis, consultation, applications | NCI CA014195; Helmsley Trust ; Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility |
Open | SCR_014842 | , Integrative Genomics, Salk, Core Facility, Institute, Razavi Newman, UCSD, Bioinformatics | 2026-02-14 02:08:24 | 940 | ||||||||
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RPPA Core Facility Resource Report Resource Website 10+ mentions |
RPPA Core Facility (RRID:SCR_016649) | RPPA | core facility, access service resource, service resource | Core provides technology for functional proteomics studies and centralized, standardized and quality controlled services locally and globally. | technology, functional, proteomics, studies, centralized, standardized, quality, controlled, service | has parent organization: University of Texas MD Anderson Cancer Center | NCI CA16672 | Commercially available, Registration required | SCR_016649 | MD Anderson RPPA Core, RPPA, Reverse Phase Protein Array Core, Reverse Phase Protein Array (RPPA) Core | 2026-02-14 02:08:39 | 34 | |||||||
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University of Texas MD Anderson Cancer Center Proteomics Core Facility Resource Report Resource Website |
University of Texas MD Anderson Cancer Center Proteomics Core Facility (RRID:SCR_017731) | core facility, access service resource, service resource | Facility provides mass spectrometry analysis of proteins. Provides access to mass spectrometry based proteomics technologies and services including Protein Identification, Molecular Weight Determination, Quantitative Protein Analysis, Post-translational Modification Analysis, LC or LC-MS Analysis, Equipment Usage, Additional Data Analysis:Bioinformatics, statistics, pathway analysis and Assistance preparing materials for manuscripts or grants.Consultations for custom assays for other MS Services are also available. | Mass, spectrometry, analysis, protein, proteomics, service | NCI P30 CA016672; NIH Office of the Director S10 OD012304 |
Open | ABRF_186 | SCR_017731 | Proteomics Facility | 2026-02-14 02:08:09 | 0 | ||||||||
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Chicago University Cytometry and Antibody Technology Core Facility Resource Report Resource Website 50+ mentions |
Chicago University Cytometry and Antibody Technology Core Facility (RRID:SCR_017760) | CAT Facility | core facility, access service resource, service resource | Core offers services in cytometry and antibody technology, helps to design projects, data acquisition, analysis and/or interpretation beyond routine practices,critical drafting and/or revision of manuscript for intellectual content purposes. | Cytometry, antibody, technology, project, design, data, acquisition, analysis, service, core | NCI P30 CA014599 | Open | ABRF_293 | SCR_017760 | Cytometry and Antibody Technology Core Facility | 2026-02-14 02:08:41 | 64 | |||||||
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North Carolina University at Chapel Hill School of Medicine High Throughput Peptide Synthesis and Array Core Facility Resource Report Resource Website 1+ mentions |
North Carolina University at Chapel Hill School of Medicine High Throughput Peptide Synthesis and Array Core Facility (RRID:SCR_017837) | core facility, access service resource, service resource | Core offers services for: High quality synthetic peptides, stable isotope labeled peptides, peptides with PTM and fluorescent and affinity tags, synthesis of peptide libraries. Analysis of synthetic peptides. Purification, lyophilization and aliquoting of synthetic peptides. | Synthetic, peptide, stable, isotope, labeled, library, analysis, purification, lyophilization, aliquoting, service, core, ABRF | is listed by: ABRF CoreMarketplace | NCI P30 CA016086 | Open | ABRF_626 | SCR_017837 | UNC High-Throughput Peptide Synthesis and Array Facility | 2026-02-14 02:08:12 | 6 | |||||||
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North Carolina University at Chapel Hill School of Medicine Macromolecular X-Ray Crystallography Core Facility Resource Report Resource Website |
North Carolina University at Chapel Hill School of Medicine Macromolecular X-Ray Crystallography Core Facility (RRID:SCR_017839) | MX Facility | core facility, access service resource, service resource | Core provides support and infrastructure necessary to initiate and successfully complete structural biology or structural chemistry project. Offers services in Crystallization,X-Ray DiffractionData Collection,Structure Determination and Refinement. | Structural, biology, chemistry, X-ray, crystallography, diffraction, data, collection, refinement, service, core, ABRF | is listed by: ABRF CoreMarketplace | NCI P30 CA016086 | Open | ABRF_629 | SCR_017839 | Macromolecular X-Ray Crystallography | 2026-02-14 02:08:05 | 0 |
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