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| 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 | NIH T32 HG003284; NSF IIS-0612231; NSF PECASE MCB-0093399; NIGMS GM076275; NIH P50 GM071508 |
PMID:17519246 | Free, Available for download | SCR_016064 | Conservation-code | 2026-08-04 09:43:47 | 1564 | |||||||
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ESRseq score Resource Report Resource Website 1+ mentions |
ESRseq score (RRID:SCR_022270) | software application, software resource | Software for comprehensive quantitative measure of splicing impact of complete set of RNA 6-mer sequences by deep sequencing successfully spliced transcripts. | Splicing impact quantitative measure, set of RNA 6-mer sequences, deep sequencing, successfully spliced transcripts | NIGMS GM072740 | PMID:21659425 | SCR_022270 | 2026-08-04 09:45:03 | 2 | ||||||||||
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Coarse grained co-translational folding analysis Resource Report Resource Website 1+ mentions |
Coarse grained co-translational folding analysis (RRID:SCR_022271) | software application, software resource | Software for statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved, and also co-translational protein folding model. | statistical approach, identify loci within genes, significantly enriched in slowly translated codons, co-translational protein folding model evolutionarily conserved, | NIGMS R01GM124044; NIGMS F32GM116231 |
PMID:29073068 | Free, Freely available | SCR_022271 | Coarse-grained co-translational folding analysis | 2026-08-04 09:44:58 | 1 | ||||||||
|
PyRosetta Resource Report Resource Website 10+ mentions |
PyRosetta (RRID:SCR_018541) | software application, standalone software, software resource | Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions. | Molecular modeling, custom structure prediction, design algorithm, energy function, scoring function, bio.tools |
uses: Python Programming Language is listed by: bio.tools is listed by: Debian is related to: Rosetta has parent organization: Johns Hopkins University; Maryland; USA |
NIGMS R01 GM73151; NIGMS R01 GM078221; NSF 0846324 |
PMID:20061306 | Free, Freely available | biotools:pyrosetta | https://bio.tools/pyrosetta | SCR_018541 | Python Rosetta | 2026-08-04 09:44:21 | 20 | |||||
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National Center for Macromolecular Imaging Resource Report Resource Website 1+ mentions |
National Center for Macromolecular Imaging (RRID:SCR_001445) | NCMI | access service resource, biomedical technology research center, training resource, service resource | Biomedical technology research center establishing the infrastructure for fast, routine, atomic structure determination of subcellular complexes by electron cryo-microscopy, computer reconstruction and modeling. Their emphasis is on specimens that cannot currently be studied by conventional structural techniques such as x-ray crystallography or NMR. The ultimate outcome of their research is a three-dimensional image of the complex that can be used for design of drugs and vaccines for a variety of diseases. The center is focused on extending the resolution, speed and flexibility of cryo-electron microscopy for the three-dimensional structure determination of biological macromolecular assemblies. Cryo-electron microscopy can visualize molecules under near-native conditions at resolutions ranging from 0.3 to 5 nm and can yield images of individual molecules in a range of different conformations as they exist in solution. Other cryo-electron mycroscopy techniques, such as cryo-electron tomography, are being developed to capture molecular structures in situ. The equipment, techniques and expertise developed are available to the research community through collaborative projects. The NCMI also provides training through workshops and other forms of dissemination via both traditional and modern Internet-based methods. | cryo-electron microscopy, structure determination, structure, macromolecule, assembly, model, reconstruction, subcellular complex, electron cryo-microscopy, 3d spatial image, structural biology technology center |
is related to: EMDataResource.org has parent organization: Baylor University; Texas; USA |
NIGMS 3R01GM079429-05S1 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152670 | SCR_001445 | 2026-08-04 09:40:23 | 1 | |||||||
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Proteomics Research Center for Integrative Biology Resource Report Resource Website |
Proteomics Research Center for Integrative Biology (RRID:SCR_001098) | Proteomics Resource for Integrative Biology | biomedical technology research center, training resource | Biomedical technology research center that develops and integrates new proteomic technologies for collaborative and service studies, disseminating the new technologies and training scientists in their use. | systems biology technology center, proteomics, mass spectrometry, data management, analysis | has parent organization: Pacific Northwest National Laboratory | NIGMS 4P41GM103493-14 | nlx_152684 | SCR_001098 | Proteomics Research Resource for Integrative Biology | 2026-08-04 09:40:18 | 0 | |||||||
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ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data set, data or information resource | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | 2026-08-04 09:40:28 | 35 | ||||||
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National Center for X-ray Tomography Resource Report Resource Website 1+ mentions |
National Center for X-ray Tomography (RRID:SCR_001433) | NCXT | biomedical technology research center, training resource | Biomedical technology research center that develops novel cellular imaging technologies, specifically soft X-ray tomography, for visualizing and quantifying the internal structure of whole, hydrated cells, and high-numerical aperture fluorescence microscopy for locating the position of specific cellular molecules. Data from these two imaging modalities can be combined to form a single, correlated imaging view of a cell. | x-ray tomography, cell, imaging, microscopy, x-ray, tomography, imaging technology center |
has parent organization: Lawrence Berkeley National Laboratory has parent organization: University of California at San Francisco; California; USA |
NIGMS ; DOE |
Free, Freely Available | nlx_152657 | http://ncxt.lbl.gov/ | SCR_001433 | National Center for X-ray Tomography: Cellular imaging at the mesoscale | 2026-08-04 09:40:23 | 6 | |||||
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South Carolina Medical University Mass Spectrometry Core Facility Resource Report Resource Website 1+ mentions |
South Carolina Medical University Mass Spectrometry Core Facility (RRID:SCR_017959) | access service resource, core facility, service resource | Core provides expertise, services, education, and instrumentation to enhance biomedical research through LC-MS/MS-based proteomics. Services are offered for protein identification; characterization of post-translational modifications; and quantitative proteomics to identify differentially expressed/degraded proteins, regulated sites of post-translational modification, protein-protein interactions, and protein targets of drugs identified in phenotypic screens. Analyses include sample preparation, LC-MS/MS, database searching, generation of reports, and assistance with data interpretation. Faculty and staff assist with experimental design and development/optimization of customized methodology for analysis of post-translationally modified peptides (e.g. phosphorylation and O-GlcNAc modification, N- and O-linked glycosylation, Cys modifications including S-glutathionylation, and glycation of Lys and Arg). Quantitative approaches including metabolic labeling (SILAC), isobaric tagging (iTRAQ/TMT), and label free proteomics (LFQ) are performed on Orbitrap Elite or Orbitrap Fusion Lumos Mass Spectrometers. Developes methodology to identify alterations in post-translational modifications that impact signal transduction, transcription, translation, and response to therapeutics with goal of enabling investigators to discover molecular mechanisms underlying disease progression and therapeutic response. | Mass, spectrometry, expertise, service, education, instrumentation, proteomics, protein, identification, characterization, post translational, modification, target, drug, identification, phenotypic, screen, analysis, disease, service, core, ABRF | is listed by: ABRF CoreMarketplace | NIH Office of the Director S10 OD010731; NIGMS P20 GM103542 |
ABRF_985 | SCR_017959 | MUSC Mass Spectrometry Facility | 2026-08-04 09:44:19 | 1 | ||||||||
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Vermont University Proteomics Core Facility Resource Report Resource Website 10+ mentions |
Vermont University Proteomics Core Facility (RRID:SCR_018667) | access service resource, core facility, service resource | Provides central resource of mass spectrometry based proteomics technologies to identify, characterize and quantify target proteins in various biological and biomedical samples. Provides mass spectrometry expertise for analyzing proteins and peptides for proteomics studies, support for data analysis from proteomics measurements, training in proteomics methods, and experimental design. | USEDit, mass spectrometry, proteomics technology, protein, biomedical sample, protein analysis, peptide, measurement, experimental design, ABRF | is listed by: ABRF CoreMarketplace | NIGMS P20 GM103449 | Open | ABRF_44 | https://coremarketplace.org/?FacilityID=44 | https://vgn.uvm.edu/proteomics/ | SCR_018667 | UVM-Proteomics Facility, University of Vermont Proteomics Facility | 2026-08-04 09:44:23 | 11 | |||||
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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 1429282; NSF 1828319; NSF 1337897; NSF OIA 1757371 |
open | ABRF_640 | https://coremarketplace.org/?FacilityID=640 | SCR_021101 | University Instrumentation Center, University of New Hampshire University Instrumentation Center | 2026-08-04 09:44:43 | 0 | |||||
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lapdftext Resource Report Resource Website |
lapdftext (RRID:SCR_006167) | lapdftext, LA-PDFText, | text extraction software, software application, software resource | Software that facilitates accurate extraction of text from PDF files of research articles for use in text mining applications. It is intended for both scientists and natural language processing (NLP) engineers interested in getting access to text within specific sections of research articles. The system extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles. The current version of LA-PDFText is a baseline system that extracts text using a three-stage process: * identification of blocks of contiguous text * classification of these blocks into rhetorical categories * extraction of the text from blocks grouped section-wise. | text mining, pdf, text extraction, natural language processing |
is listed by: FORCE11 has parent organization: University of Southern California; Los Angeles; USA |
NSF 0849977; NIGMS RO1-GM083871; NIMH 1R01MH079068-01A2; NCRR U24 RR025736-01 |
PMID:22640904 | Acknowledgement requested, GNU General Public License, v3 | nlx_151668 | SCR_006167 | Layout-Aware PDF Text Extraction, Layout-Aware Text Extraction from Full-text PDF of Scientific Articles, lapdftext: Layout-Aware Text Extraction from Full-text PDF of Scientific Articles | 2026-08-04 09:41:31 | 0 | |||||
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BioGPS: The Gene Portal Hub Resource Report Resource Website 500+ mentions |
BioGPS: The Gene Portal Hub (RRID:SCR_006433) | BioGPS | database, data or information resource | An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database. | gene, ortholog, plug-in, report, literature, genetics, expression, reagent, protein, pathway, snp, genomics, gene annotation, function, FASEB list |
is listed by: Biositemaps is related to: bioDBcore is related to: aGEM has parent organization: Scripps Research Institute |
Novartis Research Foundation ; NIGMS R01GM083924 |
PMID:19919682 | Free, The community can contribute to this resource | r3d100012402, nif-0000-10168 | http://biogps.gnf.org/, https://doi.org/10.17616/R33J20 | SCR_006433 | 2026-08-04 09:41:36 | 725 | |||||
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Add Health (National Longitudinal Study of Adolescent Health) Resource Report Resource Website 10+ mentions |
Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) | Add Health | database, data or information resource | Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database. | adolescent, longitudinal, adult human, interview, social, behavior, health, early adult human, FASEB list | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | Aging | NICHD ; NCI ; CDC ; NIAID ; NIMHD ; NIDCD ; NIGMS ; NIMH ; NINR ; NIA ; NIAAA ; NIDA ; NSF ; NIH ; Department of Health and Human Services ; MacArthur Foundation ; Robert Wood Johnson Foundation |
Restricted use | nif-0000-00621 | SCR_007434 | National Longitudinal Study of Adolescent Health | 2026-08-04 09:41:51 | 37 | |||||
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ESEfinder 3.0 Resource Report Resource Website 100+ mentions |
ESEfinder 3.0 (RRID:SCR_007088) | ESEfinder | data analysis service, analysis service resource, production service resource, service resource | A web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements. | exonic splicing enhancer, sr protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Cold Spring Harbor Laboratory |
NIGMS GM42699; NCI CA88351; NHGRI HG01696 |
PMID:12824367 | Free for non-profit use, Non-commercial, Acknowledgement requested, Commercial use with license | biotools:esefinder, nif-0000-30496 | http://rulai.cshl.edu/tools/ESE2/, https://bio.tools/esefinder | http://exon.cshl.edu/ESE/ | SCR_007088 | 2026-08-04 09:41:46 | 211 | ||||
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FATCAT Flexible Structural Neighborhood Resource Report Resource Website |
FATCAT Flexible Structural Neighborhood (RRID:SCR_007665) | FSN | database, data or information resource | Flexible Structural Neighborhood is a database of structural neighbors of proteins as seen by FATCAT - a flexible protein structure alignment program. The server accepts either a protein (PDB ID) or a domain (SCOP ID) as a query. For the former case, the server first displays the information of chains and domains of a given protein. Afterwards, users can retrieve similar structures for a domain (if domain information is available, i.e., the protein is collected by SCOP), or for a chain otherwise. The protein structure database we collected for similar structure search includes a representative set at 90% sequence identity of SCOP domains, and of up-to-date PDB entries that are not included in the latest release of SCOP. | server, database, molecule structure, protein structure, flexibility, structure, structural neighbor, protein, domain | is related to: FATCAT | NIGMS GM101457; NIGMS GM63208; NIGMS GM076221; NSF DBI-0349600 |
nif-0000-02854 | http://fatcat.ljcrf.edu/fatcat-cgi/cgi/FSN/fsn.pl | SCR_007665 | FATCAT Flexible Structural Neighborhood Database, FSN Database | 2026-08-04 09:41:55 | 0 | ||||||
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PEPATAC Resource Report Resource Website 1+ mentions |
PEPATAC (RRID:SCR_024758) | software resource, software toolkit | Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats. | ATAC-seq analysis pipeline, ATAC-seq data, analysis, serial alignments, | NHGRI RM1 HG007735; NIGMS R35 GM128636; Howard Hughes Medical Institute ; American Society of Hematology |
PMID:34859208 | Free, Available for download, Freely available | https://github.com/databio/PEPATAC/releases | SCR_024758 | 2026-08-04 09:45:35 | 2 | ||||||||
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LABRAT Resource Report Resource Website 1+ mentions |
LABRAT (RRID:SCR_025006) | software application, software resource, source code | Software application to quantify usage of alternative polyadenylation and cleavage sites in RNAseq data and identify genes whose usage of these sites varies across experimental conditions. | quantify usage, alternative polyadenylation, cleavage sites, RNAseq data, identify genes, | NIGMS R35 GM133885; NIGMS R35 GM118051; RNA Bioscience Initiative at the University of Colorado Anschutz Medical Campus ; NIGMS T32 GM008730 |
DOI:10.1186/s12864-021-07781-1 | Free, Available for download, Freely available | SCR_025006 | Lightweight Alignment Based Resolution of Alternative Three prime ends | 2026-08-04 09:45:39 | 1 | ||||||||
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MAGeCK Resource Report Resource Website 100+ mentions |
MAGeCK (RRID:SCR_025016) | data processing software, software application, software resource, data analysis software | Software tool to identify important genes from genome-scale CRISPR-Cas9 screens. Used for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. | identify genes, genome scale CRISPR-Cas9 screens, | NIGMS R01 GM099409; Dana-Farber Cancer Institute |
PMID:25476604 | Free, Available for download, Freely available | https://github.com/liulab-dfci/MAGeCK | SCR_025016 | Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout | 2026-08-04 09:45:42 | 182 | |||||||
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CRAPome Resource Report Resource Website 10+ mentions |
CRAPome (RRID:SCR_025008) | web service, software resource, data access protocol, database, data or information resource | Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions. | Mass Spectrometry contaminants, standardized negative controls, contaminant repository, AP-MS analysis, affinity purification, mass spectrometry data, | NIGMS 5R01GM94231; NIDA DP1DA026192; NHLBI HL112618-01; Canadian Institutes of Health Research ; government of Ontario ; Austrian Academy of Sciences ; Austrian Federal Ministry for Science and Research ; European Research Council ; Austrian Science Fund ; European Molecular Biology Organisation ; Netherlands Proteomics Center ; European Union 7th Framework Program ; Stowers Institute for Medical Research ; Human Frontier Science Program ; NCI R21 CA16006001A1 |
PMID:23921808 | Free, Freely available, | https://reprint-apms.org/ | SCR_025008 | CRAPome:Contaminant Repository for Affinity Purification | 2026-08-04 09:45:39 | 16 |
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