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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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FATCAT Flexible Structural Neighborhood Resource Report Resource Website |
FATCAT Flexible Structural Neighborhood (RRID:SCR_007665) | FSN | data or information resource, database | 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 | 2026-02-14 02:06:06 | 0 | ||||||
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GlyGen Resource Report Resource Website 10+ mentions |
GlyGen (RRID:SCR_023438) | data or information resource, portal, project portal | Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression. | Gly-glycobiology Gen-information, glycobiology, glycans molecular properties, glycans biophysical properties, glycans functional properties properties, glycans, genes, proteins, lipids, pathways and ontologies, data, mutation and expression data, carbohydrate and glycoconjugate related data, | NIGMS 1U01GM125267; NIGMS R24 GM146616 |
PMID:31616925 PMID:32324859 |
Free, Freely available | SCR_023438 | GlyGen Portal | 2026-02-14 02:05:38 | 11 | ||||||||
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Minimum Information about Biosynthetic Gene cluster Resource Report Resource Website 50+ mentions |
Minimum Information about Biosynthetic Gene cluster (RRID:SCR_023660) | MIBiG | data or information resource, portal, database, project portal | MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters. | Genomic standards consortium project, community standard, annotations and metadata standards, biosynthetic gene clusters, sequence framework, biosynthetic gene cluster data, | Netherlands Organization for Scientific Research VENI grant ; NSF CAREER Award ; UK Biotechnology and Biological Sciences Research Council ; Novo Nordisk Foundation ; NIH U41 AT008718; Danish National Research Foundation ; NCCIH U24 AT010811; NCCIH F32 AT011475; Natural Sciences and Engineering Council of Canada Discovery grant ; European Union Horizon 2020 projects CARTNET ; Horizon 2020 Marie Skłodowska-Curie ; U.S. Department of Energy ; Portuguese Science and Technology Foundation ; U.S. National Science Foundation ; National Research Foundation of Korea ; NIGMS GM134688; NIAID R01AI155694; Netherlands eScience Center Accelerating Scientific Discoveries Grant ; Funds of the Chemical Industry Germany ; UK government Department for Environment ; Food and Rural Affairs ; German Chemical Industry ; Natural Sciences and Engineering Council of Canada |
PMID:36399496 DOI:10.1093/nar/gkz882 |
Free, Freely available | SCR_023660 | MIBiG 3.0, MIBiG 2.0 | 2026-02-14 02:05:38 | 55 | |||||||
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BindingDB Resource Report Resource Website 10+ mentions |
BindingDB (RRID:SCR_000390) | data or information resource, database | Web accessible database of data extracted from scientific literature, focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in Protein Data Bank . Website supports query types including searches by chemical structure, substructure and similarity, protein sequence, ligand and protein names, affinity ranges and molecular weight . Data sets generated by BindingDB queries can be downloaded in form of annotated SDfiles for further analysis, or used as basis for virtual screening of compound database uploaded by user. Data are linked to structural data in PDB via PDB IDs and chemical and sequence searches, and to literature in PubMed via PubMed IDs . | drug, drug discovery, drug target, binding affinity, protein interaction, small molecule-protein interaction, interaction, protein, small molecule, FASEB list |
is related to: PSICQUIC Registry is related to: canSAR has parent organization: University of California at San Diego; California; USA |
NIGMS GM070064; NSF 9808318; National Institute of Standards and Technology ; NIGMS R24 GM144232 |
PMID:26481362 PMID:17145705 |
Free, Freely available | r3d100012074, nif-0000-02603 | https://doi.org/10.17616/R3ZS9T | SCR_000390 | BindingDB | 2026-02-14 02:05:57 | 41 | |||||
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Hanalyzer Resource Report Resource Website |
Hanalyzer (RRID:SCR_000923) | software resource, source code, software application | An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download. | genomic, visualization, reading, reasoning, reporting, throughput analyzer, data network |
has parent organization: University of Colorado Denver; Colorado; USA has parent organization: SourceForge |
NIDCR R01DE15191; NLM R01LM008111; NLM R01LM009254; NIGMS R01GM083649; NLM T15LM009451; NHGRI 5R01HG004483-09 |
PMID:19325874 | nlx_48287 | SCR_000923 | Hanalyzer: A 3R System | 2026-02-14 02:06:03 | 0 | |||||||
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WTCHG Genome Scan Viewer Resource Report Resource Website 1+ mentions |
WTCHG Genome Scan Viewer (RRID:SCR_001635) | GSCANDB | data or information resource, service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database / display tool of genome scans, with a web interface that lets the user view the data. It does not perform any analyses - these must be done by other software, and the results uploaded into it. The basic features of GSCANDB are: * Parallel viewing of scans for multiple phenotypes. * Parallel analyses of the same scan data. * Genome-wide views of genome scans * Chromosomal region views, with zooming * Gene and SNP Annotation is shown at high zoom levels * Haplotype block structure viewing * The positions of known Trait Loci can be overlayed and queried. * Links to Ensembl, MGI, NCBI, UCSC and other genome data browsers. In GSCANDB, a genome scan has a wide definition, including not only the usual statistical genetic measures of association between genetic variation at a series of loci and variation in a phenotype, but any quantitative measure that varies along the genome. This includes for example competitive genome hybridization data and some kinds of gene expression measurements. | genome, gene, snp, trait, genotype, phenotype, visualization, region, chromosome, quantitative trait locus, hybridization, gene expression | has parent organization: University of Oxford; Oxford; United Kingdom | NIAAA U01AA014425; NCRR R24RR015116; NIGMS R01GM072863; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153902 | SCR_001635 | Wellcome Trust Centre for Human Genetics Genome Scan Viewer, Genome Scan Viewer, Genome Scan Database | 2026-02-14 02:05:45 | 3 | ||||||
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Bioscholar Resource Report Resource Website 1+ mentions |
Bioscholar (RRID:SCR_001380) | BioScholar | software resource, source code, software application | Knowledge management and engineering system software for experimental biomedical scientists permitting a single scientific worker (at the level of a graduate student or postdoctoral worker) to design, construct and manage a shared knowledge repository for a research group derived on a local store of PDF files. Usability is especially emphasized within a laboratory so that this software could provide support to experimental scientists attempting to construct a personalized representation of their own knowledge on a medium scale. The BioScholar system uses a graphical interface to create experimental designs based on the experimental variables in the system. The design is then analyzed to construct a tabular input form based on the data flow. They call this methodology "Knowledge Engineering from Experimental Design" or "KEfED". The approach is domain-independent but domain-specific modules reasoning can be constructed to generate interpretations from the observational data represented in the KEfED model. The application is available for download as platform-specific installers including Linux, Unix, Mac OS, and Windows. The installer will install an application that will run the BioScholar server. This server uses Jetty as its integrated web server. | knowledge engineering from experimental design, protocol, lab data management, knowledge engineering, kefed, experimental design, curate, model, scientific experiment, data repository, experimental variable, biomedical, bioinformatics |
is related to: Knowledge Engineering from Experimental Design has parent organization: University of Southern California; Los Angeles; USA |
NCRR 1 U24 RR025736; NIGMS R01-GM083871 |
PMID:21859449 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152541 | SCR_001380 | 2026-02-14 02:06:04 | 1 | ||||||
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Kinase Enrichment Analysis 3 Resource Report Resource Website 10+ mentions |
Kinase Enrichment Analysis 3 (RRID:SCR_023623) | KEA3 | data access protocol, software resource, web service | Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations. | overrepresentation of upstream kinases, upstream kinases, upstream kinases substrates, user inputted list of proteins, | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | NHLBI U54 HL127624; NCI U24 CA224260; NIGMS T32 GM062754; NIH Office of the Director OT3 OD025467 |
PMID:34019655 | Free, Freely available | SCR_023623 | 2026-02-14 02:05:07 | 11 | |||||||
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MicrobeJ Resource Report Resource Website 1+ mentions |
MicrobeJ (RRID:SCR_023914) | data processing software, data analysis software, software application, image processing software, software resource | Software tool for high throughput bacterial cell detection and quantitative analysis. Used to analyze bacterial cells. Used to process images derived from variety of microscopy experiments with special emphasis on large image sets. Performs intensity and morphology measurements as well as customized detection of poles, septa, fluorescent foci, and organelles, determines their sub-cellular localization with sub-pixel resolution, and tracks them over time. | bacterial cell detection, analyze bacterial cells, bacteria quantitative analysis, process images, intensity and morphology measurements, | is a plug in for: ImageJ | NIGMS GM51986; NIGMS GM113172; Indiana University Office of the Vice President for Research ; NCATS UL1TR001108 |
PMID:27572972 | Free, Available for download, Freely available | SCR_023914 | 2026-02-14 02:05:15 | 6 | ||||||||
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microbeMASST Resource Report Resource Website 1+ mentions |
microbeMASST (RRID:SCR_024713) | data access protocol, software resource, web service | Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. | Identification of microbial derived metabolites, microbial metabolomics data, microbial metabolite annotation, taxonomy, mass spectrometry search tool, searching tool, bacteria, fungi, metabolomics, microbiome, search known and unknown MS/MS spectra, | is related to: GNPS MASST | NIDDK U24DK133658; NIA U19AG063744; NIGMS 1DP2GM137413; Korean Government ; Austrian Science Fund ; German Research Foundation ; Sao Paulo Research Foundation ; Mexican National Council of Science and Technology ; NIGMS R01GM107550; NSF ; Research Council of Norway ; NIAID R01AI167860; NIDDK T32DK007202; NIGMS 1R01GM132649; NIGMS R35GM142938; NIDDK U01DK119702; NIH Office of the Director S10 OD021750; NLM 1R01LM013115 |
PMID:37577622 | Free, Freely available, | SCR_024713 | 2026-02-14 02:05:22 | 6 | ||||||||
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nTracer Resource Report Resource Website |
nTracer (RRID:SCR_023032) | image processing software, software resource, data processing software, software application | Software tool as plug-in for ImageJ software. Used for tracing microscopic images. | tracing microscopic images | is a plug in for: ImageJ | Michigan miBRAIN initiative ; NIAID R01AI130303; NSF NSF-1707316; NIMH R01MH110932; NIGMS F31GM116517; NINDS R01NS095367; NIMH P50MH09427; NIH Office of the Director DP2OD006514; NINDS R01NS076467; NINDS U01NS090449; NIGMS P41GM10371; Multidisciplinary University Research Initiative Army Research Office |
PMID:30715234 | Free, Available for download, Freely available | SCR_023032 | 2026-02-14 02:05:00 | 0 | ||||||||
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APA-Scan Resource Report Resource Website |
APA-Scan (RRID:SCR_022974) | data visualization software, data processing software, data analysis software, software application, software resource | Software Python tool for detection and visualization of annotated and potential alternative polyadenylation events in downstream 3'-UTR of gene among two different biological conditions. Used for detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data. | annotated and potential alternative polyadenylation events, gene downstream 3'-UTR, RNA-seq and 3'-end-seq data, two different biological conditions, polyadenylation events | NSF FET2003749; NIGMS R01GM113952; NIDDK DK097771 |
PMID:36171568 | Free, Available for download, Freely available | SCR_022974 | 2026-02-14 02:04:42 | 0 | |||||||||
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ChIP-X Enrichment Analysis 3 Resource Report Resource Website 100+ mentions |
ChIP-X Enrichment Analysis 3 (RRID:SCR_023159) | ChEA3 | software resource, web application | Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries. | Transcription Factor, gene sets, transcription factor enrichment analysis, TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, TF-gene co-occurrence, prediction of correct upstream, | NHLBI U54HL127624; NCI U24CA224260; NIGMS T32GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114921 | Free, Freely available | SCR_023159 | ChIP-X Enrichment Analysis Version 3 (ChEA3) | 2026-02-14 02:04:46 | 108 | |||||||
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rMATS Resource Report Resource Website 10+ mentions |
rMATS (RRID:SCR_023485) | software resource | Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P-value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user-defined threshold. From RNA-Seq data can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design. | detection of differential alternative splicing, replicate RNA-Seq data, analysis of paired and unpaired replicates, clinical RNA-Seq datasets, genome studies, | NIGMS R01GM088342; NINDS R01NS076631; NIEHS R01ES024995; NIGMS R01GM105431; NSF DMS1055286; NSF DMS1310391; Alfred Sloan Research Fellowship |
PMID:25480548 | Free, Available to download, Freely available | SCR_023485 | 2026-02-14 02:05:11 | 18 | |||||||||
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SPRING Resource Report Resource Website 10+ mentions |
SPRING (RRID:SCR_023578) | data access protocol, software resource, web service | Interactive web tool to visualize single cell data using force directed graph layouts. Kinetic interface for visualizing high dimensional single cell expression data. Collection of pre-processing scripts and web browser based tool for visualizing and interacting with high dimensional data. | visualizing high dimensional single cell expression data, single cell expression data visualization, high dimensional data, | has parent organization: Harvard University; Cambridge; United States | NIGMS 5T32GM080177; NCI 1R33CA212697; Burroughs-Wellcome Career Award at the Scientific Interface ; Edward J Mallinckrodt Foundation Fellowship |
PMID:29228172 | Free, Available for download, Freely available | https://github.com/AllonKleinLab/SPRING/ https://github.com/AllonKleinLab/SPRING_dev |
SCR_023578 | 2026-02-14 02:04:57 | 24 | |||||||
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R/qtl2 Resource Report Resource Website 10+ mentions |
R/qtl2 (RRID:SCR_018181) | data analysis software, software resource, data processing software, software application | Software R package for mapping quantitative trait loci with high dimensional data and multiparent populations. Used for analysis of high dimensional data and complex crosses. Interactive software environment for mapping quantitative trait loci in experimental populations.R/qtl2 software expands scope of R/qtl software package to include multiparent populations derived from more than two founder strains, such as Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. | High density genotyping data, molecular phenotype, gene expression, proteomics, mapping trait loci, diversity outbred mice, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM074244; NIGMS R01 GM070683; NIGMS R01 GM123489 |
PMID:30591514 | Free, Available for download, Freely available | biotools:R_qtl2, SCR_020965 | https://bio.tools/R_qtl2 https://kbroman.org/qtl2 https://github.com/rqtl/qtl2 |
SCR_018181 | QTL, R/quantitative trait loci, QTL2, Quantitative Trait Locus 2, quantitative trait loci 2, R/qtl, qtl2 | 2026-02-14 02:04:39 | 13 | |||||
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ClusPro Resource Report Resource Website 500+ mentions |
ClusPro (RRID:SCR_018248) | data access protocol, software resource, web service, service resource | Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results. | Protein-protein docking, protein structure, energy function, energy parameter selection, analysis, data |
has parent organization: Boston University; Massachusetts; USA has parent organization: Stony Brook University; New York; USA |
NIGMS R35 GM118078; NIGMS R01 GM061867 |
PMID:28079879 | Free, Freely available | SCR_018248 | ClusPro 2.0 | 2026-02-14 02:04:58 | 858 | |||||||
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ConnecTF Resource Report Resource Website 1+ mentions |
ConnecTF (RRID:SCR_022577) | data access protocol, software resource, web service | Software platform to integrate transcription factor gene interactions and validate regulatory networks. Gene regulatory network validation. | integrate transcription factor gene interactions, validate regulatory networks, gene regulatory network validation | NIGMS RO1-GM121753; NSF PGRP IOS-1339362; NSF PGRP IOS-1840761; NIGMS F32GM116347 |
PMID:33631799 | Free, Available for download, Freely available | https://github.com/coruzzilab/connectf_server | SCR_022577 | 2026-02-14 02:05:02 | 3 | ||||||||
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PILGRM Resource Report Resource Website 1+ mentions |
PILGRM (RRID:SCR_004749) | PILGRIM | data analysis service, production service resource, service resource, analysis service resource | PILGRM (the platform for interactive learning by genomics results mining) puts advanced supervised analysis techniques applied to enormous gene expression compendia into the hands of bench biologists. This flexible system empowers its users to answer diverse biological questions that are often outside of the scope of common databases in a data-driven manner. This capability allows domain experts to quickly and easily generate hypotheses about biological processes, tissues or diseases of interest. Specifically PILGRM helps biologists generate these hypotheses by analyzing the expression levels of known relevant genes in large compendia of microarray data. PILGRM is for the biologist with a set of proteins relevant to a disease, biological function or tissue of interest who wants to find additional players in that process. It uses a data driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets using lists of relevant and irrelevant genes (standards). PILGRM produces publication quality PDFs usable as supplementary material to describe the computational approach, standards and datasets. Each PILGRM analysis starts with an important biological question (e.g. What genes are relevant for breast cancer but not mammary tissue in general?). For PILGRM to discover relevant genes, it needs examples of both genes that you would (positive) and would not (negative) find interesting. Lists of these genes are what we call standards and in PILGRM you can build your own standards or you can use standards from common sources that we pre-load for your convenience. PILGRM lets you build your own literature-documented standards so that processes, disease, and tissues that are not well covered in databases of tissue expression, disease, or function can still be used for an analysis. | data mining, gene expression, user directed data mining, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Princeton University; New Jersey; USA |
NSF DBI-0546275; NIGMS R01 GM071966; NIGMS P50 GM071508; NCI T32 CA005928 |
PMID:21653547 | nlx_75372, biotools:pilgrm | https://bio.tools/pilgrm | SCR_004749 | Platform for Interactive Learning by Genomics Results Mining | 2026-02-14 02:06:19 | 1 | |||||
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Biomedical Computation Review Resource Report Resource Website |
Biomedical Computation Review (RRID:SCR_004866) | Biomedical Computation Review | data or information resource, narrative resource, blog | Magazine published by Simbios, a National NIH Center for Biomedical Computing, covering the latest research wherever computation, biology, and medicine intersect. In addition to disseminating information about the latest research in biomedical computation, they aim to foster community amongst the wide audience interested in any and all aspects of biomedical computing. Whether you are a long time researcher in this area or new to it, please consider joining those who have already started to participate in Biomedical Computation Review. You are encouraged to: * Write a letter to the editor on any relevant topics * Suggest your favorite topics that should receive more attention * Suggest an idea for a feature article * Propose an idea for an Under the Hood tutorial * Tell us any other way in which we can better serve this community | biomedical computing, computation, biology, medicine |
is related to: Simbios has parent organization: Simbios |
NIH Roadmap for Medical Research ; NIGMS U54 GM072970 |
nlx_84418 | http://biomedicalcomputationreview.org/index.html | SCR_004866 | 2026-02-14 02:06:20 | 0 |
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