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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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WEBLOGO Resource Report Resource Website 1000+ mentions |
WEBLOGO (RRID:SCR_010236) | service resource, software resource, data access protocol, web service | Web application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator. | Generate sequence logo, pattern graphical representation, multiple sequence alignment, sequence logo generator, amino acid sequence alignment, nucleic acid sequence alignment, sequence alignment representation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
NHGRI K22 HG00056; Searle Scholars program ; NIGMS P50 GM62412 |
PMID:15173120 | Free, Available for download, Freely available | nlx_156853, biotools:weblogo_3 | http://weblogo.threeplusone.com/, https://bio.tools/weblogo_3 | SCR_010236 | WebLogo Version 2.8.2, WebLogo3, WebLogo | 2026-07-28 09:42:40 | 3653 | |||||
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HOMER Resource Report Resource Website 5000+ mentions |
HOMER (RRID:SCR_010881) | HOMER | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++. | motif, discovery, next, generation, sequencing, analysis, genomic, data |
is listed by: OMICtools is related to: findMotif.pl has parent organization: University of California at San Diego; California; USA |
NURSA consortium grant ; NIH HC088093; NIDDK DK063491; NCI CA52599; NIGMS P50 GM081892; Foundation Leducq Transatlantic Network Grant |
PMID:20513432 | OMICS_00483 | http://biowhat.ucsd.edu/homer/index.html | SCR_010881 | HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 | 2026-07-28 09:42:59 | 5370 | |||||
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Zebra Finch Expression Brain Atlas Resource Report Resource Website 10+ mentions |
Zebra Finch Expression Brain Atlas (RRID:SCR_012988) | ZEBrA | data or information resource, expression atlas, database, atlas | Expression atlas of in situ hybridization images from large collection of genes expressed in brain of adult male zebra finches. Goal of ZEBrA project is to develop publicly available on-line digital atlas that documents expression of large collection of genes within brain of adult male zebra finches. | gene, expression, brain, in-situ, hybridization, taeniopygia, vocal learning, anatomical, atlas, data set, molecular neuroanatomy, adult, male, gene, image, bird, image, avian | has parent organization: Oregon Health and Science University; Oregon; USA | NINDS R03 NS059755; NIGMS R24 GM092842 |
Free, Freely available | nif-0000-24345, SCR_000641, nlx_152091 | http://ignrhnet.ohsu.edu/finch/songbird/index.php | SCR_012988 | zebra, , Zebra Finch Expression Brain Atlas, atlas, Zebra Finch Brain Atlas, ZEBrA, finch | 2026-07-28 09:43:09 | 38 | |||||
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bNAber Resource Report Resource Website 1+ mentions |
bNAber (RRID:SCR_010510) | bNAber | data or information resource, database | bNAber is the Broadly Neutralizing Antibody E-Resource Database, analysis, visualization, and data discovery tool for broadly neutralizing HIV-1 antibodies (bNAbs). bNAber seeks to be a vital tool in the search for an AIDS vaccine. | sanford burnham medical research institute, hiv, aids | is related to: CHAVI-ID | HIV, AIDS | NIAID UM1AI100663; NIGMS R01GM101457 |
nlx_158732 | SCR_010510 | 2026-07-28 09:42:47 | 7 | |||||||
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miRanda Resource Report Resource Website 100+ mentions |
miRanda (RRID:SCR_017496) | data or information resource, service resource, database | Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Whole, genome, prediction, miRNA, target, gene, expression, profile, data, FASEB list | is listed by: SoftCite | NIGMS ; Atlantic Philanthropies ; Alfred W. Bressler Scholars Endowment Fund |
PMID:18158296 | THIS RESOURCE IS NO LONGER IN SERVICE | http://www.microrna.org/microrna/home.do | SCR_017496 | MicroRNA.org. microrna.org | 2026-07-28 09:44:30 | 210 | ||||||
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Viral Integrated Structural Evolution Dynamic Database Resource Report Resource Website 1+ mentions |
Viral Integrated Structural Evolution Dynamic Database (RRID:SCR_018793) | VIStEDD | data or information resource, database | Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein. | Virus, SARS-CoV-2, COVID-19, proteins coded by virus, viral evolution, protein, data, amino acid, protein modeling, molecular dynamic simulation, evolutionary analysis, protein-protein interaction, protein- protein interaction mapping, protein data folder system, rotating protein video, protein function, molecular dynamic simulation | has parent organization: Michigan State University; Michigan; USA | COVID-19 | NIGMS R01 GM108618; NIEHS K01 ES025435 |
PMID:32511397 | Free, Freely available | SCR_018793 | Viral Integrated Structural Evolution Dynamic Database, SARS-CoV-2 dynamicome database | 2026-07-28 09:44:45 | 3 | |||||
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CIS-BP Resource Report Resource Website 100+ mentions |
CIS-BP (RRID:SCR_017236) | data or information resource, database, data access protocol, software resource, web service | Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs. | catalog, inferred, sequence, binding, preference, transcription, factor, DNA, motif, FASEB list | Canadian Institutes of Health Research ; Canadian Institute for Advanced Research Junior Fellows Genetic Networks Program ; NICHD P01 HD39691; NIGMS GM082971; EU Marie Curie International Outgoing Fellowship ; NSF MCB-1024999; Howard Hughes Medical Institute ; Gordon and Betty Moore Foundation ; Millennium Nucleus for Fungal Integrative and Synthetic Biology ; Fondo Nacional de Desarrollo Científico y Tecnológico |
PMID:25215497 | Free, Freely available | r3d100013971 | https://doi.org/10.17616/R31NJN9V | SCR_017236 | Catalog of Inferred Sequence Binding Preferences | 2026-07-28 09:44:32 | 104 | ||||||
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SRMAtlas Resource Report Resource Website 1+ mentions |
SRMAtlas (RRID:SCR_016996) | SRM Atlas, SRMatlas | data or information resource, database, atlas | Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome. | collection, proteomic, assay, detect, quantify, protein, mass, spectrometry, peptide | American Recovery and Reinvestment Act ; NHGRI RC2 HG005805; NIGMS R01 GM087221; NCRR S10 RR027584; NIGMS P50 GM076547; Luxembourg Centre for Systems Biomedicine University Luxembourg ; European Research Council ; Swiss National Science Foundation |
PMID:27453469 | Publicly available, Registration required | SCR_016996 | 2026-07-28 09:44:27 | 3 | ||||||||
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Integrative Modeling Platform Resource Report Resource Website 50+ mentions |
Integrative Modeling Platform (RRID:SCR_002982) | IMP | software toolkit, software resource | An open source C++ and Python toolbox for solving complex modeling problems, and a number of applications for tackling some common problems in a user-friendly way. Its broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies, by integrating data from diverse biochemical and biophysical experiments. It can also be used from the Chimera molecular modeling system, or via one of several web applications. | integrative modeling, structure determination, hybrid modeling, macromolecular assembly, c++, python, peptide, biomolecule, model, structural characterization, structure |
is related to: UCSF Chimera has parent organization: University of California at San Francisco; California; USA |
NIGMS R01 GM083960 | PMID:22272186 | GNU Lesser General Public License, v2.1 or later, Acknowledgement requested, GNU General Public License | SciRes_000187 | SCR_002982 | IMP - the Integrative Modeling Platform, Integrative Modeling Platform (IMP), IMP the Integrative Modeling Platform | 2026-07-28 09:40:42 | 54 | |||||
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Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure Resource Report Resource Website 10+ mentions |
Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure (RRID:SCR_001300) | SCORE imaging | data or information resource, narrative resource | Narrative resource describing a visual data analysis and collection approach that takes advantage of the cylindrical nature of the zebrafish allowing for an efficient and effective method for image capture called, Specimen in a Corrected Optical Rotational Enclosure (SCORE) Imaging. To achieve a non-distorted image, zebrafish were placed in a fluorinated ethylene propylene (FEP) tube with a surrounding, optically corrected imaging solution: water. By similarly matching the refractive index of the housing (FEP tubing) to that of the inner liquid and outer liquid (water), distortion was markedly reduced, producing a crisp imagable specimen that is able to be fully rotated 360 degrees. A similar procedure was established for fixed zebrafish embryos using convenient, readily available borosilicate capillaries surrounded by 75% glycerol. The method described could be applied to chemical genetic screening and other, related high-throughput methods within the fish community and among other scientific fields. | format, authoring tool, embryo, microscopy, publishing format, image |
is listed by: FORCE11 has parent organization: Mayo Clinic Minnesota; Minnesota; USA has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NIGMS GM63904; NIDA DA14546 |
PMID:20528262 | nif-0000-07749 | SCR_001300 | Specimen in a Corrected Optical Rotational Enclosure imaging | 2026-07-28 09:40:13 | 11 | ||||||
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NIGMS Computing Life Resource Report Resource Website |
NIGMS Computing Life (RRID:SCR_005850) | Computing Life | data or information resource, narrative resource | An NIGMS magazine that showcases the exciting ways that scientists are using the power of computers to expand our knowledge of biology and medicine. From text messaging friends to navigating city streets with GPS technology, we''re all living the computing life. But as we''ve upgraded from snail mail and compasses, so too have scientists. Computer advances now let researchers quickly search through DNA sequences to find gene variations that could lead to disease, simulate how flu might spread through your school and design three-dimensional animations of molecules that rival any video game. By teaming computers and biology, scientists can answer new and old questions that could offer insights into the fundamental processes that keep us alive and make us sick. This booklet introduces you to just some of the ways that physicists, biologists and even artists are computing life. Each section focuses on a different research problem, offers examples of current scientific projects and acquaints you with the people conducting the work. You can follow the links for online extras and other opportunities to learn aboutand get involved inthis exciting new interdisciplinary field. | computer, biology, medicine, human, health | has parent organization: National Institute of General Medical Sciences | NIGMS | nlx_149381 | SCR_005850 | 2026-07-28 09:41:21 | 0 | ||||||||
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Berkeley Drosophila Genome Project Resource Report Resource Website 100+ mentions |
Berkeley Drosophila Genome Project (RRID:SCR_013094) | BDGP, BDGP EST, BDGP INS | data or information resource, database | Database on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs. | drosophila genome, cdna, est, transposon insertions, genomic sequencing, gene, FASEB list |
is related to: Bgee: dataBase for Gene Expression Evolution is related to: OpenFlyData.org has parent organization: University of California at Berkeley; Berkeley; USA is parent organization of: Patterns of Gene Expression in Drosophila Embryogenesis |
NHGRI ; NIGMS |
PMID:21177961 | nif-0000-02867, r3d100010624 | http://www.bdgp.org/ | SCR_013094 | 2026-07-28 09:43:10 | 463 | ||||||
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ADMIXTOOLS Resource Report Resource Website 100+ mentions |
ADMIXTOOLS (RRID:SCR_018495) | software toolkit, software resource | Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates. | Formal test support, admixture, infer admixture proportion, infer admixture date, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Harvard University; Cambridge; United States |
U.S. National Science Foundation HOMINID ; NIGMS GM100233 |
PMID:22960212 | Free, Available for download, Freely available | biotools:admixtools | http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html., https://bio.tools/admixtools | SCR_018495 | 2026-07-28 09:44:45 | 205 | ||||||
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FluCalc Resource Report Resource Website 1+ mentions |
FluCalc (RRID:SCR_019322) | software application, data analytics software, software resource | Software tool as MSS-MLE calculator for Luria–Delbrück fluctuation analysis. | Estimator, fluctuation calculation, MSS-MLE, Ma-Sandri-Sarkar Maximum Likelihood Estimator, calculator, fluctuation analysis | has parent organization: Tufts University; Massachusetts; USA | NIGMS GM105473; NIGMS GM60987 |
PMID:29043640 | Free, Available for download, Freely available | SCR_019322 | flucalc, fluctuation calculation | 2026-07-28 09:45:05 | 1 | |||||||
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CellChat Resource Report Resource Website 500+ mentions |
CellChat (RRID:SCR_021946) | software toolkit, software resource | Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets. | inference, visualization, analysis, cell-cell communication, single cell data, intercellular communication networks, single-cell RNA-sequencing data | NSF DMS1763272; Simons Foundation ; NIH U01 AR073159; NIGMS R01 GM123731; NIH P30 AR07504; Pew Charitable Trust ; LEO Foundation ; UC Irvine ; Howard Hughes Medical Institute |
PMID:33597522 | Free, Available for download, Freely available | http://www.cellchat.org/ | SCR_021946 | 2026-07-28 09:45:21 | 536 | ||||||||
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SYGNAL Resource Report Resource Website 1+ mentions |
SYGNAL (RRID:SCR_023080) | software toolkit, software resource | 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 | 2026-07-28 09:45:51 | 1 | ||||||||
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AmpliconArchitect Resource Report Resource Website 10+ mentions |
AmpliconArchitect (RRID:SCR_023150) | software toolkit, software resource | Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers. | call circular DNA, short read WGS data, connected genomic regions identification, simultaneous copy number amplification, amplicon | NIGMS R01GM114362; NHGRI HG010149; NSF NSF-DBI-1458557 |
DOI:10.1038/s41467-018-08200-y | SCR_023150 | 2026-07-28 09:45:52 | 42 | ||||||||||
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CarbonylDB Resource Report Resource Website 1+ mentions |
CarbonylDB (RRID:SCR_023924) | data or information resource, database | Curated data resource of protein carbonylation sites.Manually curated data resource of experimentally confirmed carbonylated proteins and sites.Provides information on other related resources such as list of other oxidative protein modification databases, list of protein oxidation and carbonylation prediction tools. | Curated data, protein carbonylation site, chemically diverse form, irreversible oxidative post translational modifications, | NIGMS R01 GM100701; Danish Council for Independent Research–Technology and Production Sciences |
PMID:29509874 | Free, Available for download, Freely available | SCR_023924 | 2026-07-28 09:45:59 | 1 | |||||||||
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National Resource for Automated Molecular Microscopy Resource Report Resource Website 1+ mentions |
National Resource for Automated Molecular Microscopy (RRID:SCR_001448) | NRAMM | training resource, biomedical technology research center | Biomedical technology research center that develops, tests and applies technology aimed toward completely automating the processes involved in solving macromolecular structures using cryo-electron microscopy. The goal is to establish a resource that will serve both as a center for high-throughput molecular microscopy as well as for transferring this technique to the research community. Current Core Technology Research and Development is focused on 4 areas: improving grid substrates and specimen preparation; further automation and optimization of image acquisition; development of an integrated single particle analysis and processing pipeline; and the development of automated high throughput EM screening. NRAMM welcomes applications of both collaborative and service projects. | macromolecular structure, cryo-electron microscopy, macromolecule, structure, microscopy, automation, high throughput, specimen handling, image acquisition, data processing, data information integration, structural biology technology center | NIGMS 9 P41 GM103310; NCRR 2P41RR017573 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152671 | SCR_001448 | 2026-07-28 09:40:11 | 2 | ||||||||
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National Magnetic Resonance Facility at Madison Resource Report Resource Website 1+ mentions |
National Magnetic Resonance Facility at Madison (RRID:SCR_001449) | NMRFAM | access service resource, service resource, training resource | Provides access and developes NMR technology to advance range of applications and improves the efficiency, rigor and reproducibility of NMR data acquisition and analysis. Houses NMR spectrometers equipped with state-of-the-art probe technology and protocols to support acquisition of high-quality data. Spectrometers range from 500 MHz to 1100 MHz. Service is tailored to the needs of individual users and projects. Provides training and advice on experimental design, best practices for data acquisition, and data analysis. Experienced staff support users with training opportunities including workshops, video tutorials and protocols. | nmr spectrometer, structure, function, protein, rna, dynamics, complex, membrane protein, paramagnetic protein, metabolomics, analysis, spectroscopy, nucleic acid, automation, data analysis, macromolecule, small angle x-ray scattering, structural biology technology center | has parent organization: University of Wisconsin-Madison; Wisconsin; USA | NIGMS R24GM141526; NIGMS P41136463 |
Free, Freely Available | nlx_152672 | SCR_001449 | 2026-07-28 09:40:11 | 4 |
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