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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
arcasHLA
 
Resource Report
Resource Website
1+ mentions
arcasHLA (RRID:SCR_022286) software resource, data processing software, software application Software tool for high resolution HLA typing from RNAseq. Fast and accurate in silico inference of HLA genotypes from RNA-seq. in silico inference of HLA genotypes, RNA-seq data, HLA typing DARPA ;
Phillip A. Sharp award ;
NCI U54CA193313;
NIGMS R01GM117591
PMID:31173059 Free SCR_022286 2026-02-14 02:05:37 8
plusTipTracker
 
Resource Report
Resource Website
10+ mentions
plusTipTracker (RRID:SCR_021890) software resource, image analysis software, data processing software, software application Software package as quantitative image analysis software for measurement of microtubule dynamics. MATLAB software for tracking full dynamics of microtubules based on plusTIP marker live cell image sequences. microtubule tracking, microtubule dynamics, microtubule dynamics measurement, plusTIP marker, live cell image sequences NIGMS U01 GM67230 PMID:21821130 Free, Available for download, Freely available SCR_021890 2026-02-14 02:05:48 10
Phenologs
 
Resource Report
Resource Website
1+ mentions
Phenologs (RRID:SCR_005529) Phenologs data or information resource, database Database for identifying orthologous phenotypes (phenologs). Mapping between genotype and phenotype is often non-obvious, complicating prediction of genes underlying specific phenotypes. This problem can be addressed through comparative analyses of phenotypes. We define phenologs based upon overlapping sets of orthologous genes associated with each phenotype. Comparisons of >189,000 human, mouse, yeast, and worm gene-phenotype associations reveal many significant phenologs, including novel non-obvious human disease models. For example, phenologs suggest a yeast model for mammalian angiogenesis defects and an invertebrate model for vertebrate neural tube birth defects. Phenologs thus create a rich framework for comparing mutational phenotypes, identify adaptive reuse of gene systems, and suggest new disease genes. To search for phenologs, go to the basic search page and enter a list of genes in the box provided, using Entrez gene identifiers for mouse/human genes, locus ids for yeast (e.g., YHR200W), or sequence names for worm (e.g., B0205.3). It is expected that this list of genes will all be associated with a particular system, trait, mutational phenotype, or disease. The search will return all identified model organism/human mutational phenotypes that show any overlap with the input set of the genes, ranked according to their hypergeometric probability scores. Clicking on a particular phenolog will result in a list of genes associated with the phenotype, from which potential new candidate genes can identified. Currently known phenotypes in the database are available from the link labeled ''Find phenotypes'', where the associated gene can be submitted as queries, or alternately, can be searched directly from the link provided. gene, phenotype, ortholog, genotype, human, mouse, yeast, worm has parent organization: University of Texas at Austin; Texas; USA Texas Advanced Research Program ;
Welch Foundation ;
Packard Fellowship ;
March of Dimes ;
Texas Institute for Drug and Diagnostic Development ;
NSF ;
NIH ;
NIGMS
PMID:20308572 nlx_144624 SCR_005529 phenologs.org, Phenologs - Systematic discovery of non-obvious disease models and candidate genes 2026-02-14 02:06:24 4
BiGG Database
 
Resource Report
Resource Website
100+ mentions
BiGG Database (RRID:SCR_005809) BiGG data or information resource, database A knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest. biochemical, genetics, genomics, genome, metabolic network, reconstruction, model, metabolic pathway, gene, protein, reaction, metabolite, metabolic reconstruction, compound, pathway, FASEB list uses: SBML
is used by: BiGGR
is listed by: 3DVC
has parent organization: University of California at San Diego; California; USA
NIH ;
Ruth L. Kirschstein National Research Service Award - NIH Bioinformatics Training ;
University of California at San Diego; California; USA ;
Calit2 summer research scholarship ;
NIGMS GM00806-06
PMID:20426874 nlx_149299, r3d100011567 https://doi.org/10.17616/R3MG9M SCR_005809 BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions, BiGG - a Biochemical Genetic and Genomic knowledgebase 2026-02-14 02:05:58 124
NIGMS - YouTube
 
Resource Report
Resource Website
NIGMS - YouTube (RRID:SCR_005678) NIGMS - YouTube data or information resource, video resource YouTube videos provided by the National Institute of General Medical Sciences (NIGMS). has parent organization: National Institute of General Medical Sciences NIGMS nlx_149378 SCR_005678 National Institute of General Medical Sciences - YouTube 2026-02-14 02:05:53 0
WorfDB
 
Resource Report
Resource Website
1+ mentions
WorfDB (RRID:SCR_006028) data or information resource, database Database that integrates and disseminates the data from the cloning of complete set of predicted protein-encoding ORFs of Caenorhabditis elegans. It also allows the community to search for availability and quality of cloned ORFs. So far, ORF sequence tags (OSTs) obtained for all individual clones have allowed exon structure corrections for ORFs originally predicted by the C. elegans sequencing consortium. The database contains this OST information along with data pertinent to the cloning process. open reading frame, c elegans, orf sequence tag has parent organization: Dana-Farber Cancer Institute
has parent organization: Harvard Medical School; Massachusetts; USA
NIGMS ;
MGRI ;
NHGRI 5R01HG01715-02;
NCI 7 R33 CA81658-02
PMID:12519990 nif-0000-03644 SCR_006028 WorfDB - Worm ORF Database, Worm ORFeome DataBase, Worm ORFeome 2026-02-14 02:05:54 9
Recon x
 
Resource Report
Resource Website
10+ mentions
Recon x (RRID:SCR_006345) Recon x data or information resource, database A comprehensive biochemical knowledge-base on human metabolism, this community-driven, consensus metabolic reconstruction integrates metabolic information from five different resources: * Recon 1, a global human metabolic reconstruction (Duarte et al, PNAS, 104(6), 1777-1782, 2007) * EHMN, Edinburgh Human Metabolic Network (Hao et al., BMC Bioinformatics 11, 393, 2010) * HepatoNet1, a liver metabolic reconstruction (Gille et al., Molecular Systems Biology 6, 411, 2010), * Ac/FAO module, an acylcarnitine/fatty acid oxidation module (Sahoo et al., Molecular bioSystems 8, 2545-2558, 2012), * a human small intestinal enterocytes reconstruction (Sahoo and Thiele, submitted). Additionally, more than 370 transport and exchange reactions were added, based on a literature review. Recon 2 is fully semantically annotated (Le Nov��re, N. et al. Nat Biotechnol 23, 1509-1515, 2005) with references to persistent and publicly available chemical and gene databases, unambiguously identifying its components and increasing its applicability for third-party users. Here you can explore the content of the reconstruction by searching/browsing metabolites and reactions. Recon 2 predictive model is available in the Systems Biology Markup Language format. metabolism, annotation, metabolite, reaction, genome, reconstruction has parent organization: University of Iceland; Reykjavik; Iceland Knut and Alice Wallenberg Foundation ;
Marie Curie International Reintegration Grant 249261;
European Research Council 232816;
Rannis research 100406022;
Manchester Centre for Integrative Systems Biology BB/C008219/1;
Bioprocessing Research Industry Club ;
European Union FP7 201142;
BBSRC BB/F005938;
BBSRC BB/F00561X;
DFG 0315756;
DFG 0315741;
NIGMS GM088244;
NSF 0643548;
Cystic Fibrosis Research Foundation 1060
PMID:23455439 Free, Acknowledgement requested nlx_152079 SCR_006345 Recon x Reconstruction of The Human Genome, Recon x - Reconstruction of The Human Genome, Recon x: Reconstruction of The Human Genome, Recon 2 2026-02-14 02:06:34 11
RNA CoSSMos
 
Resource Report
Resource Website
1+ mentions
RNA CoSSMos (RRID:SCR_006120) RNA CoSSMos data or information resource, database Database to search through the nucleic acid structures from the Protein Data Bank and examine structural motifs, including (a)symmetric internal loops, bulge loops, and hairpin loops. They have compiled over 2,000 three-dimensional structures, which can now be searched using different parameters, including PDB information, experimental technique, sequence, and motif type. RNA secondary structure is important for designing therapeutics, understanding protein-RNA binding and predicting tertiary structure of RNA. Several databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. To create the RNA CoSSMos database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop''''s structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the database. False positives were defined, identified and reclassified or omitted from the database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos database is updated weekly. secondary structure motif, rna, three-dimensional structure, internal loop, bulge loop, hairpin loop, motif, nucleic acid, structure, secondary structure, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
has parent organization: Saint Louis University; Missouri; USA
NIGMS 1R15GM085699-01A1 PMID:22127861 Freely accessible, Acknowledgement requested nlx_151597, biotools:rna_cossmos https://bio.tools/rna_cossmos SCR_006120 Znosko Lab RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database, Znosko Lab CoSSMos Database, RNA Characterization of Secondary Structure Motifs (RNA CoSSMos), RNA CoSSMos Database, RNA CoSSMos - Characterization of Secondary Structure Motifs, RNA Characterization of Secondary Structure Motifs 2026-02-14 02:06:25 1
Worldwide Protein Data Bank (wwPDB)
 
Resource Report
Resource Website
1000+ mentions
Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) wwPDB data or information resource, database Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations. 3-dimentional, bioinformatics, protein, research, structure, macromolecule, structural data, 3d spatial image, gold standard is used by: Ligand Expo
is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is related to: Biological Magnetic Resonance Data Bank (BMRB)
is related to: Proteopedia - Life in 3D
is related to: NRG-CING
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is related to: DNA DataBank of Japan (DDBJ)
is related to: PDBe - Protein Data Bank in Europe
is related to: PDBe - Protein Data Bank in Europe
is related to: PDBj - Protein Data Bank Japan
is related to: Biological Magnetic Resonance Data Bank (BMRB)
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is related to: PDB Validation Server
is related to: Structural Antibody Database
is parent organization of: PDB-Dev
works with: PDB-REDO
NSF ;
NIGMS ;
DOE ;
NLM ;
NCI ;
NINDS ;
NIDDK ;
European Molecular Biology Laboratory ;
Heidelberg; Germany ;
Wellcome Trust ;
BBSRC ;
NIH ;
European Union ;
NBDC - National Bioscience Database Center ;
Japan Science and Technology Agency
PMID:14634627 Free, Freely available nif-0000-23903, r3d100011104 https://doi.org/10.17616/R3462V SCR_006555 World Wide Protein DataBank, wwPDB, Worldwide Protein Data Bank (wwPDB), World Wide Protein Data Bank, Worldwide Protein DataBank 2026-02-14 02:06:26 1215
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 2026-02-14 02:07:07 0
MORGAN
 
Resource Report
Resource Website
100+ mentions
MORGAN (RRID:SCR_006906) MORGAN software resource, software application Software programs for segregation and linkage analysis, using a variety of Markov chain Monte Carlo (MCMC) methods. Includes MCMC methods for multilocus gene identity by descent (including homozygosity mapping) and Monte Carlo Lod scores. Also, other programs for EM analysis of quantitative traits. gene, genetic, genomic, c, unix, compaq-alpha, solaris, linux, linkage disequilibrium, gl_lods, ibd_haplo, identity by descent, segregation, linkage analysis, markov chain monte carlo is listed by: OMICtools
is listed by: Genetic Analysis Software
has parent organization: University of Washington; Seattle; USA
NIGMS GM-46255 PMID:22298700 nlx_154201, OMICS_00205 SCR_006906 MOnte caRlo Genetic ANalysis PANGAEA 2026-02-14 02:07:09 305
ShapeWorks
 
Resource Report
Resource Website
1+ mentions
ShapeWorks (RRID:SCR_000424) ShapeWorks software resource, software application THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2022. Software that is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results. c++, console (text based), linux, macos, microsoft, magnetic resonance, posix/unix-like, rendering, shape analysis, surface rendering, visualization, win32 (ms windows), windows, workflow is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of Utah; Utah; USA
NCRR 5P41RR012553-15;
NIGMS 8 P41 GM103545-15
THIS RESOURCE IS NO LONGER IN SERVICE nlx_155961 http://www.nitrc.org/projects/shapeworks SCR_000424 2026-02-14 02:06:58 1
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 2026-02-14 02:06:59 11
Integrative Modeling Platform
 
Resource Report
Resource Website
50+ mentions
Integrative Modeling Platform (RRID:SCR_002982) IMP software resource, software toolkit 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 2026-02-14 02:06:56 54
Gemma
 
Resource Report
Resource Website
1000+ mentions
Gemma (RRID:SCR_008007) Gemma data or information resource, database Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results. chip, microarray, functional genomics, gene expression, coexpression, differential expression, FASEB list is used by: NIF Data Federation
is used by: Integrated Data Annotation
is listed by: Debian
is listed by: SoftCite
is related to: Gene Ontology
is related to: Gene Expression Omnibus
is related to: Phenocarta
has parent organization: University of British Columbia; British Columbia; Canada
is parent organization of: Neurocarta
NIGMS GM076990;
Canadian Foundation for Innovation ;
Michael Smith Foundation for Health Research ;
Canadian Institutes for Health Research
PMID:22782548 Free, Freely available nif-0000-08127, r3d100012747 https://sources.debian.org/src/gemma/
https://doi.org/10.17616/R36R54
https://doi.org/10.17616/R36R54
SCR_008007 2026-02-14 02:06:41 1112
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 2026-02-14 02:06:44 7
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 2026-02-14 02:06:48 210
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 2026-02-14 02:06:33 3
CIS-BP
 
Resource Report
Resource Website
100+ mentions
CIS-BP (RRID:SCR_017236) web service, data or information resource, data access protocol, software resource, database 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 2026-02-14 02:06:31 104
SRMAtlas
 
Resource Report
Resource Website
1+ mentions
SRMAtlas (RRID:SCR_016996) SRM Atlas, SRMatlas data or information resource, atlas, database 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 2026-02-14 02:06:47 3

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