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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MassQL Resource Report Resource Website 1+ mentions |
MassQL (RRID:SCR_025106) | software resource, source code | Software application for universal searching of Mass Spectrometry data. Open source MS query language for flexible and mass spectrometer manufacturer-independent mining of MS data. Implements common MS terminology to build consensus vocabulary to search for MS patterns in single mass spectrometry run. Enables set of mass spectrometry patterns to be queried directly from raw data. | Mass Spectrometry data searching, mass spectrometry data, mining of MS data, common MS terminology, mass spectrometry patterns, raw data query, | NIGMS R01 GM125943; NIGMS R01 GM107550; NIGMS R35 GM128690; NIAID R21 AI156669; NIAID R15 AI137996; NSF ; Burroughs Wellcome Fund ; University of Michigan ; National Research Foundation of Korea ; German Research Foundation ; Swedish Research Council ; Ministry of Innovative Development of the Republic of Uzbekistan ; German Ministry for Education and Research ; Horizon 2020 programme of the European Union ; Czech Science Foundation ; U.S. Department of Energy Joint Genome Institute ; National Cancer Center Research and Development Fund ; AMED Japan Program for Infectious Diseases Research and Infrastructure ; Novo Nordisk Foundation ; Denmark ; Betty and Gordon Moore Foundation |
DOI:10.1101/2022.08.06.503000 | Free, Available for download, Freely available | https://pypi.org/project/massql/ | SCR_025106 | Mass Spec Query Language | 2026-08-03 09:39:00 | 1 | |||||||
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MEGA Resource Report Resource Website 1000+ mentions |
MEGA (RRID:SCR_000667) | MEGA, MEGA6, MEGA4, MEGA 4, MEGA 11 | data processing software, data analysis software, software resource, sequence analysis software, software application, software toolkit | Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny. | comparative, analysis, DNA, protein, sequence, molecular, evolution, pattern, gene, genome, evolution, FASEB list | has parent organization: Pennsylvania State University | Japan Society for the Promotion of Science ; NHGRI HG006039; NHGRI HG002096; Burroughs-Wellcome Fund ; NIGMS R01GM126567; NSF ABI 1661218; NIGMS R35GM139504 |
DOI:10.1093/molbev/msab120 PMID:24132122 PMID:31904846 PMID:22923298 PMID:21546353 PMID:17488738 PMID:15260895 PMID:11751241 PMID:8019868 |
Free, Available for download, Freely available | SCR_023017, nlx_156838 | https://www.megasoftware.net/mega4/ | SCR_000667 | MEGA11, Molecular Evolutionary Genetics Analysis, Molecular Evolutionary Genetics Analysis 6, Molecular Evolutionary Genetics Analysis 4 | 2026-08-04 09:40:11 | 2763 | ||||
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Structure-function linkage database Resource Report Resource Website 10+ mentions |
Structure-function linkage database (RRID:SCR_001375) | SFLD | database, data or information resource | A database of hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities. The SFLD classifies evolutionarily related enzymes according to shared chemical functions and maps these shared functions to conserved active site features. The classification is hierarchical, where broader levels encompass more distantly related proteins with fewer shared features. It thus serves as the analysis and archive site for superfamilies targeted by the Enzyme Function Initiative, and is developed by the Babbitt Laboratory in collaboration with the UCSF Resource for Biocomputing, Visualization, and Informatics. The resource also provides a collection of tools and data for investigating sequence-structure-function relationships and hypothesizing function. | software, enzyme, structure-function relationship, blast, reaction, superfamily, hidden markov model, sequence alignment, protein similarity network, sequence, structure, function |
uses: UCSF Chimera has parent organization: Resource for Biocomputing Visualization and Informatics |
NIGMS R01GM60595; NIGMS P01GM071790; NIGMS U54GM093342 |
PMID:18428763 PMID:16489747 |
Free, Freely available, | nlx_152532 | SCR_001375 | 2026-08-04 09:40:21 | 17 | ||||||
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ALFRED Resource Report Resource Website 50+ mentions |
ALFRED (RRID:SCR_001730) | ALFRED | storage service resource, data repository, service resource, database, data or information resource | A public curated compilation of allele frequency data on anthropologically defined human population samples linked to the molecular genetics-human genome databases. Only data on well defined population samples that are large enough to yield reasonably accurate frequencies and for polymorphisms sufficiently defined to be replicable can be included in ALFRED. Researchers wishing to have their data entered into ALFRED should contact them. Initially, ALFRED contained primarily data generated in the laboratories of K.K. and J.R. Kidd in the Department of Genetics at Yale, including extensive unpublished data. Data from the published literature are being entered into ALFRED in a systematic way, with a focus on polymorphisms studied in many different populations. ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation. ALFRED's focus is on allele frequencies in diverse anthropologically defined populations. It is not a compendium of human DNA polymorphisms but of frequencies of selected polymorphisms with an emphasis on those that have been studied in multiple populations. All of the data in ALFRED are considered to be in the public domain and available for use in research and teaching. ALFRED provides easy searching options including versatile "Keyword search" and also has numerous summary tables providing quick overviews of contents by chromosome, population, average heterozygosity, Fst and others, all available under various tabs from the ALFRED homepage. | allele frequency, dna polymorphism, haplotype, high throughput, genome, population, sample, education, polymorphism, allele, chromosome, heterozygosity, fst, loci, pathway, genetics, FASEB list | has parent organization: Yale School of Medicine; Connecticut; USA | NIGMS P01GM 57672 | PMID:19325849 PMID:11125124 PMID:12209575 |
Free, Freely Available | nif-0000-02541, r3d100012700 | https://doi.org/10.17616/R3GZ2J | SCR_001730 | The ALlele FREquency Database, ALlele FREquency Database | 2026-08-04 09:40:27 | 71 | ||||
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ASAP Resource Report Resource Website 50+ mentions |
ASAP (RRID:SCR_001849) | ASAP | storage service resource, data repository, service resource, database, data or information resource | Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene expression, genome, genome sequence, multiple genome sequence, post sequencing functional analysis, preliminary experiment, blast, annotation, data analysis service |
is used by: NIF Data Federation is listed by: SoftCite is related to: AmiGO has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
USDA 2001-52100-11316; NIGMS GM62994-02; NIGMS GM35682-15A1 |
PMID:12519969 | Free, Freely available | nif-0000-02571, r3d100010666 | https://omictools.com/asap-3-tool | SCR_001849 | A Systematic Annotation Package for Community Analysis of Genome, ASAP: a systematic annotation package for community analysis of genomes, A systematic annotation package for community analysis of genomes | 2026-08-04 09:40:29 | 53 | ||||
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PhosphoSitePlus: Protein Modification Site Resource Report Resource Website 500+ mentions |
PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) | PSP | portal, knowledge environment resource, data or information resource | A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published. | portal, mass spectroscopist, molecular model, mouse, post translational, subcellular localization, protein modification, post-translational modification, protein phosphorylation, protein structure, protein function, ubiquitinylation, acetylation, cellular component, cell type, visualization, data repository, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: Cytoscape is related to: ConsensusPathDB has parent organization: Cell Signaling Technology |
NCI ; NIAAA R44 AA014848; NIGMS R43 GM65768 |
PMID:22135298 | Free, Freely available | biotools:phosphositeplus, nif-0000-10399 | https://bio.tools/phosphositeplus | SCR_001837 | PhosphoSitePlus, PhosphoSite | 2026-08-04 09:40:29 | 903 | ||||
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SPP Resource Report Resource Website 1+ mentions |
SPP (RRID:SCR_001790) | data processing software, software application, software resource, data analysis software | R analysis and processing package for Illumina platform Chip-Seq data. | chip seq data, illummina, r package, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U01HG004258; NIGMS R01GM082798; NCRR UL1RR024920 |
DOI:10.1038/nbt.1508 | Free, Available for download, Freely available | OMICS_00425, biotools:spp | https://bio.tools/spp | https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq | SCR_001790 | SPP Package | 2026-08-04 09:40:28 | 9 | ||||
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SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | data analysis service, source code, analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available. | gene, genetic, genomic, amino acid, substitution, protein function, coding region, single nucleotide variant, coding indel, deletion, insertion, sequence, protein, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SIFT 4G has parent organization: Genome Institute of Singapore; Singapore; Singapore has parent organization: J. Craig Venter Institute |
Agency for Science Technology and Research ; NIGMS GM29009 |
PMID:19561590 PMID:12824425 PMID:11337480 DOI:10.1038/nprot.2009.86 |
Non-commercial | biotools:sift, OMICS_00137, nlx_154618 | http://sift.jcvi.org/, https://bio.tools/sift, https://sources.debian.org/src/sift/ | http://sift.bii.a-star.edu.sg/SIFT.html | SCR_012813 | Sorting Intolerant From Tolerant | 2026-08-04 09:43:05 | 10223 | |||
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Pathway Tools Resource Report Resource Website 10+ mentions |
Pathway Tools (RRID:SCR_013786) | software application, software resource, software toolkit, data management software | A software application which supplies software tools to develop and maintain pathway/genome databases (PGDBs). These include the development of organism-specific databases, metabolic reconstruction and metabolic-flux modeling, scientific visualization and web publishing of organism-specific databases, analysis of gene-expression and metabolomics datasets, comparative genome and pathway analyses, and analysis of biological networks. | software application, bioinformatics, software, software system, pathway genome database, PGDB, bio.tools |
is used by: BioCyc is used by: EcoCyc is used by: MetaCyc is listed by: BioCyc is listed by: bio.tools is listed by: Debian is related to: BioCyc is related to: MetaCyc is related to: EcoCyc is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: BioCyc |
NIGMS GM077678; NIGMS GM080746; NIGMS GM75742 |
DOI:10.1093/bib/bbp043 | biotools:pathway_tools | http://bioinformatics.ai.sri.com/ptools/ptools-overview.html, https://bio.tools/pathway_tools | SCR_013786 | Pathway Tools Bioinformatics Software, Pathway Tools Software | 2026-08-04 09:43:17 | 23 | ||||||
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Phenix Resource Report Resource Website 10000+ mentions |
Phenix (RRID:SCR_014224) | data processing software, image reconstruction software, software resource, software application, image analysis software | A Python-based software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Phenix includes programs for assessing data quality, experimental phasing, molecular replacement, model building, structure refinement, and validation. It also includes tools for reflection data and creating maps and models. Phenix can also be used for neutron crystallography. Tutorials and examples are available in the documentation tab. | automation, molecular structure, xray crystallography, neutron crystallography, image reconstruction software |
is listed by: SoftCite is affiliated with: Phaser is related to: MolProbity has parent organization: Lawrence Berkeley National Laboratory has parent organization: University of California at Berkeley; Berkeley; USA provides: Phenix.refine |
NIGMS | Available for download, Free for nonprofit work, Acknowledgement requested, For profit groups may access PHENIX through a Consortium agreement | https://www.phenix-online.org/documentation/ | SCR_014224 | Python-based Hierarchical ENvironment for Integrated Xtallography | 2026-08-04 09:43:22 | 10587 | |||||||
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FATCAT Resource Report Resource Website 100+ mentions |
FATCAT (RRID:SCR_014631) | web application, software resource | Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | web server, protein, comparison, structure, flexible protein structure, protein structure comparison, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: FATCAT Flexible Structural Neighborhood |
NIGMS GM101457; NIGMS GM63208; NIGMS GM076221; NSF DBI-0349600 |
PMID:14534198 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fatcat | https://bio.tools/fatcat | SCR_014631 | (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists, (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) | 2026-08-04 09:43:29 | 139 | |||||
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Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | data processing software, alignment software, data analysis software, software resource, sequence analysis software, software application, image analysis software | Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method. | sequence, analysis, long, reference, sequence, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: HLA-HD is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Bowtie |
NHGRI R01 HG006102; NIGMS R01 GM083873 |
PMID:22388286 | Free, Available for download, Freely available | biotools:bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml, https://github.com/BenLangmead/bowtie2, https://bio.tools/bowtie2 | SCR_016368 | , bowtie 2, bowtie2 v 2.2.3 | 2026-08-04 09:43:30 | 1745 | |||||
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WebGestalt: WEB-based GEne SeT AnaLysis Toolkit Resource Report Resource Website 1000+ mentions |
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) | WebGestalt | web application, data access protocol, software resource, web service | Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish. | proteomic, gene expression, genome wide association study, statistical analysis, functional genomics, protein protein interaction, pathway, regulatory module, analysis toolkit, web application |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Entrez Gene is related to: KEGG is related to: Pathway Commons is related to: WikiPathways is related to: PheWAS Catalog is related to: webgestaltr has parent organization: Vanderbilt University; Tennessee; USA |
NIAAA U01 AA016662; NIAAA U01 AA013512; NIDA P01 DA015027; NIMH P50 MH078028; NIMH P50 MH096972; NCI U24 CA159988; NIGMS R01 GM088822 |
PMID:24233776 PMID:15980575 PMID:14975175 |
Free, Freely available | OMICS_02222, nif-0000-30622 | http://bioinfo.vanderbilt.edu/webgestalt/ | SCR_006786 | GOTM, Gene Ontology Tree Machine, WebGestalt2, WEB-based GEne SeT AnaLysis Toolkit, WebGestalt | 2026-08-04 09:41:40 | 2760 | ||||
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HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism Resource Report Resource Website 50+ mentions |
HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism (RRID:SCR_007050) | HumanCyc | data analysis service, analysis service resource, software resource, production service resource, service resource, database, data or information resource | The HumanCyc database describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. A computational pathway analysis of the human genome assigned human enzymes to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary step toward quantitative modeling of metabolism. HumanCyc contains the complete genome sequence of Homo sapiens, as presented in Build 31. Data on the human genome from Ensembl, LocusLink and GenBank were carefully merged to create a minimally redundant human gene set to serve as an input to SRI''s PathoLogic software, which generated the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome''s annotation. SRI did not re-annotate the genome, but worked with the gene function assignments in Ensembl, LocusLink, and GenBank. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze. Also included are many links to other databases and publications. The Pathway Tools software/database bundle includes HumanCyc and the Pathway Tools software suite and is available under license. This form of HumanCyc is faster and more powerful than the Web version. | enzyme, function, functional, gene, genome, genomic, human, human genome, metabolic, metabolism, mitochondrion, nucleotide, pathway, position, reaction, sequence, metabolomics, gene expression, bioreaction, metabolic pathway, nutrition, FASEB list |
is listed by: BioCyc is related to: Pathway Commons is related to: ConsensusPathDB is related to: BioCyc is related to: Pathway Tools has parent organization: Stanford Research Institute International |
Pharmaceutical company ; NIGMS GM092729 |
PMID:15642094 | Public | r3d100011286, nif-0000-21206 | https://doi.org/10.17616/R3ZS72 | SCR_007050 | 2026-08-04 09:41:45 | 60 | |||||
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microRNA.org Resource Report Resource Website 1000+ mentions |
microRNA.org (RRID:SCR_006997) | microRNA.org | software resource, database, data or information resource | Database of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. This website enables users to explore: * The set of genes that are potentially regulated by a particular microRNA. * The implied cooperativity of multiple microRNAs on a particular mRNA. * MicroRNA expression profiles in various mammalian tissues. The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation. The microRNA Target Detection Software, miRanda, is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microrna, gene, expression, gene regulation, FASEB list |
is listed by: OMICtools is listed by: SoftCite |
NIGMS ; Atlantic Philanthropies ; Alfred W. Bressler Scholars Endowment Fund |
PMID:18158296 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03127, OMICS_00402 | SCR_006997 | microRNA.org - Targets and Expression | 2026-08-04 09:41:43 | 2648 | |||||
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Physiobank Resource Report Resource Website 10+ mentions |
Physiobank (RRID:SCR_006949) | PhysioBank | database, storage service resource, data repository, service resource, catalog, data or information resource | Archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. The PhysioBank Archives now contain over 700 gigabytes of data that may be freely downloaded. PhysioNet is seeking contributions of data sets that can be made freely available in PhysioBank. Contributions of digitized and anonymized (deidentified) physiologic signals and time series of all types are welcome. If you have a data set that may be suitable, please review PhysioNet''s guidelines for contributors and contact them. | physiologic, signal, data, biomedical, research, community, cardiopulmonary, neural, biomedical, health, cardiac, death, congestive heart failure, epilepsy, gait, disorder, sleep apnea, bibliographic, normal, physiologic signal, time series, FASEB list |
is used by: NIF Data Federation is used by: Integrated Datasets is related to: PhysioToolkit is parent organization of: Gait in Aging and Disease Database is parent organization of: Gait in Parkinson's Disease is parent organization of: Gait Dynamics in Neuro-Degenerative Disease Data Base is parent organization of: Noise Enhancement of Sensorimotor Function |
Healthy, Sudden cardiac death, Congestive heart failure, Epilepsy, Gait disorder, Sleep apnea, Aging | NIGMS ; NIBIB U01-EB-008577 |
PMID:10851218 | Free, The community can contribute to this resource, Acknowledgement requested | nlx_48903, r3d100011236 | https://doi.org/10.17616/R3J048 | SCR_006949 | 2026-08-04 09:41:43 | 39 | ||||
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Rankprop - Protein Ranking by Network Propagation Resource Report Resource Website |
Rankprop - Protein Ranking by Network Propagation (RRID:SCR_007159) | source code, web service, software resource, data access protocol, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on May,18,2020. Ranking algorithm that exploits global network structure of similarity relationships among proteins in database by performing diffusion operation on protein similarity network with weighted edges. Source code and web server for searching non-redundant protein database. Web server ranks proteins found in NRDB40 (from PairsDB) against query sequence of amino acids using Rankprop algorithm. | Ranking algorithm, network structure, protein database, similarity relationship, protein similarity network, weighted adges, non redundat protein database, protein database search | has parent organization: University of Washington; Seattle; USA | NSF EIA-0312706; NSF DBI-0243257; NIGMS GM74257 |
PMID:16723003 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_50351 | http://rankprop.gs.washington.edu/info.php | SCR_007159 | Rankprop | 2026-08-04 09:41:46 | 0 | |||||
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Function BIRN Resource Report Resource Website 1+ mentions |
Function BIRN (RRID:SCR_007291) | FBIRN | topical portal, portal, data or information resource | The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source. | fmri, 3d model, data storage, imaging, map, morphology, mri, neuroinformatics, segmentation, software, talairach, volume, warping, analyze, application, c++, csh/tcsh, data, database, database application, data resource, dicom, javascript, linux, magnetic resonance, nifti, ontology, pl/sql, posix/unix-like, python, quality metrics, spatial transformation, statistical operation, tcl/tk, unix shell, visualization, web resource, web service, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network is parent organization of: BXH/XCEDE Tools is parent organization of: FBIRN Image Processing Scripts |
NIGMS ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01 |
nif-0000-00070 | http://www.nitrc.org/projects/fbirn | http://nbirn.net/tools/browse_tools.shtm | SCR_007291 | Functional Imaging BIRN | 2026-08-04 09:41:49 | 2 | |||||
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Yeast snoRNA Database Resource Report Resource Website 1+ mentions |
Yeast snoRNA Database (RRID:SCR_007980) | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | A database of S. cerevisiae H/ACA and C/D box snoRNAs, useful for research on rRNA nucleotide modifications in the ribosome, especially those created by small nucleolar RNA:protein complexes (snoRNPs). The interactive service enables a user to visualize the positions of pseudouridines, 2'-O-methylations, and base methylations in three-dimensional space in the ribosome and also in linear and secondary structure formats of ribosomal RNA. The tools provide additional perspective on where the modifications occur relative to functional regions within the rRNA and relative to other nearby modifications. This package of tools is presented as a major enhancement of an existing but significantly upgraded yeast snoRNA database. The other key features of the enhanced database include details of the base pairing of snoRNAs with target RNAs, genomic organization of the yeast snoRNA genes, and information on corresponding snoRNAs and modifications in other model organisms. | saccharomyces cerevisiae |
is related to: 3D Ribosomal Modification Maps Database has parent organization: University of Massachusetts Amherst; Massachusetts; USA |
U.S. Public Health Service ; NIGMS GM19351 |
PMID:17283215 | nif-0000-03651 | http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html | SCR_007980 | Yeast snoRNA Database at UMass-Amherst | 2026-08-04 09:42:00 | 1 | ||||||
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LAPACK linear algebra library Resource Report Resource Website 10+ mentions |
LAPACK linear algebra library (RRID:SCR_008661) | software development tool, software resource, documentation generation software, software application, database, data or information resource | This project is the SimTK Core implementation of the extremely reliable, high speed linear algebra package LAPACK and the underlying BLAS library on which LAPACK is built. It uses ATLAS to generate hand tuned BLAS kernels for a variety of hardware platforms, including multiprocessors, using a variety of operating systems including Windows, Mac, and Red Hat Linux. These platforms are pre-built and make the binaries available as a single shared library which can be conveniently used by any program. This means that users who are not experts in high performance scientific computation can nonetheless use the fastest linear algebra methods available for their machines. | BLAS, linear algebra, database |
is related to: Simtk.org has parent organization: Simtk.org is required by: TomoMiner |
NIGMS U54 GM072970 | nif-0000-33176 | SCR_008661 | LAPACK | 2026-08-04 09:42:11 | 28 |
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We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
