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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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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
GOnet
 
Resource Report
Resource Website
1+ mentions
GOnet (RRID:SCR_018977) web service, data access protocol, analysis service resource, software resource, production service resource, service resource Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools is listed by: Debian
is listed by: bio.tools
works with: Gene Ontology
NIH Common Fund ;
NIGMS ;
NHGRI R24 HG010032;
NIAID U19 AI118610;
NIAID U19 AI118626
PMID:30526489 biotools:GOnet https://github.com/mikpom/gonet
https://bio.tools/GOnet
SCR_018977 2026-02-16 09:49:37 3
ColabFold
 
Resource Report
Resource Website
100+ mentions
ColabFold (RRID:SCR_025453) source code, software resource Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding. prediction of protein structures and complexes, protein folding, protein structure prediction, Max Planck Society ;
University of Göttingen ;
National Research Foundation of Korea ;
Seoul National University ;
NIH Office of the Director DP5OD026389;
NIAID R21AI156595;
NSF
PMID:35637307 Free, Available for download, Freely available https://github.com/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb SCR_025453 2026-02-15 09:23:00 391
Type 1 Diabetes Genetics Consortium
 
Resource Report
Resource Website
1+ mentions
Type 1 Diabetes Genetics Consortium (RRID:SCR_001557) T1DGC research forum portal, resource, topical portal, portal, data or information resource, disease-related portal Data and biological samples were collected by this consortium organizing international efforts to identify genes that determine an individual risk of type 1 diabetes. It originally focused on recruiting families with at least two siblings (brothers and/or sisters) who have type 1 diabetes (affected sibling pair or ASP families). The T1DGC completed enrollment for these families in August 2009. They completed enrollment of trios (father, mother, and a child with type 1 diabetes), as well as cases (people with type 1 diabetes) and controls (people with no history of type 1 diabetes) from populations with a low prevalence of this disease in January 2010. T1DGC Data and Samples: Phenotypic and genotypic data as well as biological samples (DNA, serum and plasma) for T1DGC participants have been deposited in the NIDDKCentral Repositories for future research. gene, genetics, genotyping, analytic, dna, serum, plasma, data set, biomaterial supply resource, phenotypic, genotypic, autoantibody, hla, phenotype, genotype is listed by: One Mind Biospecimen Bank Listing
is listed by: NIDDK Information Network (dkNET)
is listed by: NIDDK Central Repository
Type 1 diabetes, Diabetes NIDDK ;
NIAID ;
NHGRI ;
JDRF
PMID:17130525 Free, Freely available nlx_152867 SCR_001557 Type 1 Diabetes Genetics Consortium (T1DGC) 2026-02-16 09:45:31 2
Immune Tolerance Network (ITN)
 
Resource Report
Resource Website
10+ mentions
Immune Tolerance Network (ITN) (RRID:SCR_001535) ITN funding resource, clinical trial, topical portal, portal, data or information resource International clinical research consortium dedicated to the clinical evaluation of novel tolerogenic approaches for the treatment of autoimmune diseases, asthma and allergic diseases, and the prevention of graft rejection. They aim to advance the clinical application of immune tolerance by performing high quality clinical trials of emerging therapeutics integrated with mechanism-based research. In particular, they aim to: * Establish new tolerance therapeutics * Develop a better understanding of the mechanisms of immune function and disease pathogenesis * Identify new biomarkers of tolerance and disease Their goals are to identify and develop treatment game changers for tolerance modulating therapies for the treatment of immune mediated diseases and disabling conditions, and to conduct high quality, innovative clinical trials and mechanistic studies not likely to be funded by other sources or to be conducted by private industry that advance our understanding of immunological disorders. In the Immune Tolerance Network's (ITN) unique hybrid academic/industry model, the areas of academia, government and industry are integral to planning and conducting clinical studies. They develop and fund clinical trials and mechanistic studies in partnership. Their development model is a unique, interactive process. It capitalizes on their wide-ranging, multidisciplinary expertise provided by an advisory board of highly respected faculty from institutions worldwide. This model gives investigators special insight into developing high quality research studies. The ITN is comprised of leading scientific and medical faculty from more than 50 institutions in nine countries worldwide and employs over 80 full-time staff at the University of California San Francisco (UCSF), Bethesda, Maryland and Benaroya Research Institute in Seattle, Washington. immune tolerance, prevent, cure, disease, multiple sclerosis, therapy, biomarker, transplant is listed by: NIDDK Information Network (dkNET)
is listed by: NIDDK Research Resources
is related to: Immune Tolerance Network TrialShare
has parent organization: Benaroya Research Institute
Type 1 diabetes, Diabetes, Allergy, Asthma, Autoimmune disease, Transplantation, Immunological disorder NIAID N01AI15416 nlx_152838 SCR_001535 2026-02-16 09:45:30 14
Cinteny
 
Resource Report
Resource Website
10+ mentions
Cinteny (RRID:SCR_002147) web application, software resource, database, data or information resource Online database for finding and analyzing syntenic regions across multiple genomes and measuring the extent of genome rearrangement using reversal distance as a measure. syntenic genes, genome rearrangement, online genome database is listed by: OMICtools NIAID R21 AI055338;
NIAMS R01 AR050688
PMID:17343765 Free, Freely available OMICS_00931 SCR_002147 Cinteny Server for Synteny Identification and Analysis of Genome Rearrangement 2026-02-16 09:45:39 17
ASPGD
 
Resource Report
Resource Website
100+ mentions
ASPGD (RRID:SCR_002047) ASPGD, ASPGD LOCUS, ASPGD REF data repository, database, storage service resource, service resource, data or information resource Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions. function, gene, gene name, annotation, aspergillus, aspergillus nidulans, chromosome, community, dna, genome, genomic, localization, orthology, phenotype, protein, protein-coding genes, s. cerevisiae, sequence, allele, data analysis service, bio.tools, FASEB list is used by: NIF Data Federation
is listed by: bio.tools
is listed by: Debian
is related to: Candida Genome Database
is related to: AmiGO
has parent organization: Stanford University School of Medicine; California; USA
has parent organization: Broad Institute
NIAID R01 AI077599 PMID:19773420 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-12244, biotools:aspgd http://www.aspergillusgenome.org/
https://bio.tools/aspgd
SCR_002047 Aspergillus Genome Database, ASPGD REF, ASPGD LOCUS 2026-02-16 09:45:38 212
Stanford Genomics Service Center Core Facility
 
Resource Report
Resource Website
10+ mentions
Stanford Genomics Service Center Core Facility (RRID:SCR_002050) SFGF, service resource, core facility, access service resource Stanford Genomics formerly Stanford Functional Genomics Facility provides services for high throughput sequencing, single cell assays, gene expression and genotyping studies utilizing microarray and real time PCR, and related services. High throughput sequencing (Illumina HiSeq 4000, NextSeq 500, MiSeq and MiniSeq), microarray gene expression and genotyping services (Affymetrix, Agilent and Illumina). Provides 24/7 access to instruments, equipment and software utilized within genomics field. ABRF, Stanford Genomics, genomics, high throughput sequencing, single cell assays, gene expression, genotyping, microarray, real time PCR, is listed by: ABRF CoreMarketplace
has parent organization: Stanford University; Stanford; California
NIAID ;
Comprehensive Cancer Center
Open SCR_008627, ABRF_200, nif-0000-31997, nif-0000-12246 https://coremarketplace.org/?FacilityID=200&citation=1 http://www.microarray.org/sfgf/ SCR_002050 Stanford Medicine Stanford Functional Genomics Facility, Stanford University Functional Genomics Core Facility, Stanford Functional Genomics Facility, Stanford Genomics, Stanford Genomics Service Center, Stanford School of Medicine Stanford Functional Genomics Facility 2026-02-16 09:45:43 10
ReBATE
 
Resource Report
Resource Website
ReBATE (RRID:SCR_017139) software resource, software toolkit Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity . compare, relief, feature, algorithm, data, mining, variable, heterogeneous, pattern, genetic has parent organization: University of Pennsylvania; Philadelphia; USA NIAID AI116794;
NIDDK DK112217;
NIEHS ES013508;
NEI EY022300;
NHLBI HL134015;
NLM LM009012;
NLM LM010098;
NLM LM011360;
NCATS TR001263;
Warren Center for Network and Data Science
PMID:30030120 Free, Available for download, Freely available https://epistasislab.github.io/ReBATE/ SCR_017139 Relief Based Algorithm Training Environment 2026-02-16 09:49:10 0
MaAsLin2
 
Resource Report
Resource Website
100+ mentions
MaAsLin2 (RRID:SCR_023241) software resource, software toolkit SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. Microbiome Multivariable Associations with Linear Models, NSF DEB-2028280;
NIAID U19AI110820;
NHGRI R01HG005220;
NIDDK R24DK110499;
NIDDK U54DK102557
DOI:10.1371/journal.pcbi.1009442 Free, Available for download, Freely available https://huttenhower.sph.harvard.edu/maaslin/ SCR_023241 2026-02-16 09:50:36 170
Pathogens Portal Node Toolbox
 
Resource Report
Resource Website
Pathogens Portal Node Toolbox (RRID:SCR_027086) software toolkit, source code, software resource Software package and code for Pathogen Portal node (i.e. a local Pathogens Portal, such as the Swedish and Dutch Pathogens Portals). Allows users to create their own node quickly and easily. Pathogen Portal node, Swedish Pathogens Portal, Dutch Pathogens Portal, SciLifeLab NIAID U24AI183840 Free, Available for download, Freely available SCR_027086 2026-02-16 09:51:18 0
Penn machine learning benchmark repository
 
Resource Report
Resource Website
Penn machine learning benchmark repository (RRID:SCR_017138) PMLB data set, data or information resource Python wrapper for Penn Machine Learning Benchmark data repository. Large, curated repository of benchmark datasets for evaluating supervised machine learning algorithms. Part of PyPI https://pypi.org/ benchmark, suite, machine, learning, evaluation, comparison, repository, curated, dataset NIAID AI116794;
NIDDK DK112217;
NIEHS ES013508;
NEI EY022300;
NHLBI HL134015;
NLM LM009012;
NLM LM010098;
NLM LM011360;
NCATS TR001263;
Warren Center for Network and Data Science
PMID:29238404 Free, Restricted https://github.com/EpistasisLab/penn-ml-benchmarks SCR_017138 Penn Machine Learning Benchmark 2026-02-16 09:49:10 0
New York University School of Medicine IonLab Core Facility
 
Resource Report
Resource Website
1+ mentions
New York University School of Medicine IonLab Core Facility (RRID:SCR_021754) service resource, core facility, access service resource Electrophysiology core facility that is part of Ion Channels and Transporters in Immunity Research Program.Research area includes ion channel and transporter function and ionic signaling in immune cells.Users who are studying other cell types or organ systems are welcome.Provides assistance with experimental design, training, implementation, and data analysis. USEDit, ABRF, ion channel, transporter function, ionic signaling, immune cells is listed by: ABRF CoreMarketplace
has parent organization: New York University School of Medicine; New York; USA
NIAID AI097302 open ABRF_1221 https://coremarketplace.org/?FacilityID=1221 SCR_021754 IonLab 2026-02-16 09:50:08 8
ClipKIT
 
Resource Report
Resource Website
10+ mentions
ClipKIT (RRID:SCR_026411) software application, software resource, source code Software fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others. Multiple sequence alignment-trimming algorithm for accurate phylogenomic inference. multiple sequence, alignment trimming, accurate phylogenomic inference, Howard Hughes Medical Institute ;
National Science Foundation ;
Guggenheim Foundation ;
Burroughs Wellcome Fund ;
NIAID 1R56AI146096;
Zhejiang University ;
Fundamental Research Funds for the Central Universities
PMID:33264284 Free, Available for download, Freely available SCR_026411 2026-02-16 09:51:09 35
Fungal Genome Initiative
 
Resource Report
Resource Website
10+ mentions
Fungal Genome Initiative (RRID:SCR_003169) FGI data set, data or information resource Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics. sequence, fungi, gene annotation, genome is listed by: 3DVC
has parent organization: Broad Institute
NHGRI ;
NSF ;
NIAID ;
USDA
Free, Freely available nif-0000-30591 SCR_003169 2026-02-16 09:45:56 18
InterProSurf
 
Resource Report
Resource Website
InterProSurf (RRID:SCR_027791) web application, data access protocol, software resource, web service Web server for predicting interacting sites on protein surfaces. Analyzes solvent-accessible residues likely to participate in PPIs.Predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of protein complex. Analyzes solvent-accessible residues, predicting interacting sites on protein surfaces, interacting amino acid residues in proteins, proteins that are most likely to interact with other proteins, NIAID R21 AI055746;
NIAID R01 AI064913
PMID:17933856 Free, Freely available, SCR_027791 2026-02-16 09:51:28 0
Cryptococcus Neoformans cDNA Sequencing
 
Resource Report
Resource Website
1+ mentions
Cryptococcus Neoformans cDNA Sequencing (RRID:SCR_008462) software resource Cryptococcus neoformans is an encapsulated yeast that infects the human host via the respiratory tract where it usually causes an inapparent infection. In the susceptible host, it may disseminate, typically producing a chronic and life-threatening meningitis. The Cryptococcus neoformans serotypes A and D are responsible for the overwhelming majority of pulmonary infections in AIDS patients. Cryptococcus neoformans strain H99 Latest Data Release - May 19, 2004 To date, we have isolated ca. 3750 cDNA clones from Cryptococcus neoformans strain H99 in collaboration with Drs. Juneann Murphy and Dave Dyer at the University of Oklahoma Health Sciences Center''s Department of Microbiology and Immunology in Oklahoma City and Kent Buchanan at the Tulane University Medical School, New Orleans, LA. The Cryptococcus neoformans strain H99 EST''s have been generated by Doris Kupfer, Heather Bell, Sunkyoung So, Yuong Tang, and Jennifer Lewis at the University of Oklahoma''s Advanced Center for Genome Technology, in the Department of Chemistry and Biochemistry. We now have end sequenced all available templates (ca. 7500 reactions) from both ends of the directionally cloned inserts after excision into pBlueScript SK-. . All of our data is available from our ftp site, and we now have added the ability to perform blast searches on this data. A keyword search of a blastx search of GenBank with this data also is available but we have not yet linked this to a unigene database as the number of EST''s sequenced doesn''t warrent this yet. has parent organization: University of Oklahoma; Oklahoma; USA NIAID AI147079 nif-0000-30397 SCR_008462 cDNA Sequencing 2026-02-14 02:01:34 1
MS-GF+
 
Resource Report
Resource Website
100+ mentions
MS-GF+ (RRID:SCR_015646) software resource Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. protein idenitification, peptide sequence, ms, ms spectrum, proteomic, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
has parent organization: Pacific Northwest National Laboratory
NCRR RR018522;
NCRR 1-P41-RR024851;
NIAID ;
W.R. Wiley Environmental Molecular Science Laboratory
PMID:25358478 Free, Available for download, Acknowledgment requested biotools:ms-gf https://github.com/sangtaekim/msgfplus
https://bio.tools/ms-gf
SCR_015646 MSGF+, MSGFPlus 2026-02-14 02:03:07 155
Add Health (National Longitudinal Study of Adolescent Health)
 
Resource Report
Resource Website
10+ mentions
Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) Add Health data or information resource, database Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database. adolescent, longitudinal, adult human, interview, social, behavior, health, early adult human, FASEB list has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA Aging NICHD ;
NCI ;
CDC ;
NIAID ;
NIMHD ;
NIDCD ;
NIGMS ;
NIMH ;
NINR ;
NIA ;
NIAAA ;
NIDA ;
NSF ;
NIH ;
Department of Health and Human Services ;
MacArthur Foundation ;
Robert Wood Johnson Foundation
Restricted use nif-0000-00621 SCR_007434 National Longitudinal Study of Adolescent Health 2026-02-14 02:06:03 37
CharProtDB: Characterized Protein Database
 
Resource Report
Resource Website
CharProtDB: Characterized Protein Database (RRID:SCR_005872) CharProtDB data or information resource, database The Characterized Protein Database, CharProtDB, is designed and being developed as a resource of expertly curated, experimentally characterized proteins described in published literature. For each protein record in CharProtDB, storage of several data types is supported. It includes functional annotation (several instances of protein names and gene symbols) taxonomic classification, literature links, specific Gene Ontology (GO) terms and GO evidence codes, EC (Enzyme Commisssion) and TC (Transport Classification) numbers and protein sequence. Additionally, each protein record is associated with cross links to all public accessions in major protein databases as ��synonymous accessions��. Each of the above data types can be linked to as many literature references as possible. Every CharProtDB entry requires minimum data types to be furnished. They are protein name, GO terms and supporting reference(s) associated to GO evidence codes. Annotating using the GO system is of importance for several reasons; the GO system captures defined concepts (the GO terms) with unique ids, which can be attached to specific genes and the three controlled vocabularies of the GO allow for the capture of much more annotation information than is traditionally captured in protein common names, including, for example, not just the function of the protein, but its location as well. GO evidence codes implemented in CharProtDB directly correlate with the GO consortium definitions of experimental codes. CharProtDB tools link characterization data from multiple input streams through synonymous accessions or direct sequence identity. CharProtDB can represent multiple characterizations of the same protein, with proper attribution and links to database sources. Users can use a variety of search terms including protein name, gene symbol, EC number, organism name, accessions or any text to search the database. Following the search, a display page lists all the proteins that match the search term. Click on the protein name to view more detailed annotated information for each protein. Additionally, each protein record can be annotated. protein, annotation, functional annotation, taxonomic classification, literature, gene ontology, evidence code, enzyme commission, transport classification, protein sequence, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
has parent organization: J. Craig Venter Institute
NHGRI R01 HG004881;
NIAID contract HHSN266200100038C
PMID:22140108 biotools:charprotdb, nlx_149421 https://bio.tools/charprotdb SCR_005872 Characterized Protein Database 2026-02-14 02:06:25 0
ApiDB CryptoDB
 
Resource Report
Resource Website
10+ mentions
ApiDB CryptoDB (RRID:SCR_013455) ApiDB CryptoDB data or information resource, database An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data cryptosporidium parvum, cryptosporidium, cryptosporidium genome, cryptosporidium orf, cryptosporidium sage tag alignments, cryptosporidium snp, genomic sequence, dna motif, snp, est, orf, data set, bio.tools uses: SynView
is listed by: 3DVC
is listed by: Debian
is listed by: bio.tools
has parent organization: Eukaryotic Pathogen Database Resources
NIAID contract HHSN266200400037C PMID:16381902 nif-0000-02698, biotools:cryptodb https://bio.tools/cryptodb http://cryptodb.org/ SCR_013455 CryptoDB, Cryptosporidium Genomics Resource 2026-02-14 02:06:43 25

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