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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | ||||||
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SpikeHunter Resource Report Resource Website 1+ mentions |
SpikeHunter (RRID:SCR_024831) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins. | identifying phage tailspike proteins, phage tailspike protein, deplolymerase, right-handed beta-helix, | NLM ; NSF |
PMID:37503040 | Free, Available for download, Freely available | SCR_024831 | 2026-02-16 09:50:56 | 1 | |||||||||
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T Cell ExTRECT Resource Report Resource Website |
T Cell ExTRECT (RRID:SCR_027742) | software toolkit, source code, software resource | Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes. | T-cell, T cell receptor excision circle, WES data, hg19 or hg38 aligned genomes, | NHLBI U54HL108460; NCATS UL1TR000100; NCI R21CA177519; NCI P30CA023100; NCI U01CA196406; NLM T15LM011271; NIH Office of the Director DP5OD017937; NSF |
PMID:34497419 | Free, Available for download, Freely available | SCR_027742 | , T cell exome TREC, T cell exome T cell Receptor Excision Circle | 2026-02-16 09:51:28 | 0 | ||||||||
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OligoGenome Resource Report Resource Website 1+ mentions |
OligoGenome (RRID:SCR_006025) | OligoGenome | data or information resource, database, resource | The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets. | oligonucleotide, genome, probe, coding region, oligonucleotide sequence, chromosome | has parent organization: Stanford University; Stanford; California | NHGRI RC2 HG005570-01; NCI R21CA12848; NCI 5K08CA96879?6; NIDDK DK56339; NHGRI 2P01HG000205; NLM T15-LM007033; Doris Duke Clinical Foundation ; Reddere Foundation ; Liu Bie Ju Cha and Family Fellowship in Cancer ; Wang Family Foundation ; Howard Hughes Medical Foundation |
PMID:22102592 | nlx_151422 | SCR_006025 | Stanford Human Oligo Genome Project, Human OligoGenome Resource, Stanford Human Oligo Genome, Human Oligo Genome, Human OligoGenome | 2026-02-14 02:01:13 | 2 | ||||||
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Coremine Medical Resource Report Resource Website 1+ mentions |
Coremine Medical (RRID:SCR_005323) | Coremine Medical | service resource | Service to access comprehensive information on diseases, drugs, treatments and medical biology. It is ideal for those seeking an overview of a complex subject while allowing the possibility to drill down to specific details. Search results are presented in a dashboard format comprized of panels containing various categories of information ranging from introductory sources to the latest scientific articles. | disease, drug, treatment, medical biology, text mining, health, medicine, biology, network, database |
is listed by: OMICtools is related to: MeSH is related to: Entrez Gene is related to: MEDLINE is related to: PubMed is related to: DrugBank is related to: Gene Ontology is related to: UniProt has parent organization: PubGene |
NLM ; European Union FP7 ; Research Council of Norway ; Innovation Norway |
Copyrighted | OMICS_01179 | SCR_005323 | 2026-02-14 02:01:05 | 6 | |||||||
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NCBI BioProject Resource Report Resource Website 10000+ mentions |
NCBI BioProject (RRID:SCR_004801) | data or information resource, database | Database of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project''''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP. | genome sequencing, sequencing, genotype, phenotype, sequence variant, epigenetic, data set, genome, assembly, annotation, mapping, cellular organism, gene mapping, gene expression, biological tag, gene rearrangement, genetic algorithm, genetic code, genetic genealogy, gold standard, bio.tools |
is listed by: 3DVC is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: INSDC has parent organization: NCBI |
NLM | PMID:22139929 | Free, Freely available | r3d100013330, nlx_143909, biotools:bioproject | http://www.ncbi.nlm.nih.gov/genomeprj https://bio.tools/bioproject https://doi.org/10.17616/R31NJMS2 |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=genomeprj | SCR_004801 | NCBI BioProject Database, BioProject | 2026-02-14 02:05:53 | 13968 | ||||
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Developmental and Reproductive Toxicology Database Resource Report Resource Website 1+ mentions |
Developmental and Reproductive Toxicology Database (RRID:SCR_002326) | DART | data or information resource, database | Bibliographic database providing references to developmental and reproductive toxicology literature on the National Library of Medicine's Toxicology Data Network. It covers teratology and other aspects of developmental and reproductive toxicology. It contains over 200,000 references to literature published since 1965. DART/ETIC is easily accessible and free of charge. Search by subject terms, title words, chemical name, Chemical Abstracts Service Registry Number (RN), and author. Search results can easily be viewed, printed or downloaded. Search results are displayed in relevancy ranked order, but may be sorted by publication date, author or title. | chemical, developmental, medicine, reproductive, teratology, toxicology, development | has parent organization: National Library of Medicine | U.S. Environmental Protection Agency ; NIEHS ; National Center for Toxicological Research ; NLM |
PMID:24698185 | Free | nif-0000-21110 | SCR_002326 | 2026-02-14 02:06:09 | 1 | ||||||
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Protein Clusters Resource Report Resource Website 1+ mentions |
Protein Clusters (RRID:SCR_003459) | ProtClustDB | data or information resource, database | Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP | bacteriophage, mitochondrial organelle, chloroplast organelle, plasmid, phylogeny, nucleotide sequence, chloroplast, dna, virus, genome, organelle, gold standard |
is listed by: re3data.org has parent organization: NCBI |
NIH ; Intramural Research Program ; NLM |
PMID:18940865 | Free, Available for download, Freely available | nif-0000-03354, r3d100010861 | https://doi.org/10.17616/R3TS52 | SCR_003459 | Protein Clusters Database, NCBI Protein Clusters, Entrez Protein Clusters | 2026-02-14 02:05:44 | 4 | ||||
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NMR Restraints Grid Resource Report Resource Website |
NMR Restraints Grid (RRID:SCR_006127) | NMR Restraints Grid | image collection, data or information resource, database | Original NMR (nuclear magnetic resonance) data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED) respectively as described in the references. There are 9,672,968 parsed constraints in 7159 entries. (Mar. 2013) | nmr, biomolecule, structure, magnetic resonance, database of converted restraint, filtered restraints database, fred, mri, protein, nucleic acid |
is related to: NRG-CING is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Biological Magnetic Resonance Data Bank (BMRB) |
European Union FP6 contract QLG2-CT-2000-01313; NLM LM05799 |
PMID:12766409 PMID:16041478 |
Please acknowledge the references in publications where the data from this site have been utilized. | nlx_151606 | SCR_006127 | BMRB NMR Restraints Grid | 2026-02-15 09:19:09 | 0 | |||||
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Virtual Human Embryo Resource Report Resource Website 10+ mentions |
Virtual Human Embryo (RRID:SCR_006921) | VHE | image collection, data or information resource, database | A digital image database of serially sectioned human embryos from the Carnegie Collection originally developed as a collaboration between embryologist Dr. Raymond Gasser at Louisiana State University Health Science Center (LSUHSC) and the Human Developmental Anatomy Center (HDAC) in Washington D.C. The aim of the project is to increase understanding of human embryology and to encourage study of human embryonic development by providing students and researchers with reliable resources for human embryo morphology. The VHE project has several components: * DREM: The Digitally Reproduced Embryonic Morphology (DREM) project, with funding from NICHD, project has produced 27 image databases of labeled serial sections from representative human embryos at each of the 23 Carnegie stages. These databases, together with animations and reconstructions of the embryos are available on DVD and CD. * HEIRLOOM: The HEIRLOOM Collection (Human Embryo Imaging and Reconstruction, Library Of Online Media) was funded by the National Library of Medicine to provide greater access to the DREM databases. NLM provided funding to set up this website and to produce additional 3D-reconstructions and animations that are included on the DREM disks. Original website, http://virtualhumanembryo.lsuhsc.edu/HEIRLOOM/heirloom.htm * EHD: Starting in 2011, The Endowment for Human Development (EHD) will also host the VHE databases. They have made the project accessible to everyone and include a comprehensive cataloging of all the terms used to label the embryos. Their website enables users to browse through the complete VHE atlas of human embryology, http://www.ehd.org/virtual-human-embryo/ | embryo, embryonic human, development, embryology, morphology, carnegie stage, 3d-reconstruction | has parent organization: Louisiana State University Health Sciences Center New Orleans; Louisiana; USA | NICHD R01 HD37811; NLM R01 LM007591 |
nlx_152029 | SCR_006921 | Virtual Human Embryo Project | 2026-02-15 09:19:24 | 23 | |||||||
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Limitation-Recognizer Resource Report Resource Website |
Limitation-Recognizer (RRID:SCR_018747) | software application, data processing software, data analysis software, software resource | Software tool to recognize self acknowledged limitation sentences in biomedical articles. Automatic recognition of self acknowledged limitations in clinical research literature to support efforts in improving research transparency. | ASWG, automatic recognition, self acknowledged limitation, clinical research literature, research transparency, limitation sentence recognition |
uses: Stanford CoreNLP has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NLM | PMID:29718377 | Free, Freely available | SCR_018748 | SCR_018747 | limitationrecognizer, limitation recognizer, limitation-recognizer | 2026-02-15 09:22:16 | 0 | ||||||
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ClinicalTrials.gov Resource Report Resource Website 10000+ mentions |
ClinicalTrials.gov (RRID:SCR_002309) | ClinicalTrials.gov | clinical trial, data repository, database, storage service resource, catalog, service resource, data or information resource | Registry and results database of federally and privately supported clinical trials conducted in United States and around world. Provides information about purpose of trial, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care professionals.Offers information for locating federally and privately supported clinical trials for wide range of diseases and conditions. Research study in human volunteers to answer specific health questions. Interventional trials determine whether experimental treatments or new ways of using known therapies are safe and effective under controlled environments. Observational trials address health issues in large groups of people or populations in natural settings. ClinicalTrials.gov contains trials sponsored by National Institutes of Health, other federal agencies, and private industry. Studies listed in database are conducted in all 50 States and in 178 countries. | clinical trial, intervention, treatment, therapy, observation, drug, adverse event, result, outcome, data set, FASEB list |
is used by: NIF Data Federation is used by: Patients to Trials Consortium is used by: Corengi is used by: Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations is used by: Limited Access Datasets From NIMH Clinical Trials is used by: Integrated Clinical Trials is used by: Integrated Datasets is used by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases lists: Epidemiology of Diabetes Interventions and Complications lists: Behavior Enhances Drug Reduction of Incontinence lists: Diabetes Prevention Program lists: Diabetes Prevention Program Outcomes Study lists: Folic Acid for Vascular Outcome Reduction in Transplantation lists: Family Investigation of Nephropathy of Diabetes lists: Frequent Hemodialysis Network Daily Trial lists: HALT PKD lists: HEALTHY study lists: RiVuR lists: Study of Nutrition in Acute Pancreatitis lists: TINSAL-T2D lists: Treatment Options for type 2 Diabetes in Adolescents and Youth lists: TOMUS lists: TRIGR lists: CATIE - Alzheimers Disease lists: CATIE - Clinical Antipsychotic Trials in Intervention Effectiveness lists: Gastroparesis Clinical Research Consortium lists: Diabetes Control and Complications Trial lists: Efficacy and Mechanisms of Glutamine Dipeptide in the Surgical Intensive Care Unit lists: Evaluating Predictors and Interventions in Sphincter of Oddi Dysfunction lists: Frequent Hemodialysis Network Nocturnal Trial lists: Minimally Invasive Surgical Therapies Treatment Consortium for Benign Prostatic Hyperplasia lists: Focal Segmental Glomerulosclerosis in Children and Young Adults Interventional Study lists: Complementary and Alternative Medicine for Urological Symptoms lists: Program to Reduce Incontinence by Diet and Exercise lists: TEDDY lists: Diabetes Prevention Type 1 lists: HALT-C Trial lists: Viral Resistance to Antiviral Therapy of Chronic Hepatitis C lists: Medical Therapy of Prostatic Symptoms is listed by: OMICtools is related to: NIMH Clinical Trials is related to: cthist is related to: Clinical Trials Viewer has parent organization: National Library of Medicine is parent organization of: LinkedCT is parent organization of: Functional Dyspepsia Treatment Trial is parent organization of: High-dose Ursodiol Therapy of Primary Sclerosing Cholangitis is parent organization of: Peginterferon and Ribavirin for Pediatric Patients with Chronic Hepatitis C is parent organization of: Maryland Genetics of Interstitial Cystitis is parent organization of: Treatment of SSRI-resistant Depression in Adolescents (TORDIA) is parent organization of: Systematic Treatment Enhancement Program for Bipolar Disorder (STEP-BD) is parent organization of: TADS - Treatment for Adolescents with Depression Study is parent organization of: Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations is parent organization of: Renin Angiotensin System Study |
NIH ; NLM |
PMID:27631620 | Free, Freely available | OMICS_01792, r3d100010211, nif-0000-21091 | https://doi.org/10.17616/R3H887 | SCR_002309 | Clinical Trials Database, ClinicalTrials.gov, Clinicaltrials.gov: A Service Of The National Institutes Of Health, ClinicalTrials, Clinical Trials gov | 2026-02-16 09:45:43 | 49607 | ||||
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dbSNP Resource Report Resource Website 5000+ mentions |
dbSNP (RRID:SCR_002338) | dbSNP | data repository, database, storage service resource, service resource, data or information resource | Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource. | insertion, polymorphism, short, deletion, single, nucleotide, genetic, variation, genomics, genotype, disease, allele, microsatellite, marker, multinucleotide, heterozygous, sequence, gold standard, bio.tools |
is used by: ExAc is used by: GEMINI is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl Variation is related to: GWAS Central is related to: TopoSNP is related to: GWAS Central has parent organization: NCBI has parent organization: National Human Genome Research Institute works with: Open Regulatory Annotation Database |
NLM | PMID:21154707 | Free, Freely available | nif-0000-02734, biotools:dbsnp, OMICS_00264, r3d100010652 | http://www.ncbi.nlm.nih.gov/projects/SNP/ https://bio.tools/dbsnp https://doi.org/10.17616/R3XG81 |
SCR_002338 | dbSNP: Database for Short Genetic Variations, Entrez SNP - Single Nucleotide Polymorphism, SNV Database, NCBI SNV Database, NCBI Short Genetic Variations Database, NCBI Short Genetic Variations, NCBI Single Nucleotide Polymorphism, Entrez SNP, dbSNP, NCBI Short Genetic Variations (SNV) database | 2026-02-16 09:45:48 | 8619 | ||||
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Protein Information Resource Resource Report Resource Website 50+ mentions |
Protein Information Resource (RRID:SCR_002837) | PIR | data or information resource, topical portal, portal | Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. Provides databases and protein sequence analysis tools to scientific community, including Protein Sequence Database which grew out from the Atlas of Protein Sequence and Structure. Conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PRO. | annotation, genomic, mining, protein, protein bioinformatics, proteomic, research, sequence, structure, systems biology, gold standard, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: NCBI Protein Database has parent organization: University of Delaware; Delaware; USA has parent organization: Georgetown University; Washington D.C.; USA is parent organization of: PRO is parent organization of: PIRSF is parent organization of: PR is parent organization of: UniProt |
NLM P41 LM05798 | PMID:12520019 | Free, Freely available | biotools:pir, nif-0000-21327, nif-0000-00143, SCR_008229 | https://bio.tools/pir http://pir.georgetown.edu/ |
SCR_002837 | PIR - Protein Information Resource | 2026-02-16 09:45:53 | 83 | ||||
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SHRINE Resource Report Resource Website 1+ mentions |
SHRINE (RRID:SCR_006293) | SHRINE | software application, source code, software resource | Software providing a scalable query and aggregation mechanism that enables federated queries across many independently operated patient databases. This platform enables clinical researchers to solve the problem of identifying sufficient numbers of patients to include in their studies by querying across distributed hospital electronic medical record systems. Through the use of a federated network protocol, SHRINE allows investigators to see limited data about patients meeting their study criteria without compromising patient privacy. This software should greatly enable population-based research, assessment of potential clinical trials cohorts, and hypothesis formation for followup study by combining the EHR assets across the hospital system. In order to obtain the maximum number of cases representing the study population, it is useful to aggregate patient facts across as many sites as possible. Cutting across institutional boundaries necessitates that each hospital IRB remain in control, and that their local authority is recognized for each and every request for patient data. The independence, ownership, and legal responsibilities of hospitals predetermines a decentralized technical approach, such as a federated query over locally controlled databases. The application comes with the SHRINE Core Ontology but it can be used with any ontology, even one that is disease specific. The Core Ontology is designed to enable the widest range of studies possible using facts gathered in the EMR during routine patient care. SHRINE allows multiple ontologies to be used for different research purposes on the same installed systems. | software network, clinical database, data sharing, clinical, medical record, federated, platform, network |
is related to: i2b2 Cross-Institutional Clinical Translational Research project is related to: i2b2 Research Data Warehouse has parent organization: Harvard Medical School; Massachusetts; USA |
Informatics for Integrating Biology and the Bedside ; NLM 5 U54 LM008748; NCRR 1 UL1 RR025758-01 |
PMID:19567788 | Available under a BSD3 Open unspecified license Software license. | nlx_151949 | SCR_006293 | Shared Health Research Informatics NEtwork | 2026-02-15 09:19:12 | 8 | |||||
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RFMix Resource Report Resource Website 1+ mentions |
RFMix (RRID:SCR_027030) | software application, software resource | Software tool for local ancestry and admixture inference. Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference. | Discriminative Modeling, local ancestry and admixture inference, | NLM LM007033; NHGRI 2R01HG003229; NSF |
PMID:23910464 | Restricted | SCR_027030 | 2026-02-15 09:23:29 | 5 | |||||||||
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eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software application, software resource | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS P50 GM071558; NIDDK R01 DK088541; NLM RC2 LM010994; NIDDK P01 DK056492; NIDDK RC4DK090860; NCRR KL2 RR029885 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k http://www.maayanlab.net/X2K/ |
SCR_016307 | eXpression2Kinases, X2K | 2026-02-15 09:21:04 | 4 | ||||
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GlimmerHMM Resource Report Resource Website 500+ mentions |
GlimmerHMM (RRID:SCR_002654) | GlimmerHMM | source code, software resource | A gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single). | gene, hidden markov model |
is related to: Glimmer has parent organization: Johns Hopkins University; Maryland; USA |
NIH ; NLM R01-LM06845; NLM R01-LM007938 |
PMID:15145805 | Free, Available for download, Freely available | nlx_156092 | SCR_002654 | GlimmerHMM - Eukaryotic Gene-Finding System | 2026-02-15 09:18:22 | 576 | |||||
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Hanalyzer Resource Report Resource Website |
Hanalyzer (RRID:SCR_000923) | software application, source code, software resource | An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download. | genomic, visualization, reading, reasoning, reporting, throughput analyzer, data network |
has parent organization: University of Colorado Denver; Colorado; USA has parent organization: SourceForge |
NIDCR R01DE15191; NLM R01LM008111; NLM R01LM009254; NIGMS R01GM083649; NLM T15LM009451; NHGRI 5R01HG004483-09 |
PMID:19325874 | nlx_48287 | SCR_000923 | Hanalyzer: A 3R System | 2026-02-15 09:18:01 | 0 | |||||||
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LONI Visualization Tool Resource Report Resource Website |
LONI Visualization Tool (RRID:SCR_000765) | LONI Viz, LONI_Viz, LOVE | software application, data processing software, data visualization software, software resource | A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html | brain, atlas, visualization, gene mapping, atlas application, magnetic resonance, surface analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: Laboratory of Neuro Imaging |
Aging | NIA P50 AG16570; NLM 2R01 LM05639-06; NIA K08 AG100784; NCRR 2 P41 RR13642; NIMH 5 P01 MN52176; NSF DUE 0442992; NCRR U52 RR021813 |
PMID:16598642 | Free, Available for download, Freely available | nif-0000-23313 | http://www.nitrc.org/projects/incf_loni-viz | http://www.loni.ucla.edu/Software/LOVE | SCR_000765 | LONI Visualization Environment, LONI Viz environment, LOVE | 2026-02-16 09:45:20 | 0 |
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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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
