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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Tissue Solutions Resource Report Resource Website 1+ mentions |
Tissue Solutions (RRID:SCR_010672) | material resource, tissue bank, biomaterial supply resource | Tissue Solutions offers you a single point to access the entire range of human biological materials for all your research and development needs. This includes diseased and normal tissues in fresh, frozen and FFPE formats. Using our large network of ethical sources we find the tissues you require, to your specifications and will deliver them to your door. Our goal is to provide high quality and well characterized samples to biotech companies, the pharmaceutical community and contract research organizations worldwide. We also organize customized and prospective tissue acquisition projects and give specialized advice relating to all aspects of the acquisition process, including intellectual input on project design. We appreciate that you would rather spend your time finding new biomarkers and developing, testing and validating novel drugs to cure human disease than spend your time sourcing material to help you do your work, so let our dedicated Tissue Acquisitionists lessen your workload and become a virtual part of your team. | is listed by: One Mind Biospecimen Bank Listing | nlx_75586 | SCR_010672 | Tissue Solutions Ltd. | 2026-08-10 09:34:03 | 5 | ||||||||||
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T-REX Resource Report Resource Website 100+ mentions |
T-REX (RRID:SCR_010715) | T-REX | production service resource, data analysis service, analysis service resource, service resource | T-REX is a free, platform-independent online tool that allows for an integrated, rapid, and more robust analysis of T-RFLP data. Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data. Analysis of T-RFLP data generated from a multiple-factorial study was performed with T-REX. With this software, we were able to i) label raw data with attributes related to the experimental design of the samples, ii) determine a baseline threshold for identification of true peaks over noise, iii) align terminal restriction fragments (T-RFs) in all samples (i.e., bin T-RFs), iv) construct a two-way data matrix from labeled data and process the matrix in a variety of ways, v) produce several measures of data matrix complexity, including the distribution of variance between main and interaction effects and sample heterogeneity, and vi) analyze a data matrix with the additive main effects and multiplicative interaction (AMMI) model. | has parent organization: Cornell University; New York; USA | Microsoft Corporation ; NSF DGE 0221658 |
PMID:19500385 | nlx_89468 | SCR_010715 | T-REX (T-RFLP analysis EXpedited), T-REX: Software for the processing and analysis of T-RFLP data, T-RFLP analysis EXpedited | 2026-08-10 09:34:04 | 122 | |||||||
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CoMet Resource Report Resource Website 500+ mentions |
CoMet (RRID:SCR_011925) | CoMet | production service resource, data analysis service, analysis service resource, service resource | A web-server for fast comparative functional profiling of metagenomes. | is listed by: OMICtools | OMICS_01477 | SCR_011925 | CoMet - a web-server for fast comparative functional profiling of metagenomes | 2026-08-10 09:34:21 | 991 | |||||||||
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omiRas Resource Report Resource Website 10+ mentions |
omiRas (RRID:SCR_010833) | omiRas | production service resource, data analysis service, analysis service resource, service resource | A web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23946503 | biotools:omiras, OMICS_00383 | https://bio.tools/omiras | SCR_010833 | 2026-08-10 09:34:06 | 14 | |||||||
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PhyloPythiaS Resource Report Resource Website 10+ mentions |
PhyloPythiaS (RRID:SCR_011923) | PPS | production service resource, data analysis service, analysis service resource, service resource | Web Server for Taxonomic Assignment of Metagenome Sequences that is a fast and accurate sequence composition-based classifier that utilizes the hierarchical relationships between clades. Taxonomic assignments with the web server can be made with a generic model, or with sample-specific models that users can specify and create. Several interactive visualization modes and multiple download formats allow quick and convenient analysis and downstream processing of taxonomic assignments. | metagenome, sequence, taxonomy, classification | is listed by: OMICtools | PMID:22745671 PMID:21358620 |
OMICS_01460 | http://phylopythias.cs.uni-duesseldorf.de/index.php?phase=wait | SCR_011923 | 2026-08-10 09:34:21 | 12 | |||||||
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University of Pittsburgh, Health Sciences Library System Resource Report Resource Website 10+ mentions |
University of Pittsburgh, Health Sciences Library System (RRID:SCR_011975) | HSLS | data or information resource, database | Database access to information services, educational opportunities, and resources in print and electronic format to faculty, students, and researchers in the schools of the health sciences. | journal, book, video |
is listed by: OMICtools has parent organization: University of Pittsburgh; Pennsylvania; USA |
PMID:17108360 | SCR_011975 | Pitt Health Sciences Library System, Pitt HSLS, Health Sciences Library System | 2026-08-10 09:34:22 | 10 | ||||||||
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CGHweb Resource Report Resource Website 10+ mentions |
CGHweb (RRID:SCR_010923) | CGHweb | production service resource, data analysis service, analysis service resource, service resource | Data analysis service enabling users to analyse their array-CGH data with multiple algorithms simultaneously. |
is listed by: OMICtools has parent organization: Harvard Medical School; Massachusetts; USA |
OMICS_00713 | SCR_010923 | 2026-08-10 09:34:07 | 12 | ||||||||||
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Align-GVGD Resource Report Resource Website 50+ mentions |
Align-GVGD (RRID:SCR_010772) | Align-GVGD | production service resource, data analysis service, analysis service resource, service resource | A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral. | is listed by: OMICtools | Free | OMICS_00125 | SCR_010772 | 2026-08-10 09:34:05 | 93 | |||||||||
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MutationTaster Resource Report Resource Website 1000+ mentions |
MutationTaster (RRID:SCR_010777) | MutationTaster | production service resource, data analysis service, analysis service resource, service resource | Evaluates disease-causing potential of sequence alterations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20676075 | Acknowledgement requested | biotools:mutation_taster, OMICS_00153 | https://bio.tools/mutation_taster | SCR_010777 | 2026-08-10 09:34:05 | 4781 | ||||||
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Mouse ES Stem Cell Bank Resource Report Resource Website 1+ mentions |
Mouse ES Stem Cell Bank (RRID:SCR_010660) | material resource, tissue bank, biomaterial supply resource | Not yet vetted by NIF curator | nlx_69742 | SCR_010660 | 2026-08-10 09:34:03 | 2 | ||||||||||||
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Genomic HyperBrowser Resource Report Resource Website 10+ mentions |
Genomic HyperBrowser (RRID:SCR_010909) | Genomic HyperBrowser | production service resource, data analysis service, analysis service resource, service resource | A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets. | genomic, genomic track, gene regulation, disease association, epigenetic modification, genome |
is listed by: OMICtools has parent organization: University of Oslo; Oslo; Norway |
PMID:23632163 PMID:21182759 |
OMICS_00638 | SCR_010909 | The Genomic HyperBrowser | 2026-08-10 09:34:07 | 20 | |||||||
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UCSC Cancer Genomics Browser Resource Report Resource Website 500+ mentions |
UCSC Cancer Genomics Browser (RRID:SCR_011796) | Cancer Genomics Browser | data or information resource, database, service resource | A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets. | genome, genomics, clinical, next-generation sequencing, chromosome, gene, FASEB list |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
Cancer | NCI ; NHGRI ; American Association for Cancer Research ; UCSF Comprehensive Cancer Center ; California Institute for Quantitative Biosciences |
PMID:23109555 PMID:21059681 PMID:19333237 |
Acknowledgement requested | OMICS_00925 | SCR_011796 | 2026-08-10 09:34:20 | 589 | |||||
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WebMGA Resource Report Resource Website 100+ mentions |
WebMGA (RRID:SCR_011951) | WebMGA | production service resource, data analysis service, analysis service resource, service resource | A customizable web server for fast metagenomic analysis. |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
OMICS_01524 | SCR_011951 | 2026-08-10 09:34:22 | 196 | ||||||||||
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Genomics of Drug Sensitivity in Cancer Resource Report Resource Website 1000+ mentions |
Genomics of Drug Sensitivity in Cancer (RRID:SCR_011956) | Genomics of Drug Sensitivity in Cancer | data or information resource, database | A genomics database project is an academic research program to identify molecular features of cancers that predict response to anti-cancer drugs. | compound, gene, molecule, drug, FASEB list |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Cancer | Wellcome Trust | OMICS_01581 | SCR_011956 | 2026-08-10 09:34:22 | 2388 | |||||||
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DGIL Porcine Immunology and Nutrition Datebase Resource Report Resource Website 1+ mentions |
DGIL Porcine Immunology and Nutrition Datebase (RRID:SCR_012743) | data or information resource, database | Performs studies demonstrating the nutritional and biochemical effects of trace elements with special emphasis on chromium. Performs studies to elucidate the role of natural products in the improvement of the function of insulin with emphasis on polyphenols from tea and cinnamon. Performs studies on the role of dietary polyphenols on neuropathological changes including those associated with Alzheimers disease. The ultimate goal of the research is to prevent or alleviate early signs and symptoms of the metabolic syndrome which is important in the prevention of type 2 diabetes, cardiovascular, Alzheimers and related diseases. Our database is focused on immunologically-related genes classified under the following categories: Apoptosis CD markers Chemokines Chemokine receptors Cytokines Cytokine receptors Dendritic cell associated genes Type 1 IFN induced proteins Inflammation NFKB signaling pathway Toll receptor signaling pathway T cell activation TH1 cell development TH2 cell development Partners. Partnering with the Diet, Genomics, and Immunology Laboratory | has parent organization: U.S. Department of Agriculture | Type 2 diabetes, Diabetes, Cardiovasculat disease, Alzheimer's disease | nif-0000-30452 | SCR_012743 | PIN | 2026-08-10 09:34:43 | 8 | |||||||||
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FINDbase Worldwide Resource Report Resource Website 10+ mentions |
FINDbase Worldwide (RRID:SCR_012744) | data or information resource, database | FINDbase Worldwide is an online repository of information about the frequency of different mutations leading to inherited disorders in various populations around the globe. Frequency data about 32 disorders, 25 genes within 98 populations covering 1226 mutations is now available. 28 curators worldwide contributed to this database containing data from 37 submissions. | genetic disorder, human mutation, inherited disorder, mutation pathogenesis, bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:findbase, nif-0000-02838 | https://bio.tools/findbase | SCR_012744 | FINDbase | 2026-08-10 09:34:37 | 13 | ||||||||
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VIOLIN: Vaccine Investigation and Online Information Network Resource Report Resource Website 10+ mentions |
VIOLIN: Vaccine Investigation and Online Information Network (RRID:SCR_012749) | VIOLIN | data or information resource, database | A web-based central resource that integrates vaccine literature data mining, vaccine research data curation and storage, and curated vaccine data analysis for vaccines and vaccine candidates developed against various pathogens of high priority in public health and biological safety. The vaccine data includes research data from vaccine studies using humans, natural and laboratory animals.VIOLIN extracts and stores vaccine-related, peer-reviewed papers from PubMed. Several powerful literature searching and data mining programs have been developed. These include an advanced keywords search program, a natural languagae processing (NLP) based literature retrieval program, a MeSH-based literature browser, and a literature alert program. Registered users can subscribe to our email alert service and will be notified of any newly published vaccine papers in the areas of interest. These literature mining programs are designed to help the user and VIOLIN database curators to find efficiently needed vaccine articles and sentences within full-text articles that contain searched keywords or categories.A web-based literature mining and curation system (Limix) is available for registered users/curators to search, curate, and submit structured vaccine data into the VIOLIN database. The curated vaccine-related information contains many categories such as general pathogenesis, protective immunity, vaccine preparation and characteristics, host responses including vaccination protocol and efficacy against virulent pathogen infections. All data within the database is edited manually and is derived primarily from peer-reviewed publications. The curated data is stored in a relational database and can be queried using various VIOLIN search programs. Vaccine-related pathogen and host genes are annotated and available for searchs based on a customized BLAST program. All VIOLIN data are available for download into an XML-based data exchange format.VIOLIN is designed to be a vital source of vaccine information and will provide researchers in basic and clinical sciences with curated data and bioinformatics tools to facilitate understanding and development of vaccines to fight infectious diseases. Category: Other Molecular Biology Databases Subcategory: Drugs and drug design | immunology, infectious diseases, molecular biology, pathogen, public health, vaccine | has parent organization: University of Michigan; Ann Arbor; USA | NIAID U24 AI125008 | nif-0000-03629 | SCR_012749 | Violin 2.0, Vaccine Investigation and Online Information Network | 2026-08-10 09:34:37 | 27 | |||||||
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RegTransBase Resource Report Resource Website 1+ mentions |
RegTransBase (RRID:SCR_013047) | data or information resource, database | It consists of two modules - a database of regulatory interactions based on literature and an expertly curated database of transcription factor binding sites. The literature based information in RegTransBase is a manually curated database of regulatory interactions in prokaryotes, captures the knowledge in published scientific literature using a controlled vocabulary. RegTransBase describes a large number of regulatory interactions reported in many organisms and contains various types of experimental data, in particular: * the activation or repression of transcription by an identified direct regulator * determining the transcriptional regulatory function of a protein (or RNA) directly binding to DNA or RNA * mapping or prediction of binding sites for a regulatory protein * characterization of regulatory mutations The analysis section of RegtransBase is based on a set of manually curated alignments of transcription factor binding sites and allows you to search for new binding sites and verify conservation of bindings sites across multiple species through the use of web based analysis tools. | nif-0000-03398 | SCR_013047 | RegTransBase | 2026-08-10 09:34:41 | 6 | |||||||||||
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GABI-KAT Resource Report Resource Website 50+ mentions |
GABI-KAT (RRID:SCR_012751) | data or information resource, database | GABI-Kat is a database of flanking sequence tags (FSTs) from T-DNA mutagenised A. thaliana plants. Over time, an increasing number of lines will become available from NASC. The "show sequence" page of SimpleSearch will display if a GABI-Kat line for a given FST has already been donated to NASC. Lines that have so far not been regrown and confirmed are only available from GABI-Kat directly. We have used four vectors: pAC106 (GenBank:AJ537513), pAC161 (GenBank:AJ537514), pGABI1 (GenBank:AY529716) and pADIS1 (GenBank:AY529717). Sequence and overview map data of all vectors are available from the download page. Features of interest which are not included in the map should be deduced from the sequence. For a specified line, the vector is displayed in the "Show Sequence" page of SimpleSearch. | a. thaliana, a. thaliana genome, mutagen, plant genome, FASEB list | has parent organization: Bielefeld University; North Rhine-Westphalia; Germany | nif-0000-02865 | SCR_012751 | GABI-KAT | 2026-08-10 09:34:37 | 56 | |||||||||
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Colon CFR Resource Report Resource Website 1+ mentions |
Colon CFR (RRID:SCR_013162) | Colon CFR | data or information resource, database | It is an international research infrastructure for investigators interested in conducting population and clinic-based interdisciplinary studies on the genetic and molecular epidemiology of colon cancer and its behavioral implications. A central goal of the C-CFR is the translation of this research to the clinical and prevention setting for the benefit of Registry participants and the general public. The C-CFR has information and biospecimens contributed by greater than 11,300 families across the spectrum of risk for colon cancers and from population-based or relative controls. Of particular interest are: identification and characterization of cancer susceptibility genes definition of gene-gene and gene-environment interactions in cancer etiology translational, preventive, and behavioral implications of research findings Special features include: population-based and clinic-based ascertainment systematic collection of validated family history epidemiologic risk factor data clinical and follow-up data biospecimens (including tumor blocks and EBV transformed cell lines) ongoing molecular characterization of the participating families Goals: to contribute to the development of public health measures for the general population by increasing knowledge on genetic factors affecting cancer susceptibility and modification by environmental and lifestyle factors to protect those with increased susceptibility from developing cancer to provide life-prolonging treatment to genetically susceptible individuals Objectives: to establish a comprehensive research resource infrastructure to assist with the implementation of collaborative, interdisciplinary research protocols in the genetic epidemiology of cancer to identify, characterize, and follow-up a cohort of individuals and their family members, spanning the spectrum of cancer risk to identify diverse genetically susceptible populations that could benefit from enrollment in preventive and therapeutic interventions to develop an adaptive and evolving informatics model to support ongoing and future research consortia Sponsor. This study was supported by National Cancer Institute Grants R01 CA47147, R01 CA47305, and R01 CA69664. | has parent organization: National Cancer Institute | nif-0000-30482 | SCR_013162 | Colon Cancer Family Registry, The Colon Cancer Family Registry | 2026-08-10 09:34:49 | 7 |
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