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http://trex.biohpc.org/

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.

Proper citation: T-REX (RRID:SCR_010715) Copy   

•   Source: SciCrunch Registry

http://medicine.nus.edu.sg/tissue/

Tissue bank that provides samples and associated clinical information to associated researchers.

Proper citation: National University Tissue Repository (RRID:SCR_010717) Copy   

•   Source: SciCrunch Registry

http://www.textensor.com/

Textensor Limited specializes in software development and consulting related to interactive web based information management systems, web services, data modeling, and scientific computing. Our flagship product, a.nnotate.com, was launched in January 2008. It allows on-line review, annotation and discussion of web pages and a wide range of document types, including PDF and DOC, via a web browser. In April 2007 we launched PublicationsList.org to facilitate access to scientific research papers. It allows researchers to easily keep complete and reliable records of their research output on the web and gained more than 3000 users in the first 8 months. In 2005, Textensor won a SMART:Scotland award for a pilot study into techniques for authoring structured content from text. The first commercial product developed from this technology is a.nnotate.com. Recent consultancy clients include the University of Edinburgh for the development of PSICS, the Parallel Stochastic Ion Channel Simulator, the Okinawa Institute of Science and Technology for prototype code for stochastic diffusion, Memosyne Ltd for development of on-line memory tests for children, and Pearson Assessment for implementation of the Automated Working Memory Assessment.

Proper citation: Textensor Limited (RRID:SCR_010719) Copy   

•   Source: SciCrunch Registry

https://www.twbiobank.org.tw/new_web_en/index.php

Taiwan Biobank intends to conduct large-scale cohort studies and case-control studies on local diseases. The cohort study will call for 200,000 volunteers, while the case-control study will invite 100,000 patients with the 10 to 15 most common diseases. These studies will enable Taiwan Biobank to identify the disease-causing factors and mechanisms of common diseases to facilitate the development of better treatment and prevention, reduce the cost of medical treatment and make it possible to achieve the goal of improving the island nation’s health.

Proper citation: Taiwan Biobank (RRID:SCR_010557) Copy   

•   Source: SciCrunch Registry

http://www.svffoundation.org/

Not yet vetted by NIF curator

Proper citation: SVF Foundation (RRID:SCR_010678) Copy   

•   Source: SciCrunch Registry

http://virginiahughes.com/

Virginia Hughes'' Research Blog

Proper citation: http://virginiahughes.com/ (RRID:SCR_010558) Copy   

•   Source: SciCrunch Registry

http://tools.genxpro.net/omiras/

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.

Proper citation: omiRas (RRID:SCR_010833) Copy   

•   Source: SciCrunch Registry

http://func.mshri.on.ca/yeast/

YeastFunc is a public database for browsing of quantitative S. cerevisiae gene function predictions, gene function linkage predictions, and the evidence behind the predictions, overlayed upon the experimentally verified annotations as taken from the SGD, MGI and Ensembl Gene databases, respectively. Three aspects of gene function predictions are displayed: * First, for a particular gene, users can view all functions ranked by certainty that the corresponding gene-function pair is a true annotation. * Second, for a particular function, users can view all genes ranked by certainty. * The third aspect is functional linkage predictions, displayed alongside the first two aspects as gene-centered and function-centered images, respectively, and editable via Cytoscape. These functional linkage graphs are independently informative, though they are also used as a step in one of the gene function prediction techniques whose certainty scores are displaying on this site, so they can be treated as evidence. Evidence leading to all gene function predictions in the first two aspects as well as all experimentally verified gene function annotation is displayed alongside each of the first two aspects, allowing the user to understand the basis for the certainty score. To get started type a Gene Ontology ID, an SGD ID, an ORF ID, an Ensembl gene id, an Entrez gene id, a Uniprot id, a standard gene name, or a general search term in the text box. The results of your search will appear below the search box. These results are solely Gene Ontology terms and genes for the species that you selected. Click the result that you would like to investigate further. Note the paging toolbar at the bottom of the results list. If you are interested in performing your own analyses upon all prediction scores displayed on this site you may download the file. Of the 15,633,440 scored yeast gene-function pairs, 6,368 genes have scores and 4,877 genes have at least one experimentally verified function.

Proper citation: YeastFunc (RRID:SCR_010561) Copy   

•   Source: SciCrunch Registry

http://agbase.msstate.edu/cgi-bin/maizecandidates/index.cgi

A relational database with dynamic querying and data integration that can be used by researchers to identify genetic sequences with a high probability of being associated with aflatoxin accumulation resistance, according to multiple lines of evidence. CFRAS-DB integrates genomic, proteomic, and genetic data from multiple studies in maize dealing with aflatoxin accumulation or Aspergillus flavus resistance., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Corn Fungal Resistance Associated Sequences Database (RRID:SCR_010644) Copy   

•   Source: SciCrunch Registry

http://compbio.med.harvard.edu/CGHweb/

Data analysis service enabling users to analyse their array-CGH data with multiple algorithms simultaneously.

Proper citation: CGHweb (RRID:SCR_010923) Copy   

•   Source: SciCrunch Registry

http://agvgd.iarc.fr/index.php

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.

Proper citation: Align-GVGD (RRID:SCR_010772) Copy   

•   Source: SciCrunch Registry

http://cosmoss.org/bm/plantapdb

A phylogeny-based comprehensive database of plant transcription associated proteins.

Proper citation: PlanTAPDB (RRID:SCR_010897) Copy   

•   Source: SciCrunch Registry

http://www.mutationtaster.org/

Evaluates disease-causing potential of sequence alterations.

Proper citation: MutationTaster (RRID:SCR_010777) Copy   

•   Source: SciCrunch Registry

http://esbank.nia.nih.gov/

Not yet vetted by NIF curator

Proper citation: Mouse ES Stem Cell Bank (RRID:SCR_010660) Copy   

•   Source: SciCrunch Registry

http://hyperbrowser.uio.no/hb/

A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets.

Proper citation: Genomic HyperBrowser (RRID:SCR_010909) Copy   

•   Source: SciCrunch Registry

http://www.vaccineinjury.info/vaccine-damage-reports-2010.html

Database of case reports of adverse reactions to vaccinations. There are 806 reports (May 2013). If you would like to report a case, please go to report your own vaccine reaction. The user may search by keywords or sort by vaccine, country, age, outcome, gender and hospital admission.

Proper citation: Vaccine damage reports database (RRID:SCR_010740) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/Structure/MMDB/docs/mmdb_help.html

The Molecular Modeling DataBase (MMDB), also known as Entrez Structure, is a database of experimentally determined structures obtained from the RCSB Protein Data Bank (PDB). MMDB is developed by the Structure Group of the NCBI Computational Biology Branch. The data processing procedure at NCBI results in the addition of a number of useful features that facilitate computation on the data and link them to many other data types in the Entrez system. The structure database is considerably smaller than Entrez''s Protein or Nucleotide databases, but a large fraction of all known protein sequences have homologs in this set, and one may often learn more about a protein by examining 3-D structures of its homologs. These are accessible as Related Structures in the Links menu of Entrez Protein sequence records (illustrated example). It is then possible to align the query protein to the structure-based sequence, as shown in the illustration on this page. Additional resources can be used along with MMDB to interactively view the structures, find similar 3D structures, learn about the types of interactions and bound chemicals that have been found to exist among the similar 3D structures, and more.

Proper citation: Molecular Modeling DataBase (RRID:SCR_010623) Copy   

•   Source: SciCrunch Registry

http://dhruvpolyclinic.com/

Not yet vetted by NIF curator

Proper citation: Dhruv Dental Stem Cell Bank (RRID:SCR_010744) Copy   

•   Source: SciCrunch Registry

http://mayovalidation.com/quality-biospecimens/

A core laboratory facility provides high-volume, high-quality tissue and biospecimen preparation and processing in support of Mayo research. Mayo Validation Support Services utilizes these resources to deliver extensive validation capabilities specific to individualized Sponsor requirements. Medical scientific expertise at Mayo Clinic allows for unique collaborations combining quality biospecimens linked to comprehensive clinical outcomes. Biospecimens can be accessed via archives or prospectively collected via individualized standard operating procedures. Patient information for all biospecimens is protected through oversight by an Institutional Review Board (IRB). Specimens may be collected and/or processed in a variety of customized formats for individual collaborations. Typical formats include: * Specimen Processing: Tissue RNA/DNA extraction capabilities, Paraffin and frozen sectioning, Immunostaining, Digital imaging, Laser capture microdissection, Tissue microarray construction, Preparation of protocol-collected tissue (FFPE, OCT, Snap-frozen, PBS) * Blood: Circulating tumor cells, Serum, Plasma, PBMC, Whole blood for FACS analysis, Blood smears * Other: Induced sputum, Saliva, Buccal swabs, Lip biopsies, Colonoscopy biopsies, Synovium, Stool, Urine Biospecimens located within archives are well-characterized and associated with phenotypic information. Multiple types and formats of biospecimens are available for customized validation purposes.

Proper citation: Mayo Validation Support Services Biobank (RRID:SCR_010745) Copy   

•   Source: SciCrunch Registry

http://www.biobank.org/

Genetic Alliance Registry and BioBank is a centralized, clinical data registry and sample repository (including DNA, serum, cells and tissues) that enables translational research. It is a nonprofit organization established by seven patient advocacy organizations. These organizations share resources for their BioBanks, such as the contract to the independent lab that processes the samples, but each organization will maintain ownership, control and costs associated with their sample collection. Founded in 2003, this cooperative venture provides shared infrastructure and customized solutions for disease advocacy organizations to lead sophisticated research initiatives. Genetic Alliance Registry and BioBank is an advocacy owned repository for biological samples and clinical data. It provides: * Centralized, standardized collection and archiving * Highest biorepository and participant protection standards * Open access for all organization approved researchers * Advocacy organization control

Proper citation: Genetic Alliance Biobank (RRID:SCR_010625) Copy   

•   Source: SciCrunch Registry