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CIG Projects

AVIA-Annotation, Visualization and Impact Analysis

Image showing AVIA logo

AVIA

AVIA is a web application designed to explore and interpret large sets of genomic variations (single nucleotide variations and insertion/deletions) to help guide and summarize genomic experiments. The tool is based on coupling a comprehensive annotation pipeline with a flexible visualization method.

If you already have mapped genomic data from human, please click here to get started.
URL: http://avia.abcc.ncifcrf.gov

Publication(s)

Vuong H, Stephens RM, Volfovsky N. AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations. Bioinformatics. 2014 Apr 1;30(7):1013-4. doi: 10.1093/bioinformatics/btt655. Epub 2013 Nov 9.

bioDBnet – the biological DataBase network

Image showing the network of databases integrated in bioDBnet

bioDBnet

bioDBnet was developed as an internal project at ABCC where the goal was to integrate all the biological information stored in our internal data warehouse. Researchers can use bioDBnet, through an easy to use web interface, with diverse types of biological identifiers and run identifier conversions, orthology conversions or get extensive annotation reports.
URL: http://biodbnet.abcc.ncifcrf.gov

Publication(s)

Mudunuri U, Che A, Yi M, and Stephens RM. bioDBnet: the biological database network. Bioinformatics 25(4):555-6 2009. (PMID: 19129209)

BotDB – a database resource for clostridial neurotoxins

Image of the front page of the BotDB website

BotDB

BotDB was developed in collaboration with the USAMRIID. BotDB is a database designed to serve as a comprehensive resource of data for botulinum research, BotDB offers several features to aid in the research efforts of understanding the toxicity and finding ways to counteract the toxic effects of clostridial neurotoxins.
URL: http://botdb.abcc.ncifcrf.gov

Publication(s)

Mudunuri U, Stephens R, Bruining D, Liu D, Lebeda FJ. botXminer: mining biomedical literature with a new web-based application. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W748-52. (PMID: 16845112)

Cer RZ, Mudunuri U, Stephens R, Lebeda FJ. IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W441-5. (PMID: 19395593)

Lebeda FJ, Cer RZ, Stephens RM, Mudunuri U. Temporal characteristics of botulinum neurotoxin therapy. Expert Rev Neurother. 2010 Jan;10(1):93-103. (PMID: 20021324)

non-B DNA Forming regions (nonb.abcc)

Image showing the non-B annotations in nonb.abcc website

ISRCE: non-B

The Advanced Biomedical Computing Center received funding to identify, classify, and correlate genomic non-B DNA?forming regions with respect to their involvement in forming chromosomal breakpoints and other processes leading to cancer.
URL: http://nonb.abcc.ncifcrf.gov

Publication(s)

Cer RZ, Bruce KH, Mudunuri US, Yi M, Volfovsky N, Luke BT, Bacolla A, Collins JR, Stephens RM. Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes. Nucleic Acids Res. 2010 Nov 21. (PMID: 21097885)

medXminer

Image of an author's network in medXminer

medXminer

medXminer is an application developed by mining the complete MEDLINE. Currently more than 19million articles along with abstracts are stored in an Oracle XMLDB instance. The applications allows queries like multiple search terms, grouping artcles by authors, MeSH terms, which are not feasible through PubMed. A subset of MEDLINE containing all botulinum related articles is made available through botXminer, developed for our BotDB project
URL: http://botdb.abcc.ncifcrf.gov/botXminer

Systems Biology Data Cube

SysBioCube

This Systems Biology project is in collaboration with the USACEHR. The goal of the project is to create, maintain and provide ongoing support for a systems biology data cube that will serve as a central portal for data collection, integration, analysis, mining, and knowledge sharing by Army, academic, and private institution consortium collaborators.
URL: https://sysbiocube.abcc.ncifcrf.gov/