Three New Bioinformatics Tools Available
The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute is pleased to announce the release of three new, free open-source software tools: Magnolia, Ginkgo and APEX. Magnolia is a microarray data management and export system for researchers who use PFGRC microarrays. The software greatly simplifies the tasks of organizing experimental data and submitting it to a public data repository. Ginkgo is a Comparative Genomic Hybridization (CGH) and expression microarray data analysis package. Several normalization, data filtering and imputation, and replicate microarray functions are implemented in an intuitive graphical framework. The APEX tool is an implementation of the Absolute Protein Expression quantitation technique. It can compute protein abundance values for LC-MS/MS proteomics datasets, quantifying hundreds or thousands of proteins. Links to additional information on each of these new software tools is available from the PFGRC's bioinformatics page.
Microarray Suggestion Criteria
The National Institute of Allergy and Infectious Diseases (NIAID) supported Pathogen Functional Genomics Resource Center (PFGRC) designs, constructs, and distributes glass slide DNA microarrays for pathogens and biodefense related organisms (Select A-C agents). Currently, the PFGRC supports DNA microarrays for the 38 organisms listed here. In continuing its efforts to provide the infectious disease and biodefense communities with the microarray resources most relevant to their research efforts, the PFGRC is soliciting input for selection of its next set of reference/species microarrays. The criteria for organism selection may be found here.
December 8, 2003
PFGRC announces February 9, 2004 microarray application deadline for expanded organism list
The National Institute of Allergy and Infectious Diseases (NIAID) sponsored Pathogen Functional Genomics Resource Center (PFGRC) at The Institute for Genomic Research (TIGR) announces the selection of fourteen (14) organisms for development of functional genomics resources and reagents. The fourteen (14) organisms selected are Group B Streptococcus agalactiae, Trypanosoma brucei, Helicobacter pylori, Aspergillus fumigatus, Trypanosoma cruzi, Mycobacterium smegmatis, Streptococcus mutans, Porphyromonas gingivalis, Bacillus anthracis, Yersinia pestis, Vibrio cholerae, Clostridium botulinum, Listeria monocytogenes, and selected Coronaviruses. The construction and distribution of Streptococcus mutans and Porphyromonas gingivalis DNA microarrays are supported through generous funding from the National Institute of Dental and Craniofacial Research (NIDCR). The construction of the T. cruzi array is supported through the generous funding of the Sandler Foundation.
A February 9, 2004 deadline has been set for submission of applications for acquisition of glass slide microarray resources for all fourteen organisms. In addition, the PFGRC will continue to accept and support applications for organisms selected in years one (1) and two (2). Details with respect to the application process and review criteria can be found at the NIAID PFGRC web site. The application process for the NIDCR supported DNA microarrays can be found at http://www.nidcr.nih.gov/Research/Extramural/NIDCR_TIGR_Facility.htm.