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.
June 9, 2008
The APEX Quantitative Proteomics Tool v1.0 Release data version 1.0.0 release
The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute has developed a software tool that computes protein abundance values based on standard liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics datasets. The APEX Quantitative Proteomics Tool is a free open source tool that can be utilized by proteomics researchers to simultaneously quantify hundreds to thousands of proteins based on LC-MS/MS results. The APEX Tool is an implementation of the Absolute Protein Expression (APEX) quantitation technique developed by members of the Marcotte Lab at the University of Texas at Austin [Lu et al. Nature Biotech. 25(1):117-124, 2007]. The APEX Tool provides an intuitive graphical user interface, an integrated help page system, a complete manual, and a tutorial and sample data set. Additional information and APEX downloads can be found on the APEX Tool's homepage.