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.
May 30, 2007
The Pathogen Functional Genomics Resource Center (PFGRC) announces that it will conduct a two day course titled, "Advanced Microarray Data Analysis".
The NIAID sponsored Pathogen Functional Genomics Resource Center at JCVI announces that it will conduct a two day course titled, " Advanced Microarray Data Analysis ." The workshop will be held on the JCVI campus on July 10-11, 2007. This course will cover advanced data analysis techniques that are appropriate for the two-dye spotted microarray platform. The content is designed for those with experience in microarray data analysis; prior participation in the PFGRC's Introduction to Microarray Data Analysis or Introduction to Microarray Technology courses (or their equivalent) is required. Lectures, hands-on bioinformatics sessions, and group discussions will be combined to effectively cover a wide range of topics.
Projected course topics include the characterization of microarray data, gene expression normalization strategies, CGH-specific analysis considerations and approaches, advanced data mining algorithms and statistical techniques. The course will conclude with a data analysis workshop session where students will apply a variety of advanced analysis strategies while working with a published microarray dataset. The open-source TM4 software suite will be used extensively throughout the course; CDs containing the TM4 suite as well as all course materials and datasets will be provided.
The course will be provided free of charge. Attendees will be responsible for their travel and lodging. This advanced course is one of several offered by the PFGRC on a variety of functional genomics topics. Attendance will be limited to 16 participants. Interested participants should click "here" for the list of preliminary course topics, and "here" for registration information.