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 10, 2006
The PFGRC announces that it will conduct a four day course titled, "Introduction to Microarray Technology", June 19-22, 2006.
The NIAID sponsored Pathogen Functional Genomics Resource Center at TIGR announces that it will conduct a four day course titled, "Introduction to Microarray Technology." The workshop will be held on the TIGR campus on June 19-22, 2006. The course will provide an overview of the two-dye spotted microarray platform. The course is designed for hands-on participation and attendees will actively learn to make the most of their microarrays through a combination of wet lab and bioinformatics sessions.
The wet lab portion will be taught by PFGRC staff who are directly involved in microarray production. Participants will be guided through probe preparation and hybridization protocols. The training will also consist of detailed discussions on dye coupling, slide pre-hybridization, hybridization, and scanning techniques. Other topics for discussion will include the importance of assessing source material and probe quality, comparisons of various slide surfaces, and printing techniques.
The bioinformatics portion of the course covers an introduction to the stages of microarray data analysis. Major topics include data management, image analysis, normalization, and data mining. Fundamental data analysis concepts will be taught using a mix of lectures and interactive hands-on sessions. Participants will analyze the microarrays they prepared, using the open-source TM4 software suite while working closely with the software developers. CDs containing microarray datasets and the TM4 suite will be provided.
The course will be provided free of charge. Attendees will be responsible for their travel and lodging. This introductory course is the first in a planned series of courses on a variety of functional genomics topics. Interested participants should click here for the preliminary course agenda and registraion information. Attendance will be limited to 12 participants.