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.
November 3, 2006
The NIAID sponsored Pathogen Functional Genomics Resource Center at TIGR announces that it will conduct a two day course titled, "Introduction to Microarray Data Analysis"
The NIAID sponsored Pathogen Functional Genomics Resource Center at TIGR announces that it will conduct a two day workshop titled, "Introduction to Microarray Data Analysis." The workshop will be held on the TIGR campus on December 7-8, 2006, and will provide an overview of the software and techniques used in the analysis of two-dye spotted microarrays. Fundamental data analysis concepts will be taught using a mix of lectures and interactive hands-on sessions.
This introduction to the stages of microarray data analysis will be led by members of the team who developed the TM4 microarray software suite. Major topics include data management, image analysis, normalization, and data mining. Participants will analyze sample PFGRC microarrays using the open-source TM4 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 one of several offered by the PFGRC on variety of functional genomics topics. Those who have previously attended, or are interested in attending PFGRC's four day workshop, "Introduction to Microarray Technology", should not apply for this course, as the bioinformatics content is similar. Attendance will be limited to 16 participants.
Interested participants should click here for the preliminary course schedule and registration information.