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.

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Criteria for Priority Organisms

Criteria for Choosing a Target Organism for Microarrays

Importance of Organism

Disease burden of organism; biomedical or biological importance; widespread relevance for rapid advancement of biomedical research

Source of DNA available

High quality genome sequence is publicly and freely available to the scientific community. Complete or near complete genomic sequencing information with annotation from the chosen microbe exists in the public domain. Availability of source of genomic DNA for construction of an array.

Research Community

Is the microarray reagent timely for the research community? Readiness of the research and research community for this reagent? Size of the research community that could potentially use the array. Community interest in having an array as a resource/reagent.

Availability of microarray by another publicly funded agency

Is NIAID or another publicly funded agency preparing and distributing an array to the research community at a reasonable cost?

Please submit your recommendations to dl.microarray.suggestions@jcvi.org