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.
The Gateway® Entry Clone Resource
The PFGRC, under a licensing and distribution agreement with Invitrogen Corporation, makes available, at no cost to researchers, complete and custom clone sets as Gateway® entry clones. Thus far, the PFGRC has produced eight complete Gateway® Entry Clone Sets and supports the ordering of custom Gateway® Entry Clone Sets from 37 other species and strains. The PFGRC has collaborated with several institutions to construct complete clone sets including an NIAID contract for “TB Vaccine Testing and Research Materials” at Colorado State University (Mycobacterium tuberculosis), the NIAID sponsored Harvard Institute of Proteomics and the New England Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research (Yersinia pestis) and the NIAID sponsored Harvard Institute of Proteomics (Vibrio cholerae).
The PFGRC website provides detailed information for researchers interested in the Center’s Gateway® Entry Clone Resource. The table below provides specific links to the Gateway® Entry Clone Resource and specific instructions for clone or clone set ordering.
Project Description |
Reagents and Resources |
Collaborators |
Complete Clone Sets |
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Custom Clone Sets |