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.

Home > Bioinformatics > About

Bioinformatics

The Bioinformatics department works closely with the staff in all PFGRC programs including DNA microarray and gene expression, the Invitrogen Gateway® Clone Resource, Comparative Genomics, and Proteomics. Their directive is to provide software, technical support and analysis expertise to advance the production and scientific objectives of the PFGRC and the pathogen research community. Several software tools have been released to the community under open-source licenses, including the TM4 microarray software suite and the LEM (Linear Expression Maps) and NonpaR (Nonparametric Statistical Tests) modules. The implementation of a microarray annotation pipeline and internal tool "Sanim" streamlined the process of creating current annotation files for every PFGRC microarray design. EASE filesystems for these microarrays supplement the annotation files, providing GO terms, cellular roles and PFAMs, and facilitate the analysis of functional roles. A number of comparative analysis tools have been developed to facilitate Comparative Genomics research including the development of a set of filtering tools designed to identify and distinguish valid and spurious SNP calls when using Affymetrix GeneChips for the purpose of resequencing, and data normalization and classification tools for CGH experiments.

The table below summarizes and links to bioinformatics resources provided by the PFGRC.

Project Description	Reagents and Resources	Collaborators
New Magnolia: Microarray Data Management and Export System for PFGRC Microarrays	Magnolia Application and Source Code
New Ginkgo: CGH and Expression Microarray Statistical Analysis and Normalization Platform	Ginkgo Application and Source Code
New APEX Quantitative Proteomics Tool	APEX-QPT Application and Source Code	Christine Vogel & Edward M. Marcotte, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin
TM4: Comprehensive Microarray Software Suite for Data Management and Analysis	TM4 Suite, including the MADAM, Spotfinder, MIDAS and MeV Applications, Sample Datasets and Source Code	John Quackenbush and the Computational Biology and Functional Genomics Lab, Dana Farber Cancer Institute
LEM (Linear Expression Maps): Visualizing Gene Expression on a Chromosomal Coordinate Map	LEM Module, implemented in the MeV Application (TM4 Suite) and Source Code
NonpaR: Four Nonparametric Statistical Tests for Common Microarray Experimental Designs	NonpaR Module, implemented in the MeV Application (TM4 Suite) and Source Code
Microarray Annotation Pipeline	Annotation Files for PFGRC Microarrays
EASE: Resources for Biological Role Analysis of Gene Lists	EASE Filesystems for PFGRC Microarrays (including CMR cellular roles, GO terms and PFAM annotations)
Genotyping and SNP detection of Streptococcus pneumoniae isolates by resequencing arrays	S. pneumoniae comparative analysis tool	Catherine McEllistrem, The University of Pittsburg
Whole Genome Resequencing and Single Nucleotide Polymorphism Genotyping of 40 Franciscella tularensis Strains	F. tularensis comparative analysis tool, Bioinformatic SNP filter scripts	Jeannine Peterson, Martin Schriefer, and Charles Ben Beard, Bacterial Disease Branch, CDC, Fort Collins, CO, Mark Walcott and David Bedwell, US Army Medical Research Institute of Infectious Disease (USAMRIID), and Luther Lindler, Department of Homeland Security (DHS) and Walter Reed Army Institute of Research (WRAIR)
Tutorial and Guide to Microarray Data Analysis: Image Analysis, Normalization and Data Mining	Microarray Data Analysis Tutorial Public Resource Available 6/2008