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.
News Archives - 2006
December 8, 2006 The NIAID sponsored PFGRC in collaboration with the TB Vaccine Testing and Research Materials Contract, announces the availability of a Mycobacterium tuberculosis Gateway® Entry Clone Set
The National Institute of Allergy and Infectious Diseases (NIAID) sponsored Pathogen Functional Genomics Resource Center (PFGRC) at TIGR is pleased to announce the addition of a Mycobacterium tuberculosis strains H37Rv and CDC1551 Invitrogen Gateway® Entry Clone Set to the PFGRC… more
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… more
September 29, 2006 The PFGRC announces that it will continue to accept applications for acquiring DNA microarray resources on an ongoing basis.
In order to facilitate the acquisition of DNA microarray resources by interested scientists, the NIAID sponsored Pathogen Functional Genomics Resource Center has will continue its policy of accepting applications for DNA microarray resources on an ongoing… more
September 25 , 2006 Introduction to Microarray Technology
The NIAID sponsored Pathogen Functional Genomics Resource Center at TIGR conducted its second official training course offering, titled "Introduction to Microarray Technology." The four day workshop was held on the TIGR campus and provided an overview of the two-dye spotted… more
August 16, 2006 Comparative sequence analysis of S. pneumoniae TIGR 4 and a set of diverse S. pneumoniae strains.
The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) (NIAID contract N01-AI-15447) has funded a study on the evaluation of resequencing oligonucleotide array technology to detect genotypic variations in microorganisms. The PFGRC, in collaboration with Dr. Catherine McEllistrem, Division of… more
July 6 , 2006 MultiExperiment Viewer (MeV) 4.0 with Linear Expression Map (LEM) Module Released
Version 4.0 of the MultiExperiment Viewer has been released. New modules and feature upgrades include:
- LEM - Linear Expression Map, mapping expression to chromosomal location
- TEASE - Tree EASE, biological analysis for hierarchical tree branches
- USC -… more
June 6, 2006 News studies detailing the proteome of vancomycin intermediate resistant Staphylococcus aureus released
The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) (NIAID contract N01-AI-15447) has funded two studies investigating the proteome of vancomycin intermediate resistant Staphylococcus aureus (VISA). Emerging clinical VISA isolates are also methicillin-resistant and cause increasing public health concerns, because… more
May 16, 2006 Comparative sequence analysis of B. anthracis Ames Ancestor and a set of diverse B. anthracis strains.
The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) (NIAID contract N01-AI-15447) and the National Science Foundation (NSF Grant 0202304) have funded a study on the comparative sequence analysis of several strains of Bacillus anthracis. The complete genome sequence of… more
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… more
April 3, 2006 The PFGRC announces that, beginning immediately, we will be accepting applications for acquiring DNA microarray resources on an ongoing basis through September 30, 2006, without any imposed deadlines.
In order to facilitate the acquisition of DNA microarray resources by interested scientists, the NIAID sponsored Pathogen Functional Genomics Resource Center has made a change in its policy with respect to proposal submission. Beginning immediately, the PFGRC will be accepting… more
February 8, 2006 PFGRC releases expanded website content to improve resource and data availability to the community
In order to provide a more comprehensive overview of the activities of the Pathogen Functional Genomics Resource Center (PFGRC) as well as the resources and research conducted by the PFGRC, we have and will continue to update our website with… more
January 20, 2006 The PFGRC announces three new additions to its DNA microarray resource and two new deadlines for acceptance of applications for DNA microarrays.
The National Institute of Allergy and Infectious Diseases (NIAID) sponsored Pathogen Functional Genomics Resource Center (PFGRC) at The Institute for Genomic Research (TIGR) announces the selection of three organisms for development of functional genomics resources and reagents. The three organisms… more
January 20, 2006 The PFGRC and Harvard Institute of Proteomics announce the availability of three new additions to the PFGRC Invitrogen Gateway® Entry Clone Resource.
Details with respect to the construction and ordering the S. aureus, V. cholerae, and F. tularensis Gateway® Entry Clones can be found below.
The PFGRC Announces the Availability of a Staphylococcus aureus Gateway® Entry Clone Set.
The National Institute… more