- TM4 Microarray Software
- Proteomics Tools
- APEX
- Microarray Tools
- Ginkgo
- Magnolia
- Resources
- PFGRC Microarray Data Analysis Tutorial
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.
Ginkgo: CGH and Expression Microarray Statistical Analysis and Normalization Platform
Ginkgo is a spotted microarray data pre-processing platform featuring analysis functionalities for CGH and expression data. This application provides a user-friendly graphical interface that allows viewing, analyzing, generating and reporting microarray data, easily and intuitively. Within the software there are a number of algorithms to address microarray data analysis needs, including normalization, filtering, data imputation, replicates merge, and expression statistical distribution tests.
Feature List
- Data preprocessing for CGH and expression spotted microarray
- Replicates analysis and consolidation for in-slide replicates
- Flip-dye replicates analysis
- Intuitive graphical user interface
- Customized PDF analysis report
Download Latest Version
This application is released under the GPL v3 License: View License
Click here for source code: Download Source Code
Software Manual
The Ginkgo Manual describes the functionality and operations of this software.
System Requirements
Ginkgo v1.0.0 has the following requirements for OS, RAM and disk space:
- Operating System: Windows 2000/XP/Vista, Linux
- RAM: 1024 MB
- Disk Space: 512 MB
- Java Runtime Environment: Java v1.5.0 or higher.
Contact
Contact the PFGRC's Ginkgo Development Team by email: ginkgo@jcvi.org