- TM4 Microarray Software
- Proteomics Tools
- APEX
- Microarray Tools
- Ginkgo
- Magnolia
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.
Magnolia: Microarray Data Management and Export System for PFGRC Microarrays
Since it has been an obligation to submit microarray experiment data to public repositories for publishing the experimental results, collecting and storing the data is an essential step in microarray study. Implemented with H2 DBMS as the backend storage, Magnolia provides PFGRC array users with a series of intelligent entry form to collect the information or parameters of experiment, bio-source, sample, probe, slide, scan, expression, and normalization, which is MIAME compliant (Minimal Information About a Microarray Experiment; (Brazma et al., 2001)). The collected data are saved to a relational database defined by users and can be modified easily with a set of corresponding edit pages. Working as an exporter, Magnolia can write out the entered data into GEO sample and series files in SOFT format that is acceptable by GEO, so that the files can be submitted to GEO directly. Magnolia also serves as a platform for launching other data manipulation tools, such as SQL Query Window to report the entered data, Slide Annotation to load array annotation file downloaded from PFGRC site into the database, and Database Schema to present the relationships among the tables.
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 is a detailed description of the workings of Magnolia. It contains complete instructions on entering and exporting data.
System Requirements
Magnolia v1.0 runs on the Windows 2000/NT/XP systems and requires Java v1.6.0 or higher.
Contact
Contact the PFGRC's Magnolia Development Team by email: magnolia@jcvi.org