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Abstract Detail

Large Scale Technologies and Resources

Wilkerson, Curtis [1], Larson, Matt [1], Bomhof, Andrew [1], Lu, Yan [2], Savage, Linda J. [2], Last, Robert L. [3].

Development of a database for large scale reverse genetics.

We are investigating the functions of several thousand nuclear genes predicted to be located in plastids using a reverse genetics strategy (www.plastid.msu.edu), employing homozygous mutant Arabidopsis knockout plants developed at the Salk Institute (http://signal.salk.edu/). We are using a combination of assays for morphology, chemistry and physiology to determine the phenotype of each gene disruption mutant. The investigation of this number of genes using multiple assays for each plant generates tens of thousands of samples and requires robust sample tracking as well as good data entry and analysis tools.
We have developed a suite of web-based software tools to accomplish the tasks required for the project. These tools allow us to perform a variety of tracking functions including sample ordering, tracking plants as they are grown for a variety of assays and tracking samples generated from each plant as they are used in the assays. Tools are also available to gather and organize a variety of data types including images, observations made about each plant, seed or chloroplast sample using controlled vocabularies and quantitative data generated by a variety of instruments.
We are also developing approaches to present the qualitative and quantitative data in a way that allows for efficient discovery of gene function. The software tools have been developed using the asynchronous JavaScript and XML (AJAX) approach coupled with a relational database. The AJAX approach has a number of advantages which include better management of the user interface and faster response times. The AJAX approach coupled with scalable vector graphics (SVG) has allowed us to develop query and display tools that enhance the userís ability to understand the large datasets generated by this project.

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Related Links:
Project web site

1 - Michigan State University, Research Technologies Support Facility
2 - Michigan State University, Department of Biochemistry and Molecular Biology
3 - Michigan State University, Departments of Biochemistry and Molecular Biology and Plant Biology, 301 Plant Biology, East Lansing, MI, 48824, USA

Arabidopsis 2010
systems biology.

Presentation Type: Plant Biology Abstract
Session: P
Location: Exhibit Hall (Northeast, Southwest & Southeast)/Hilton
Date: Sunday, July 8th, 2007
Time: 8:00 AM
Number: P42008
Abstract ID:934

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