From Bioinformatics Core

• Developer: Brad Sickler
• Started: June 2006
• Completed: July 2006

Overview

Elsie Campbell, a researcher working on cyanobacteria in Jack Meeks lab, wants a way to visualize microarray expression data on artemis, a genome browser, and in a circular bacterial genome for publication. The program(s) will need to be portable, easy to run and be able to incorporate in a large amount of data beyond expression.

Project Goals

• 1. Experiment with the data formats in existing genomic visualization tools.
• 2. Export the data into a format artemis can understand to display the data for analysis.
• 3. Choose a tool design a highly configurable script to integrate the gene expression information into the generated image.
• 4. Teach Elsie, Jack and lab how to use the tool(s).

Final Status

All goals were met as of June 2006. Initial program, arrayArt is capable of extracting microarray expression data into a artemis compatible file. CircularDiagram can then transform any number of artemis files into a publication quality diagram (Fig). Both programs are written in Perl as well as compiled into packaged executables with lengthy usage instructions. Generated images got rave reviews from Elsie and Jack and have been included in one publication to date.

Time Estimates

30 total working hours.