Computational and Systems Biology Summer Institute
Iowa State University

1. Datasource access plugins for CellDesigner
     I am developing plugins for CellDesigner which directly access pathway databases such as MetNet and BioCyc databases.  I need help testing all the features of my software as well as help coding.  This can be either or both a software-using project and a programming project.

2. JavaCyc API upgrade
    I'd like to improve JavaCyc, the Java port of the BioCyc API (Application Programming Interface), by making it object-oriented.  This is a programming project.

3. Massively Parallel Programming on the GPU
     I have some ideas for implementing algorithms on a Graphics Processor using the CUDA framework by NVIDIA.  These include an improvement to my existing non-parametric randomization tests for microarray data and computing partial correlation networks.  These are programming projects.

4. -Omics data processing and management
Our lab has proteomics, transcriptomics, and metabolomics data for the grapevine which needs to be stored, managed, and processed.  This could involve writing scripts to store the data as well as using existing software tools to analyze the data.