Computational Biology Resources

The Arabidopsis Information Resource

Dr. Eva Huala directs TAIR (www.arabidopsis.org), a vital resource which provides access to the Arabidopsis genome sequence along with experimental and computationally predicted gene function, gene structures and splice forms, gene products, metabolic pathways, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community.

Computational prediction of gene functions

The Rhee lab has developed AraNet, a probabilistic functional gene network of Arabidopsis thaliana, constructed by a modified Bayesian integration of 24 types of "omics" data from multiple organisms. Based on these datasets, AraNet makes predictions for the functions of poorly characterized genes.

DPB Compute Cluster

The DPB computational cluster currently contains 96 AMD Opteron cores and 128 GB of RAM spread across eight dedicated systems of 12 cores each. The cluster is managed from an NFS file server running the PBS Torque cluster engine and equipped with 10TB of storage for the cluster.

Plant Metabolic Network

The Rhee lab develops the Plant Metabolic Network (PMN), which is a collaborative project among databases and biochemists with a common goal to build a broad network of plant metabolic pathway databases. A central feature of the PMN is PlantCyc, a comprehensive plant biochemical pathway database, containing curated information from the literature and computational analyses about the enes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism. More information about the project and the searchable and downloabled databases are available online at www.plantcyc.org