A tool called Load Sharing Facility (LSF) is used to manage the queues of submitted computing jobs on the HPC cluster. See LSF on HPC Cluster for a summary of the factors considering in prioritizing submitted jobs in the queue. More information is available at the FAQ for HPC users; additional documentation on LSF commands can also be found via Google searches, e.g. LSF Basics at Stanford University.
The most current list of software available on the HPC can be obtained by logging into the HPC and listing the contents of the directory /usr/local/apps. As of mid-November, 2013, installed software useful for biological research applications included a mix of open-source and commercial tools:
Submitting to the HPC