Our High Performance Computing Cluster
WSB has its own dedicated HPC cluster, based on Dell Poweredge servers and CentOS, with 224 AMD Opteron cores and a total of 2.5 TB RAM. Parallel and distributed computing is managed the Torque/Maui resource manager/scheduler. The cluster runs a range of common open source applications and programming languages, many bespoke packages devopled in house, and the MATLAB distributed Computing Server. In addition, WSB members also have access to the HPC clusters in the Centre for Scientific Computing. There are also facilities for local mass data storage, and the creation of sophisticated websites in a rich development environment.
The following publicly available software tools are hosted on our systems
Evolutionary analysis of regulatory sequences
A web interface for the sequence analysis algorithm described in Picot et al (2010). This allows DNA sequences to be uploaded to our computational cluster for analysis and the display of results.
MEME Launcher and Browser is an online tool that allows the user to easily overview and analyse the results of motif discovery using MEME on a number of clusters of co-expressed genes. See Brown et al (2013) Bioinformatics 29(13): 1696-7.
Find transcription factor binding motifs in a single DNA sequence. See Reid et al. (2009). BMC Bioinformatics 10:218.
Bayesian Segmental Models
Software developed by David Wild and others for SPAM (Systematic Protein Annotation & Modeling) project. The SPAM project is based on work sponsored by the National Institutes of Health (NIH) and its National Institute of General Medical Sciences (NIGMS) division under Grant Number 1 P01 GM63208 (NIH/NIGMS grant title: Tools & Data Resources in Support of Structural Genomics).
Streptomyces coelicolor Pathway Reconstruction
An Approach to Pathway Reconstruction Using Whole Genome Metabolic Models and Sensitive Sequence Searching