application Archives - Page 5 of 7

Evolution of the Cape Sedges

Jul 19, 2011

Jack Viljoen, a masters student in the Botany department is working on the evolution of Cape Sedges. For reconstructing the evolutionary trees of groups like the Cypereae and Schoeneae (Fig. 1), Mr Bayes

.... we use Monte Carlo Markov Chain (MCMC) sampling…

Maintenance slot scheduled for Sunday – 19 July 2011

Jul 12, 2011

application

Our monthly ICT maintenance slots allow for system administrators at ICTS to conduct configuration changes, system and security updates. Unfortunately during this maintenance slot its a complete power shutdown and therefore no ICT services will be available during 09:00 -…

Sequencing suite

Jul 9, 2011

application, hpc

We spent this week porting a suite of packages for short sequence analysis: Velvet, Oases, FastX, FastQC and Maq. We've only tested Velvet so far, it's memory hungry and seems to run best on the 400…

Crux tandem mass spectrometry

Jul 1, 2011

application, hpc

We recently installed Crux on our cluster for researchers in the IIDMM department at UCT. Unfortunately it's not MPI aware and only runs on single cores. Additionaly the binary we downloaded did not run on the cluster due to a…

Blast!

Jun 1, 2011

application, hpc

Subsequent to the installation of MrBayes we decided to deploy BLAST on the HPC cluster to complement the package on our Grid cluster. BLAST (Basic Local Alignment Search Tool) is a free bioinformatics package…

Fully utilized

May 19, 2011

application, gLite

Our Grid cluster is seeing heavy usage at present, three users running a total of 53 jobs (some queued at present). The longest running job is still going at 1213 hours. The jobs are using Matlab, Auto07 and Root, a …

Parallel poison solution

May 10, 2011

application, MPI

Having installed Gromacs last week we decided to run some tests to see how well it performed on our cluster. We downloaded a tutorial which analysed solutions of funnel web spider venom in water. Given the bounding block size of…

6 million monkeys

May 6, 2011

application, MPI

In order to test the parallel version of MrBayes we ran several simulations of the primates.nex tutorial provided with the installation. This compares the evolutionary species change and divergence between various primates.

Running the parallel version produced predictable results. "Distributing"…

Introducing Mr Bayes

May 3, 2011

application, MPI

One of our students requested that we install MrBayes, software for the estimation of phylogeny on a genetic level. This is a fairly popular package which has been ported to numerous platforms so we thought we'd have a crack…

Getting Gromacs

Apr 22, 2011

application, hpc, MPI

Gromacs is used to perform molecular dynamics simulations. It's a popular tool and we decided to install it on our cluster based on the needs of two researchers, one at UCT and the other in Kenya. Gromacs is designed to…

application

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