Installing EMBOSS on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

EMBOSS is "The European Molecular Biology Open Software Suite", a free and open source analysis package specially developed for the molecular biology community, by allowing the retrieval of sequence data in a variety of formats as well as providing extensive libraries.

Installing Ultrascan on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

UltraScan "attempts to be a comprehensive data analysis tool for the hydrodynamic studies of macromolecules and macromolecular assemblies with analytical ultracentrifugation experiments."

Sounds like fun. Let's install it. Get the tarball, ignore the part of the site which uses frames and extract in a sensible place, such as /usr/local/src/ULTRASCAN (tar xvf ultrascan-9.9-888-qt-3.3.8-ix86-linux.tar.gz).

Now the fun starts

Google have announced Google Chrome OS. This is interesting on several fronts.

Firstly, and most obviously, this is an open statement of war on Microsoft. It is written in the text of the announcement "We hear a lot from our users and their message is clear — computers need to get better." This device will have no MS APIs on it. None. Nada. The end of the MS lock in.

Which Bank?

Which bank gets confused about some fairly trivial technical and security issues on their own helpdesk system?

Installing OpenFOAM 1.5 on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

OpenFOAM (Open Field Operationa and Manipulation) is a computational fluid dynamics toolbox which simulates "anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics, electromagnetics and the pricing of financial options." All this and free and open source as well.

Annoying older Mailman bug with certain MIME types.

Multipurpose Internet Mail Extensions (MIME) is an Internet standard that extends the format of e-mail to support various extended formats. However with older versions of Mailman there is a serious bug which affects the archives.

MIME allows the following:

  • Text in character sets other than ASCII
  • Non-text attachments
  • Message bodies with multiple parts
  • Header information in non-ASCII character sets
  • etc.,

Installing Velvet 0.7.31 on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

From their website; "Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom."

Installing Desmond-2.0.4-0 on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

Developed by D.E. Shaw Research, Desmond performs high-speed molecular dynamics simulations of biological systems using parallel algorithms and numerical techniques. The README.txt explains the horror that will prevail...

Installing NAMD 2.7b1 with CUDA on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

NAMD is a parallel molecular dynamics code for large biomolecular systems. Version 2.7b1 has some advantages over 2.6 and an extensive user's guide. CUDA (Compute Unified Device Architecture) is a parallel computing architecture developed by NVIDIA providing a computing engine in NVIDIA graphics processing units or GPUs. It should make NAMD awesome, if it works.

Dreadmwidth/Livejournal Collaboration for ARCS

Dreadmwidth/Livejournal Collaboration for ARCS v0.1, May 11, 2009

1. What is this?

A proposal to use the free and open source technologies used by Livejournal ( and further developed by Dreamwidth ( to create an effective social collaboration and journaling site for Australian researchers.

2. Background


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