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Commercialisation of scientific software; the case for open-source.
September 29th, 2010 by Will Spooner
Since the Fort Lauderdale agreement in 2003, genomics has had perhaps the most 'open' attitude to data sharing of any field of science, and this is reflected in attitudes to software, where open-source is the norm. Much like the Apache web server is invaluable to the internet, scientific open-source software, from aligners to genome browsers, are invaluable…
Single point of failure
September 21st, 2010 by Richard Holland
This should be common sense really, but the weakest point of any software system is the point that is non-redundant and cannot be avoided. No matter how many alternative paths you have that pass through that point, if none of the paths can get to their conclusion by following an alternative route that does not…
European Conference on Computational Biology, Ghent ( ECCB10)
September 17th, 2010 by Nick James
In a couple of weeks I shall be attending the ECCB10 conference in Ghent. I have just been reading through the talks and needless to say it looks interesting. I shall be presenting a poster this time, on "An Ensembl-based pipeline for microRNA prediction and expression profiling using Next Generation Sequencing data" I've already described this…
DBCLS BioHackathon
September 17th, 2010 by Richard Holland
Eagle’s Richard Holland is an author on a bio-semantics paper.
Debian Ensembl update
September 10th, 2010 by Richard Holland
Eagle’s DebianMed contribution of a fully-working .deb file to install Ensembl is almost complete. The demonstration version 57 contains only minor issues now that need to be resolved before it can be released through the Debian package management process. Those issues are: Removal of the embedded JALView as it breaks a lot of Debian’s licensing…
Eucalyptus has now a serious competitor
September 10th, 2010 by Abel Ureta-Vidal
I discovered in this article by Joseph Forn that Eucalyptus, the well known open source infrastructure software to establish cloud environment, is in fact not 100% open source. The story goes that a code contributor, namely NASA, using Eucalyptus internally could not contribute improved code back to the project in specific part of the software…
BioMart 0.8
September 3rd, 2010 by Richard Holland
BioMart will be previewing their new 0.8 version during a dedicated workshop at GMOD Europe 2010. The key change in the new system is a shift from a Perl-driven user interface and backend to a Java-driven one, complete with Web 2.0 technologies such as AJAX and advanced JavaScript toolkits used in the interface design. Under the…