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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…
Changing understandings
September 22nd, 2010 by Nick James
Often in science our understanding of whats really happening can change completely.
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…
Amazon S3 as a File System in Amazon EC2
September 20th, 2010 by Madhu Donepudi
As a cloud application developer, shared storage on EC2 is particularly challenging when GBs of data has to be accessed by 100s of EC2 instances. One particular option we explored is leveraging our Amazon S3 storage to mount on EC2 instances and use as a shared drive. Most popular software solutions for this approach are:…
Where in the world are the bioinformaticians?
September 17th, 2010 by Richard Holland
As Eagle expands, we hire new staff from time-to-time to cope with the increased workload. (We’re not currently hiring by the way, this is a general comment piece…) The UK’s tough new immigration laws make it almost impossible for us to hire anybody who doesn’t either have a UK or EU passport or already have…
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…
ProServer Das, Ensembl and EC2
September 9th, 2010 by Nick James
If you use the ProServer DAS server with some Ensembl-based adaptors ( maybe you want to server data from Ensembl, or maybe you have genomic data and want to serve it with some extra annotation that is in Ensembl ) then you may have come across the ‘mysql has gone away’ timeout error. Basically what…