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GlusterFS vs a future Distributed Bioinformatics File System
March 28th, 2013 by Mutlu Dogruel
What is GlusterFS? The main theme of this year’s Eagle symposium was Big Data and its implications on Bioinformatics budgets. We have been witnessing a dramatic departure from conventional back-end storage practices recently with the rise of technologies such as Amazon S3 and Hadoop. Hadoop coerces us to think in terms of the “divide and conquer”…
Elements of Bioinformatics table – now with Search!
March 19th, 2013 by Richard Holland
We released a new version of our Elements of Bioinformatics table this morning – otherwise known as the Periodic Table of Bioinformatics. There's been a few changes which we hope you'll like: Search tools by name – they will highlight in yellow. Filter tools by year – maybe we should call this the Bioinformatics Time…
Crowdsourcing pros and cons
February 28th, 2013 by Richard Holland
I wanted to blog about this paper on crowdsourcing in bioinformatics but had great difficulty in finding any way of getting across the message without simply cutting-and-pasting the entire paper verbatim. Readers with an interest in the field would do well to read the entire original, but here I'll try to summarise it in a…
An embargo on short read alignment tools
January 23rd, 2013 by Richard Holland
Mick Watson wrote this excellent post on his own blog just before Christmas. I couldn't resist asking if I could repost it here as I agree with so much of it, and luckily he said yes. – RH Two things happened recently that inspired this blog post. The first was an excellent review that revealed…
Private Key SSL Connection to Self-Signed Website Using Java
October 26th, 2012 by Bart Ailey
I recently had to write a Java web client to a external website with a self-signed certificate and secured with a private key. This was not something that I have done before; most of my work has been within company firewalls. There is a lot of information on the web about how to do parts…
Periodic Table version 2 released
September 24th, 2012 by Richard Holland
We have just released a useful update to our periodic table of bioinformatics tools – the Elements of Bioinformatics. New tools have been added, old ones have been updated and all the tools can now be viewed in an expanded view with extra details. We've made it easier for you to make suggestions for updating…
Four things every sequence analysis pipeline should do
September 4th, 2012 by Richard Holland
Titus Brown writes a good blog, and so I am surprised that I didn't spot his December 2011 post on "Four reasons I won't use your sequence analysis pipeline" any earlier than I did. So, somewhat belatedly, here is my response to his excellent set of arguments against commercial providers of sequence analysis pipelines and…
The power of open science
August 21st, 2012 by Richard Holland
This is a really short post – the video on the BBC website in this link gives the full story. A 15-year old teenager from the US has developed a pancreatic cancer test which greatly undercuts the cost of the existing standard test, and runs several orders of magnitude faster. Aside from this remarkable achievement…
Model Patents
August 8th, 2012 by Richard Holland
A couple of weeks ago, Stanford University published details of the first complete computational model of an organism representing every interaction that takes place within it during its entire lifecycle. Whilst only a humble single-celled organism, this is a big step forward. It has long been the desire of researchers to be able to minimise…
Apache projects around Hadoop in a nutshell
June 28th, 2012 by Mutlu Dogruel
You might be a little surprised to know that Apache Software Foundation hosts over 100 top-level software projects, but you will certainly be surprised to know that there are at least a dozen Hadoop related Apache projects, if you haven’t come across them yet. Today I will mention briefly about 4 projects in the Hadoop…