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Cloud BioLinux paper published
March 29th, 2012 by Richard Holland
About 10 days ago BMC Bioinformatics published a paper entitled "Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community" (Krampis et. al.). Two of the co-authors, Tim Booth and Brad Chapman, are long-time friends of Eagle and we are currently making use of Cloud BioLinux in some of our projects. Bioinformatics Linux distributions…
Native Amazon workflows for bioinformatics
February 22nd, 2012 by Richard Holland
Today, Amazon's Simple Workflow Service (SWF) was launched in beta mode and marketed as "a workflow service for building scalable, resilient applications". What does this mean for bioinformatics? Quite a lot, probably. One of the biggest headaches of any major bioinformatics task is orchestrating a workflow (or pipeline) to carry out batches of data analysis…
Top stats tips from Ewan Birney
June 20th, 2011 by Richard Holland
In a blog post on GenomeInformatician, Ewan Birney from the EBI lists everything the average bioinformatician should really know: http://genomeinformatician.blogspot.com/2011/06/five-statistical-things-i-wished-i-had.html
Ensembl 60 top tip #1
November 10th, 2010 by Richard Holland
Ensembl 60 came out yesterday. For those of you who are technical developers like us who do in-depth hacking of the source code, there's two things that have changed which you need to be aware of: (this information is shamelessly cribbed from the ensembl-dev mailing list – if you need more details, email the Ensembl team…
SSL and Tomcat
October 29th, 2010 by Richard Holland
A purely technical post this one, because it gave me such a headache this morning trying to figure it out and realising that nowhere was all this written down in one place. In a Java 6 + Tomcat 6 installation, installing an SSL certificate is usually as easy as uncommenting the appropriate Connector in server.xml…
Importing Ensembl into Amazon RDB
October 21st, 2010 by Richard Holland
Ensembl very kindly distributes their databases on Amazon as public datasets in a variety of forms. The most straightforward to use is the set of MySQL database files that can simply be copied into your MySQL server’s data directory and they will become instantly available. However, the most cloud-like way to use databases within Amazon…
JSON for Ajax
July 26th, 2010 by Richard Holland
JSON is so much easier to work with in Javascript than XML. This makes it perfect for coding responses from AJAX-backed web services. An example JSON data structure: { ‘projects’:[ {'ID':'1','Type':'StrangeProject','Members':['Joe','Jim','Jane']}, {‘ID’:’2′,’Type’:’NiceProject’,’Members’:['Richard','John','Joe']} ] } And here’s how to parse it in Javascript (myJSONData is a text string containing the above structure, e.g. lifted directly from…
Building an Ensembl .deb
July 21st, 2010 by Richard Holland
Quick one today – we’ve been asked to build a .deb containing the same Ensembl installation as can be found in our EagleBrowser product. Turns out to be easier said than done! Whilst the basic specifying of package dependencies and provision of bugfixed/modified source code is easy enough (the modifications are to remove references to…
Random bash shell tidbits
July 9th, 2010 by Richard Holland
This is probably common knowledge, but worth repeating since it saves so much time. 1. If you’re typing a long list of commands that all end in the same parameter, e.g. a username, you don’t need to keep on typing that last parameter out every time. Instead, type !$ in its place and bash will…
Creating Amazon EC2 AMIs – the basics
July 7th, 2010 by Richard Holland
This morning at the Codefest 2010 I was asked to give an impromptu presentation about the basics of getting an EC2 image up and running. Here is a brief summary of how it all works, using the command-line tools. Of course you can use the EC2 console as it can do it all for you,…