News and Blog

News and Blog

MapReduce Genome Assembly using Contrail

July 29, 2010 / 1 Comments / in Bioinformatics / by Richard Holland

Contrail has to be the most impressive application of MapReduce I've seen yet.

Next Generation Sequencing conference in Nottingham, UK

I shall be attending a next generation sequencing conference in Nottingham in August and hopefully presenting a talk. The talk would describe nicely a project that I have been involved over the last month or so.  I've just written an abstract for..

JSON for Ajax

JSON is so much easier to work with in Javascript than XML. This makes it perfect for coding responses from AJAX-backed web services.

Building an Ensembl .deb

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..

Security of open-source

Just a quick one today, being thoughts about how secure open-source software is. There's an argument that goes along the lines of it being less secure because hackers can read the source code and spot the vulnerabilities that way. That's not..

Solutions without problems

There are so many good ideas floating around in the bioinformatics open-source world that its hard to know what to do about them all. Sometimes it feels like almost every day yet another paper has been published on some fantastic piece of software..

Open source vs. open development

At the 2nd day of BOSC 2010, Ross Gardler of the Apache Software Foundation gave a keynote which triggered no end of discussions afterwards about the difference between sharing your project's source code, and sharing its development too.

Do web services go to heaven?

July 11, 2010 / no comments / in Bioinformatics / by Richard Holland

Sebastian Schultheiss talked at BOSC 2010 about the lack of maintenance of bioinformatics web services after the paper that describes them has been published. This also applies to bioinformatics software in general. What happens when the PhD that..

To cloud or not to cloud

July 10, 2010 / no comments / in AWS, Bioinformatics, Cloud, EC2 / by Richard Holland

Today was the 1st day of the 2 day Bioinformatics Open Source Conference (BOSC) 2010, held in Boston MA. The variety of topics covered during the 1st day was huge, but here are some highlights.

Random bash shell tidbits

This is probably common knowledge, but worth repeating since it saves so much time.

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