Releasing Chipster 2.0.1

I have just pushed out server packages for our data analysis environment Chipster, version 2.0.1.

Chipster was originally developed for microarray data, and now in version 2.0 it has been extended for next-generation sequencing data: the new version contains dozens of NGS tools, integrated genome browser and revamped infrastructure.

Typically release of the server packages follows a week or two after we have released the version to our production environment. This time, however, we decided to wait for the upcoming virtual machine packages and release them all together.

In the end, it turned out to be a learning process for us and took quite a bit longer than expected. We are rolling out the images with Ubuntu VMBuilder and distributing them to our clusters, and to everyone else, via nic.funet.fi file server. Getting the process to be robust took many iterations, and because of the almost 100 GB image size, each iteration took its time.  

But now we have Chipster 2.0 rolled into Ubuntu based virtual machine images, and released together with some small fixes as version 2.0.1. We would love to get feedback, so that the process could be improved further.

These virtual machine bundles will be the primary release format from now on. For a couple of months we have been using them exclusive to run our own development and production environments, using OpenNebula and VMware vCenter. From our experience we can say that we love those images, even though virtualisation middleware is not as mature as you would hope. For us, private clouds are a definite improvement over the previous platforms.

While I'm at it, I'll also mention three publications that I have so far forgotten to mention here. First of them is the "official" publication about Chipster, the second one in discusses massively parallel cloud computing work that we have been involved with, and the last one is a very nice example of stuff that can be done with Chipster (with contributions from Massimiliano, one of our team members).

• Kallio et al.: Chipster: user-friendly analysis software for microarray and other high-throughput data, BMC Genomics (2011).

• Niemenmaa et al.: Hadoop-BAM: Directly manipulating next generation sequencing data in the cloud, Bioinformatics (2012).

• Mäkinen et al.: MED12, the Mediator Complex Subunit 12 Gene, Is Mutated at High Frequency in Uterine Leiomyomas, Science (2011).

What next? More releases, of course. While fiddling with the 2.0/2.0.1 release, we have had the development work progressing on the side. So next ones should follow soon, hopefully. :)