Samuel's Tech Blog

As I concluded in a question on Biostar, there has been no real consensus on a short, non-hijacked hashtag to use for "High-Througput sequencing" / "Next Generation Sequencing" on social media sites such as twitter and identi.ca.

After some community voting, a new winner turned out: #deepseq (click for twitter feed)

So, do spread the word, and start using it!

This blog has been silent for a while and someone might wonder what I've been doing.

One answer is: Developing a graphical client for non-linux-experienced users to connect securely to a computer cluster and configure batch jobs for common bioinformatics software. The project is financed within the UPPNEX project, and so the focus is foremost analysis of Next Generation Sequencing data, but the client will be fully capable to use for any software installed on the cluster.

The client meets a rising need in the next generation sequencing community, since biologists generally have far less experience with *nix systems and programming, than, say physicists, while the vast amounts of sequencing data increases the need to use large scale computing resources such as the ones provided in the UPPNEX project.

I demonstrated a proof-of-concept version at the UPPNEX-SciLifeLab bioinformatics forum on Feb 22nd, and the slides are now available:

• Download slides
  

As can be seen in the slides, the client is based on the very capable Bioclipse platform.

The other day we set up a repository at the UPPNEX website, for typical workflows/scripts, used for mangling Next Generation Sequencing data at the SNIC-UPPMAX HPC clusters. Only two scripts there so far, but we are expecting more to come!

We were discussing different solutions for such a repository, including sites like gist.github.com and www.myexperiment.org, but settled for an own repository in order to provide maximally convenient access for the not-always-so-computer-mileaged NGS community. We'll encourage users to also publish their scripts on sites like myexperiment.org though (Actually, that kind of publicity should be a good thing in general for UU).

• Visit repository