Tuesday, August 25, 2009

Sun Regensburg HPC workshop FULL

Looks like there is still a lot of interest in Sun HPC despite the buy out by Oracle. This is really great news for everyone that appreciates the technical savvy of Sun Hardware and Software. Its not to great for anyone that was wanting to attend. You can still get on the wait list and hope somebody drops out at: http://hpcworkshop.com/. For those of you attending, the town of Regensburg its very beautiful with many historical sites to see as well as the conference. The beer is pretty good too.

Bioinformatics Computer Skills Chapter 1

The first chapter talks about how biological information now is being collected far faster than it can be analyzed or understood. Huge databases are being collected and stored but the only thing that can help with making all this information useful would be fast processing computers.

The first tool talked about is used for searching and finding DNA sequences using programs such as BLAST and FASTA. Which takes us to a web interface at the National Center for Biotechnology Information (NCBI). The book details out all the specifics of what this is and what it means. I will not go into that because my intention is not to copy this book. I could get into a lot of trouble and the authors I’m sure know much more about this than me.

Let’s just suffice it to say that the first tool used is a web browser. OpenSolaris comes complete with Firefox one of the most used web browsers provided by most Linux distributions.

It is spelled out that in order to use most of the powerful programs available you will need to know Unix. OpenSolaris is also Unix and it comes from the very stable Solaris base which has been around as long or longer than Linux. The book talks about the need to probably set up your computer as a dual boot system because you will want to have access to software such as word processors, graphics programs and visual programming tools. With OpenSolaris you have a complete office suite OpenOffice which is compatible with the Windows Office suite. If there happens to be some tool that just is only available for Windows than you can run a VirtualBox Virtual Machine with windows for that one piece of software.  With VirtualBox there is no need to boot and reboot back and forth between Windows and OpenSolaris. Both Operating Systems are running simultaneously and you can move files between the two systems or cut and paste data and text from one to the other.

 

Summarize tools and systems from chapter 1

Web Browser – Already there in OpenSolaris.

Office Suite – Available for OpenSolaris with OpenOffice which is provided with OpenSolaris.

No need to Dual boot, but should it be absolutely required run Windows in a Virtual Machine with VirtualBox.

 

Thanks and stay tuned for tools and systems for chapter 2.

Friday, August 21, 2009

Bioinformatics Computer Skills Chapter 2

So its been awhile since I got a chance to get back to this. Its terrible when work gets in your way of doing things which are interesting.

Not really a lot about computing in this chapter, it discusses mostly the reasons why computers and software are becoming more and more important in the field of Biology. I’ll leave that up to the authors so go and buy the book on Amazon.

What was discussed of interest to the OpenSolaris community would be the concept of Electronic Notebooks. These tools allow for researchers to share their work with each other and speed along the process of discovery. No longer does the individual scientist have his research all locked away in private notebooks never to be seen until the final results are published, or never for that matter. Now we have the concept of putting the records out for everyone to share.

The authors mention a very easy to use Notebook called DOE2000 Electronic Notebook which I tried out. The Notebook is run via a web based interface resembling pages in an actual notebook. There are 2 different version. The first a PHP based system which I installed and reviewed. Another, a Java version soon to be released. All the web needs are available on OpenSolaris by installing the amp package (Apache, MySQL and PHP). Then follow the instructions to install the Electronic Notebook. I had the best results by installing the Notebook package to the /var/apache2/2.2/htdocs directory.

More info on the Electronic Notebook can be gotten here. The project has an online demo which can be viewed at this site and access to the package can be gotten by emailing Al Geist.

Notebook

Go to Demo by clicking here

So again there was nothing in this chapter which could not be done on OpenSolaris.

 

Back to work and reading the next chapters.