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.


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.

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