nodalpoint.org

I have created a new "about" page for nodalpoint (see top right for the link), hopefully this should make things a little clearer for new visitors to the site. I didn't spend a great deal of time writing the text, so I welcome your suggestions. If anyone wants to be added as a "regular" contributor or if you want to change the text you should be able to edit it yourself. I have also attached the previous comments regarding our about page to this thread.

Update: I am retiring the old "book" module and moving all the documentaiton to the nodalpoint wiki. Please go there for the most upto-date information about nodalpoint.

The nodalpoint bioinformatics weblog takes its name from a term that William Gibson coined in is book Idoru. He used the word nodalpoint to describe a singularity or convergence point in a sea of overwhelming information. Nodalpoint is primarily maintained by me (Greg Tyrelle) as an enjoyable distraction from the daily grind of working as a bioinformatics researcher. The site has been lucky to have some excellent contributions from researchers in the school of biotechnology and biomolecular sciences at the University of New South Wales, Sydney, Australia (where I graduated from). These individuals are often referred to as "the usual suspects", they are Neil Saunders, Chris Cotsapas and Matt Hope (a.k.a Dopey). The site has been running now for almost five years, thanks to everyone that has posted or commented on the site.

For more information about the site (contact details), please see the nodalpoint documentation.

Version (0.2) of my Firefox extension to make LSIDs "clickable" is available from http://darwin.zoology.gla.ac.uk/~rpage/lsid/.

This version uses a server in Glasgow to resolve the LSID, rather than bounce you to the Biopathways site. Basically this makes browsing LSID metadata much smoother -- if the metadata refers to other LSIDs, you can simply click on those as if they were URLs.

This is still all a bit crude, but here are some example LSIDs to try:

• A North Temperate Lakes protocols (urn:lsid:limnology.wisc.edu:category:chem)
• A PubMed reference (urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed:12441807)

I don't know if I've confessed publicly to this on nodalpoint, but I am a big fan of the semantic web. The life science identification protocol (LSID) is related to the semantic web, but is yet to gain any real traction. LSID has been covered on nodalpoint in the past. There is currently a thread on the W3C semantic web for life sciences mailing list asking for suggestions on how to make LSID work. I have been meaning to reply to that thread so this post is intended a reminder for me and announcement for anyone who may be interested in contributing to the discussion.

I won't go into detail here, I'll save it for my reply, but generally speaking the problem is we don't have a clear path showing how the semantic web should benefit the life sciences. More to follow...

Once a month my Journal of Bioinformatics rss feed is updated with the latest research in the field. Herein I present my pick for bioinformatics paper of the month. Having spend many long hours pondering microarray data normalization I am thrilled to see it is still an issue for some people. However as fascinating as microarray data normalization is, my pick for bioinformatics paper of the month is:

A parallel graph decomposition algorithm for DNA sequencing with nanopores - Shahid H. Bokhari and Jon R. Sauer

That's right, a sequence assembly algorithm for a technology that doesn't exist yet. Still, it represents an interesting bioinformatics problem. How to assemble complete DNA sequence from variable read lengths up to 10^5 bases, where complementarity is unknown, the orientation is unknown and errors from the nanopore sequencer may also be unknown.

I'm finally ready with the latest release of biobar. See Post 1547 or Post 1537. Biobar is a toolbar project for firefox/mozilla/netscape, which allows a user to easily search and retrieve data for a particular search term straight from many biological data collections. The latest release provides access to 38 biological databases . Based on user input from Nodalpoint and other users this release has the following salient features:

Posts about bioinformatics tools, many created by nodalpoint readers.

Posts about content management systems: Drupal, plone, phpwebsite etc.

Posts about cluster computing

This book contains the best posts and comments to nodalpoint. We often have perma threads on nodalpoint, such as the definition of bioinformatics, the best tools to use, and how to build clusters. Post are grouped by category bellow.