nodalpoint.org

Greetings,
I have been working on a platform to facilitate the browsing of recent literature in specific fields of the life sciences. The platform displays stemmed tags extracted from abstracts and organized as a tag cloud. We have compiled a database of citation frequency for researchers and journals and we use this data to format the tags related to importance (i.e. more highly cited journals and PIs have tags with a larger font size). We are still working on optimizing the database queries, but it is now fully functioning. We are using AJAX callbacks to enhance usability and speed-up the browsing process.

Pedro mentioned it, I mentioned it but there's no harm in mentioning it again. BioPerl has a redesigned website built on MediaWiki and an associated news blog. Great stuff.

Get your grass skirt on, the proceedings from the Pacific Symposium on Biocomputing (PSB) 2006 have been recently put online. There are eight papers about semantic webs for life sciences, two of particular interest to anyone who is building and using ontologies in bioinformatics, and didn't make it to Hawaii.

There was this article at BioIT-World this week about a Malaysian company named Synamatix

...Synamatix’s approach is to find patterns in sequence data and identify relationships between the patterns. This information is used to infer the function and significance of various patterns.... automatically learns and identifies similar patterns from raw data sets and stores each unique pattern only once. This helps deal with scaling (less data needs to be stored) and computational speed.

For those of you interested in data analysis (in and out of databases), you can read the company's white papers where you might get a hint of what or how they did it...

Nathan Myhrvold is predicting the end of relational databases for *omics data storage:

'heavy reliance on relational databases like Oracle, SQL, and DB2 within the field of proteomics and genomics is "completely boneheaded."'

This quote is from a short news piece on BioIT World. On the one hand it is quite a glib statement to make, "the end of X as we know it...", however there might be some truth to it...

The January 2006 issue of Nature Biotechnology contains four letters to the editor which reply to the infamous Are the current ontologies in biology good ontologies? article by Larisa Soldatova and Ross King.

I just read this article in the Scientist. It makes interesting reading, since most of us are/have been PostDocs sometime or the other. The biggest problem, and getting worse, is the one of there not being enough tenure-track positions in Academia or industry where PostDocs can be accomodated after a few years of training.

So what use is a PostDoc stint anymore ? Do people here think that the age of the PostDoc is slowly going to be replaced with the PostDoc continuum, where PostDocs remain in limbo for 8-10 years or more ?

Welcome to nodalpoint forums.

Surfing to Nature's blog domain gives a RedHat Enterprise Aapche default page. Linux is more common than we thought...

Two related articles in the December 2005 issue of Plos Computational Biology describe the state of the art in biomedical ontologies and where they might be going in 2006.