New look and feel at RCSB PDB web site

RCSB PDB has been advised by a worldwide top consultancy about how to take the look and feel to the next level. We are planning to release the result with the next major update. Please take a look and let us know any feedback:

http://betastaging.rcsb.org/pdb/home/home.do

How Google Buzz affects my Blog

I like Google Buzz, since most of the postings that I can read there are mainly work related. It has also affected my blogging here: While I still don't seem to get many comments on my postings here, it seems people like to comment on Buzz, where this blog is listed as a connected site of my account. I will start adding links to Buzz threads of my blogs in the discussion section.

Converging the different Google technologies would be nice in this case. Google are also owning the site that is hosting this blog. Why can't Buzz threads related to this blog automatically appear here?

Google Summer of Code 2010

Our (the Open Biology Foundation's) application for the Google Summer of Code has been accepted. http://socghop.appspot.com/gsoc/program/accepted_orgs/google/gsoc2010

I am offering to mentor a project to develop an All-Java Multiple Sequence Alignment algorithm as part of the BioJava project.

If you are an interested and skilled student, take a look at the project description, and if you think you are up for the challenge, send me an email with your application.

http://biojava.org/wiki/Google_Summer_of_Code

Latest release of RCSB PDB web site contains all vs. all protein structure alignments

Last night we released the latest major version of the RCSB PDB web site. This release contains a number of exciting new features:

All vs. all protein structure alignments

* Interactive Structure Alignment Display
* Expert Mode for Protein Comparison Tool

General Site Improvements

* Home Page Layout and Customization
* OpenSearch Integration
* Resizable Viewer Applets

Query Results Page and Tabular Reports Improvements

* Bidirectional Sorting
* New Image Collage Page
* Report Table Filtering
* One-to-Many Relationships in Report Tables

Ligand Search Improvements

* Ligand Top-Bar Search
* Ligand Advanced Search
* Chemical Structure Search
* Ligand Summary Page

In our latest publication, we are discussing the benefits of the use of Widgets in bioinformatics and demonstrate a few examples that we are making available from the RCSB PDB website:

Will Widgets and Semantic Tagging Change Computational Biology?

Testing upcoming release of all v.s. all protein structure alignment comparisons

At RCSB PDB we are currently working on an all vs. all comparison of PDB. A preliminary version of this is available from the betastaging site for public testing. e.g.:

http://betastaging.rcsb.org/pdb/explore/structureCluster.do?structureId=2W72

This is a beta site so it might not always be available or some things might not work as expected, still it should give you a pretty good impression of what is in preparation. If you want to help testing, have a look there and let me know how it goes.

Some documentation on the all vs. all procedure can be found here:

http://betastaging.rcsb.org/pdb/static.do?p=general_information/cluster/structureAll.jsp

BioHackathon 2010

Currently the BioHackaton '2010 is happening in Japan. The goal is integration of biological resources with Semantic Web technologies. Brad Chapman is blogging about what is going on there. Here links to his blog:

Day 1

Day 2 - Python SPARQL query builder

Day 3 - Fish, interoperating and data retrieval

Day 4 - Improved python SPARQL query interface

Day 5 - The final day