Monday, December 10, 2012

Protein Feature View goes open source

The source code for the Protein Feature View has been released at github. This allows you to incorporate the dynamic SVG graphics visualizing UniProt and PDB relationships into your own web sites. You can either use the public JSON services provided by RCSB PDB to populate the view, or display your own data (after setting up your own services).

Saturday, December 8, 2012

RCSB PDB's NAR paper

The manuscript describing recent developments at the RCSB PDB has been released as part of the latest Nucleic Acid Research database issue.

View the manuscript at NAR

The Author Profile provides a graphical timeline on when a particular structure was released in the PDB.

Some of the highlights of this year are improvements in the following areas:
Our continuous efforts to provide a structural view of biology are also reflected by an increase in our user base.  The RCSB PDB web site currently hosts ∼240 000 unique visitors per month (based on the number of unique IP addresses), an increase from the 180 000 visitors last reported in 2011. 

Thursday, December 6, 2012

Ten Simple Rules For The Open Development of Scientific Software

Jim Procter and I drafted a new manuscript for PLOS Computational Biology describing ten simple rules for the open development of scientific software. Our motivation for writing this was to make the development of open scientific software more rewarding and the experience of using software more positive.  The ten rules are intended to serve as a guide for any computational scientist:

Ten Simple Rules For the Open Development of Scientific Software (article)

Tuesday, December 4, 2012

RCSB PDB is hiring

The RCSB PDB is one of the leading biological databases with more than 240,000 unique visitors per month. We have an open position in our team for a Lead Web Architect. The position is located in beautiful San Diego at UCSD .

A detailed job description and online application form can be found at:


* MS Degree in Computer Science or comparable combination of education and experience with considerable focus in JavaEE software development.

* Established demonstrated work experience in the role of an architect and developer on medium to large size database-driven web applications using Java EE technology and standards.

* Advanced experience developing the presentation layer of a dynamic, database-driven web application using HTML, CSS, JavaScript, JavaScript Toolkits, Ajax, JSP, XML, Java. Experience resolving browser and cross-platform compatibility issues. Advanced experience with Struts2, Tiles, jQuery.

* Advanced experience with database design, Structured Query Language and RDBMS's such as MySQL. Expertise in web application server administration and configuration such as Tomcat.

* Established expertise in software life cycle methodologies. Experience with build tools such as Maven and Ant, and continuous integration systems such as Cruise Control. Experience with project tracking tools such as Jira.