Andreas Prlic homepage

Welcome to my homepage. I am working as a Senior Scientist for the Protein Data Bank (PDB) at the University of California, San Diego (UCSD).

This site provides documentation on current and previous projects I am, or have been working on.

BioJava

I am currently the project leader of the BioJava project. I am developing and maintaining the protein structure module. I also was release coordinator for the 1.6 and 1.7 releases. A related project is HibernatePDB which is a project to serialize the protein structure modules using Hibernate to a database. To view some stats and the latest nightly BioJava builds please visit the BioJava - CruiseControl page.

Distributed Annotation System

While I was working at the Sanger Instute I was working on the DAS system:

The Distributed Annotation System (DAS) is a communication protocol for the exchange of biological annotations. It is motivated by the idea that annotations should not be provided by single centralized databases, but instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. [biodas.org]

Over the last years DAS has become widely adopted by the community and the DAS registration server now counts more than 250 DAS sources coming from around 40 institutions in 15 countries world wide.

SPICE

SPICE is a browser for the annotations for protein sequences and structures that is based on the DAS protocol (and gave this web site its name...). The official web site for SPICE can be found here: http://www.efamily.org.uk/software/dasclients/spice/.

SPICE can be launched from the Ensembl genome browser via the PDB_SPICE - DAS track [demo] or run standalone. It can also be used to visualize multiple structure alignments. [SISYPHUS database][CASP-7] [more info] [publications]