Mark Schreiber


I first became involved with BioJava in 2000. I was doing my PhD in New Zealand and I needed a Java package that could produce HMMs suitable for gene finding algorithms. BioJava had just arrived and did what I needed it to do. During this time I added some support for circular genome sequences and locations, much of the DistributionTools class, tools to read Phred data and improved the serialization of the core BioJava objects. Some of these contributions have been more succesful than others. I also used BioJava in my PhD research to calculate the information content of motifs and display these graphically.

In 2001 I joined AgResearch, an NZ based agricultural biotech company, as a Bioinformatics Consultant. There I used BioJava to detect SNPs and micro-satellites in EST contigs. While at AgResearch in 2003 I began work on the Biojava in Anger cookbook which I still try to keep up to date when I have time.

In 2004 I moved to Singapore to work as a Principal Scientist with the Novartis Institute for Tropical Diseases. Here I use BioJava to support the Tuberculosis and Dengue Fever drug discovery programs. My research interests have expanded to include evolution, phylogeny and molecular and structural modelling. Some of these may find there way into BioJava soon. I am also working with Richard Holland from GIS using biojava and biosql to make a dengue virus sequence database called dengueinfo. We are also working on an experimental extension and hopefully backwards compatable upgrade to biojava called biojavax (watch this space).

I am sporadically helping to write a book on BioJava with a projected completion date that is very fuzzy just now. My current thinking is that I will make it a Wiki manual or a DocBook xml in CVS so everyone can edit it.