Bioinformatics Comes To .NET

My interest in molecular biology grows with each issue of Scientific American and each Technology Review post I read.  For a C# and Java developer, such as myself, Bioinformatics is a natural progression from programming into cell biology. I’m also a big open source proponent. So what do you get when you throw all these together? An open source project that brings the popular BioJava bioinformatics library to .NET, where I’m the latest team addition. BioSharp is the first open source project that I am actively working on.

BioSharp was started by Doug Swisher out of curiosity about how BioJava was implemented. Since .NET lacked an equivalent framework, Doug decided to create a port of BioJava in C# to aid his learning.

Currently I’m converting the classes from the org.biojava.ontology package to the BioSharp.Core.Ontology gene ontology namespace. As a non-native English speaker, the term ontology was new to me, and immediately caught my attention. So I spontaneously started working  on BioSharp’s gene ontology.

It turns out implementing the gene ontology library requires more knowledge about parsing files and building hierarchies of related terms (which could be any term not just biological terms) than knowledge about genes and cells. This suits me very well at this early stage, since my knowledge of cellular biology is extremely limited. I’m definitely working on BioSharp out of enthusiasm for molecular biology, rather than being an expert at anything biology related.