by Mark Stone on June 01, 2009 11:15am


The 1.0 release of WinBioinfTools might seem like a modest event; as of this writing, the project has
44 downloads. High Performance Computing (HPC) is a small community, granted, and the number of HPC
applications for bioinformatics is a small subset of that. Let's not confuse popularity with importance,
however.

We use the phrase "mission critical" very frequently and somewhat casually within software development. In
talking to a friend about the swine flu outbreak, I was reminded that the phrase has its origin in
military history: an aspect of a mission so critical that failure in that aspect would result in the
loss of life. In the developing world where medical infrastructure can be a fragile thing, information about
the origins or genetic makeup of a virus can be vital. It can be mission critical.

Historically, the developing world has been dependent on developed western countries to do their research for them.
Open source is beginning to level that playing field, though. Using a cluster environment and software
projects like CoCoNUT for gene sequencing and comparison, even university research centers with modest x86
server environments can play in the HPC space. This is important because the research priorities for a
university in a developing country may be very different from the research priorities of a major western
research university. At its best, this is exactly the kind of lowering of barriers to entry that open
source should facilitate.

For all its value, CoCoNUT has two significant limitations. Its license is an academic license, not a fully
open source license. And it runs only on Linux/Unix systems. The latter is particularly important. Research
scientists are not IT professionals, and they should not have to care about the underlying platform on which
their software runs. The spirit of open source is to make software as widely available as possible, and there
is no way to meet that spirit without including Windows Server among the target platforms. Mission critical
demands no less.

So WinBioinfTools makes important steps forward on both fronts. The team at Nile University has released a
GPL-licensed project that "contains a number of programs for Bioinformatics running over Windows Cluster running
Windows HPC server 2008. The current version includes the CoCoNUT system for pairwise genome comparison,
parallel global sequence alignment, and parallel BLAST."

This is a great example of a local software community using open source to make their needs a priority,
and delivering a project that will benefit local software communities in other developing countries with
similar needs. WinBioinfTools puts us one step closer to making scientific computing software platform
neutral, and closer to making Windows Server a first class citizen in the open source world of HPC.