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BSD and Science?
Trish Lynch <[email protected]>

[ This is an article that first appeared in the October 2000 issue of Open Magazine which was submitted to us by the author for republication here. ]

Open Source software grew out of the IT industry's attempt to streamline development cycles and ease of use for computer professionals. How many times did one say, "Now if I only had the source." Still, Open Source had to be accepted by IT management. Industry analysts and IT crystal-ball watchers have all turned that question of acceptance every which way: Where doesn't Open Source work in the here and now? What fields represent hurdles to Open Source principles and methods? Can Open Source thrive in an environment where the core expertise is not specifically computer-related?

This BSD writer has found a match: An industry that has turned away from Microsoft solutions due to massive processing needs and a strong academic tradition, and has turned to commercial UNIX vendors such as SGI, Compaq/DEC, and Sun for their computing solutions. Welcome to the hot field of bioinformatics.

Bioinformatics is one of the fields where users are truly end users. Most are scientists who don't want to know anything about the underlying OS; they just want the machines to work and the OS to run. As such, we are talking about an audience where Open Source faces impediments.

[ An interdisciplinary research area where computer science is used in life sciences, bioinformatics is where the two sciences interface to solve complex biological problems. It includes the collection, organization, storage, and retrieval of biological information and databases. What's more, bioinformatics is having a major impact on drug discovery through the retrieval, storage, and analysis of genetic information. Large-scale databases of genomic information requiring high-performance computing systems are foundations for compute-intensive search and analysis algorithms and applications that make bioinformatics a major focus in drug discovery. Andrew Pollack of The New York Times casts bioinformatics in the light of a wet science, biology, shifting from work done in test tubes to partly a dry one, where crucial analysis is done on computers. ]

Considering all this, one easily sees that Open Source traditionally has worked in other kinds of settings.

The roots of Open Source are in the Internet industry, where users have computing skills, and where computers are not required to have massive processing capabilities, and where typically there is not a lot of money to throw at a problem. In turn, people in the Internet/e-commerce arenas tend to go for self-supported systems such as Linux and BSD. Bioinformatics, on the other hand, is a place where research is done entirely within the silicon structure of a computer. many biologists cannot be competitive without young, new talent in the IT fields today.

Johann Visagie of Electric Genetics says, "With new blood came new ideas, and some of the ideas we brought with us said that there are far more sensible ways of doing things than paying millions upon millions to hardware and software vendors. The idea that Open Source should play an important part in bioinformatics is quickly taking off. If Open Source bioinformatics becomes the norm, you can bet that Open Source operating systems will become common in the field. Linux is finding acceptance quickly."

Visagie is quite optimistic about BSD usage in this field. If one is going to build massive processing boxes out of inexpensive hardware, one may as well use an OS that is "stable, mature, and above all very manageable in a large, networked environment," he states.

There are several biotech software packages ported to BSD now, such as emboss, sim4, bioperl, and biopython, located in /usr/ports/biology in the FreeBSD ports collection; feedback from the authors of these packages has been very supportive. This kind of endorsement is what BSD (also Linux and other Open Source software) needs to succeed in that field.

What's more, hardware is an important factor. By nature, bioinformatics is very CPU-intensive. [ As obviously noted, bioinformatics handles enormous data volumes. ].

Besides x86 and Alpha hardware, which all of the Open Source BSDs support, NetBSD and BSD/OS (BSDi's closed-source BSD offering) have UltraSparc ports. Big Iron support is a significant advantage in the bioinformatics field due to the processing power needed.

With BSD optimists like Visagie, why has Open Source not pervaded the world of bioinformatics? Impediments are largely sociological.

The end users are set in their ways, as evidenced in many academic environments. Can an Open Source solution do the job? No question. It's a matter of acceptance within a community that is largely shielded from technical details.

Might BSD's academic background be used to leverage greater acceptance of the OS in biotechnical fields? This remains to be seen. What we do know is that people like Johann Visagie and their quest for inexpensive, powerful computing in this field are really providing the groundwork needed for long-term success.

- Trish

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