A mixed bag

There's an interesting series of notes in Macintouch on how to justify the use of Macintoshes in mixed computer environments and the rationale given by many network administrators to standardize on a Wintel platform. It seems ludicrous, particularly when such an attempt occurs in an educational institution, where choice and free thought is promoted, and in fact is supposed to be a fundamental tenet of our society. To paraphrase one post, it's time to turn the arguments around. When IT discusses the need to standardize, ask them for their cost-benefit analysis for the Windows platform. Make sure they don't forget to include the cost of installing security patches, cleaning computers of viruses, updating virus dats, etc. One university euphemistically calls this "remediation." Oh, good. Today Microsoft reported that they expect another worm/virus attack this week.

I've spent the last several days working out the last few details on the genome grant. For the sequencing phase we're down to working with my favorite university genome center (one of several built for the human genome sequencing project) or to continue to work with a commercial sequencing outfit. There are significant advantages and disadvantages to both.

The genome center is considerably cheaper which will allow my collaborators and I to carry out our original , have considerable experience in completing genomic sequence of high quality, they are close to me physically, and it will be easier to set up a collaborative agreement with them (instead of having to work on a huge contract. The genome center will also be slower (other concurrent projects), and at the quoted dollar amount, once they get to the hard part (gap closure), there may not be enough funds to cover it.

The commercial outfit will be faster, more integrated with our bioinformatics partner, and will give a high quality sequence. However, they will be considerably more expensive which will not allow us to complete some of the educational and annotation objectives, and at the budgeted amount, may not be able to actually complete the entire genome (no or few gaps) without additional money (contract is fixed for a certain number of base pairs).

Interesting process, and I'm learning a lot.