24 Feb 2005 titus   » (Journeyer)

Random Miscellany

Undefeatable spam. (Well, at least without real AI.)

Public posting of genome shotgun data can lead to the discovery of new species, sequenced unintentionally. Heh.

CatchUp! Record the refactoring of your API, then "play back" the refactoring on dependent applications. Very cool!

WaterBot. I don't get it.

Corollaries and Laws

My first rule of thumb (a.k.a. "law that I will force into every technical discussion, irrespective of relevance") is this:

Rule Z: A marshalling library isn't complete unless A = load(marshal(A))
A corollary is this:
Corollary Z_1: An analysis program isn't usable by other people unless it is possible to build a complete marshalling library for the output.
This is one of my bet bioinformatics peeves: people (or large institutions) who build otherwise useful programs that have an utterly nonregular output format, rendering these programs largely useless for pipelines.

Corollary Z_2: A list of tab-delimited lists is not a real file format.

'nuff said there. One day I hope to be inspired enough to write a rant about this; my title is already planned out: "You wouldn't use Excel as your database, so why are you using GFF?" (GFF is a simple tab-delimited format that everyone uses in bioinformatics.)

Another rule of thumb:

Rule Y: Premature standardization is the root of much evil.

Writing data export specs before you've talked about use cases with at least three other groups is one flagrant contravention. Solidifying APIs without actually developing a real application that uses them is another.

Prevayling Stochasticity

Via Max Ischenko, the Pyrasun rant about Prevayler is pretty wild. Mike Spille seems to have some serious objections to Prevayler, and after reading the interview with Klaus Wuestefeld I get a bad feeling about it, too. It's not like this guy Klaus needs any more publicity -- even (or especially?) bad publicity must feed his ego -- but there are some choice quotes in the interview:

Q. "Who are you?"
A. [ ... ] "That is, I'm an nonconformist. [sic]"
Q. "What would you say to those people who own this kind of application [SQL app], and want to migrate to OO using Prevayler?
A. " Initially, they will feel like Neo, floating on that water container, completely atrophic, for living their entire life inside a database bubble."
Q. "Have you ever been confined in an asylum?"
A. "In reality, I'm just a prophet."

Wow. Well, if attitude and arrogance equalled credibility, this guy would be even more credible than me.

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