Advogato: Personal info for nutella

nutella is currently certified at Master level.

Name: Scrambled Text?
Member since: 2005-01-14 23:43:36
Last Login: 2008-05-17 16:37:22

Notes: This bit didn't come back when I recreated my account after the Advogato glitch.

I am a Yoorpean currently working for a medium-small biotech company in the San Francisco Bay area. After getting my Ph.D. in Yoorp I was a fellow at the National Cancer Institute, a postdoc at UCSF and an investigator at a health science company in the Chicago area. I don't know where life will lead me next.

I am not a computer professional but have been hooked on them since exposure to the school's Commodore PET (1979). I prefer UNIX-like OSs and have used Linux in some shape or form since Slackware 2.0 in June 1994 (kernel 1.0.9). In addition to Intel boxes at home and work I also have a Sun Ultra 5. All run Debian.

Recent blog entries by nutella

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9 Mar 2008 »

Weird! It seems that a reasonably high proportion of the time I visit Central Computers (San Francisco or Santa Clara) Don Marti is there. Clone? Mistaken identity? Eerie coincidence?

20 Jan 2008 »

Zoiks! Is it just me (Firefox 2.0.0.11) or did someone (<cough> adulau <cough>) forget to close a [bold] tag in their RSS feed?

1 Dec 2007 (updated 1 Dec 2007 at 17:44 UTC) »

While using truly Free software allows totally unrestrained joy when passing on tips and tricks to others, there's still some happiness to be gained when the software is proprietary but the recipients of the tip are people with whom you work. Here in the Real World[TM] I have to deal with (non computer) hardware manufacturers who sell overpriced computers running horrible equipment control software and who refuse to give you the "administrator" password, presumably because they believe you'd immediately copy the kludgey software to a more affordable box. Argh! Mercifully there's also equipment specific software written by Real Programmers and they've embedded macro languages that allow you to express yourself and get the job done. Thank you, Oh Sensible Ones! Today I managed to use such a a TIMTOWTDI rich macro language in a strange way and it was clearly The Right Way. It was so beautiful. My co-workers immediately appreciated the extra stability and efficiency, if not the beauty of the code. That was reward enough.

16 Nov 2007 »

GAR! Google GAR!
I wanted to demonstrate to a colleague the prevalence of typos out in the interweb and so asked The Google to return hits containing "Gusty Gibbon" (one of my favourites). Alas the big G assumes that this is just a typo and returns many hits for the more boring correct title.

But what if I was working on a project on primate flatulence? How would I find the information I need?

1 Oct 2007 »

As I mentioned earlier, I have been allowed some time to play with Mathematica at work. I tried to assess it by transliteration of some of those popPK spreadsheets and in doing so it has grown on me. I do like the ability of the random number generator to produce real numbers over a specified range. For Excel I had been forced to use RANDBETWEEN() (which only generates integers) and scale by a large number - this led to many off-by-epsilon rounding errors. Now I can precalculate the log-normal probabilities of each of the target limits of the PK parameters with;
CDF[LogNormalDistribution[mean, cv/100*mean], Exp[value]]
and then generate a table of random parameter values for the population with;
myList = Table[Log[Quantile[LogNormalDistribution[myMedian, myCV/100*myMedian], Random[Real, {myMinProb, myMaxProb}]]], {populationSize}];
This seems to be a small price to pay for having to use studlyCaps for variable names and for forever forgetting to use square brackets instead of parentheses and double square brackets instead of singles. The other major gotcha was not realising that you have to initialise an array (e.g. by setting to Null) if you want to subsequently add values to it piecemeal (the error messages generated are way too arcane).

I also had to change my approach when switching programs as in Mathematica it is actually easier to plot a function defined symbolically than it is to generate a bunch of x,y values and use them.

227 older entries...

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