Older blog entries for nutella (starting at number 231)

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?

Zoiks! Is it just me (Firefox 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.

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?

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.

Pump up the func
I've mentioned previously that I have been experimenting with some PBPK and enzymology modeling on a Ti89. This was my first exposure to anything that allows you to work digitally with symbolic mathematics. I must have been looking too awestruck as a colleague has allowed me to play with their installations of Mathematica (not seen it before) and MATLAB (only seen very old versions previously), just to expand my horizons. They are both very cool but have way too much functionality for my needs. At first glance the capabilities of Mathematica appear to be a superset of MATLAB (although the latter likely has the edge for matrix manipulation). I've started trying to move some of my models into the two packages. MATLAB looks as if it could handily replace some of my more clunky spreadsheets, where I'm using discrete methods, as I can turn the columns into lists and functions. Scanning Mathematica's abilities suggests that I could come up with more general analytical models, and that is very appealing. I see that there are some free alternatives but I don't know if any of them could cope with the uses I have in mind (I was aware of octave but have never used it).
Oh, the Good Old Days!
While browsing the shelves in the local library I came across a copy of the DVD from a concert I attended many moons ago. Naturally I had to borrow it and scan through it looking for myself (I'm still not a fan and so couldn't muster the time to watch the entire thing through). As I mentioned nearly seven years ago I was back behind the camera booms so my vanity wasn't tweaked. One question answered by the credits is the name of the mystery camerawoman - apparently it was Amy Ocheltree. Nice job, Amy!

It has been a while since I tried DOSBox so I gave it another whirl and am amazed at just how well it copes with some old programs. I may be able to retire my old 486/66 that I keep around "just in case".

...and a sample of blood. ...and your first born child.
My experience to date with CDW has been fairly positive, although I used to have the luxury of picking items up at the will-call window. Alas, recently they seem to have taken a sharp turn for the worse. I tried to order an item earlier this week and was told that, despite the web site claim of 2 - 3 days availability, it was out of stock for at least two weeks. I wasn't particularly surprised by this as I know that the availability numbers on the site are works of fiction intended to trap buyers. In the past I've had to wait a week or two for ~30% of the items I've bought. The latest shock was being told that, although my credit card details and address were okay, they could not sell the item to me as I had not given them my home telephone number. The only option to allow the sale to take place was for me to fax them an image of my driver's license. I checked with the sales person (who like all CDW people I've dealt with was friendly and polite). The summary of the email stream is as follows;
ME: Is this company policy?
CDW: Yes.
ME: Is there any alternative? You have validated my credit card and home address. Surely that's enough.
CDW: The only alternative is to cancel your order.
ME: What would you do with all my personal information?
CDW: My job is to collect all personal details from customers and if I can't do this with google, whitepages online or zabasearch I am obliged to ask the customer.
ME: Is it okay if I warn the rest of the world about this?
CDW: (implied) Yes.

So I can cross another supplier (and another vendor I'd endorse) off my list.

In addition to frequently falling into the well-recognised wikipedia trap and being distracted by reality I've noticed that I've now come to see inane email at work as slarshdawt articles and feel the urge to apply tags appropriately. Alas there's no way of making useful tags have an effect on those that most need them.

titus I sympathise with you concerning the changes in output format. I encourage you to keep going as it is very cool when you track down an apparent problem to an error in NIH's sequence file (or other supplier). The folk at the National Library of Medicine used to be very happy that other people were debugging their files by parsing them rigorously. I haven't done this in a few years so I am guessing that such source errors are rarer now but it feels good to be the one to spot them.

Thanks to Sun I now have the free (gratis) Solaris 10 DVD set. After sending my request in January I had given up hope as the intermediary who was mailing them emailed me to tell me that I hadn't filled out an application (so how did they get my contact information?). I've dabbled with Solaris 7 and 8 in the past, both x86 and SPARC, but the inclusion of Sun Studio on the latest set was what had sparked my interest. Hmmm... I have no idea if I can add an ATAPI DVD-ROM to my Ultra 5. Otherwise I'll try it out on a spare x86 box.

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