Molecules et al

[Daniel Barker]

On Fri, 29 Aug 1997, Susan Farmer wrote:

> >At 09:14 AM 8/29/97 -0400, Stuart Fullerton wrote:
> >>I just spoke with our local supplier of wonders about this. She says that
> >>it should be on the market by the 10th of Septermber. And it will be
> >>available in "fine" hardware stores near you for only $9.95. Get two or
> >>three of them. They will make great stocking stuffers!
> >
> >Amazing! Considering that a "cheap, dust-proof, hand-held," solar-powered
> >microscope (= hand lens) will still set you back US$30-40 in these parts
> >(minus the "vast library").
> >
> >Funding, indeed!
> >
>
> Don't laugh too hard!  When Larry Morse did his first Interactive
> Identification Program for his PhD, it had to fit into a 64K computer.
> I can buy a 64K calculator; program it with his code and Bingo! a
> handheld, interactive field identifier -- at least to family -- maybe
> even to the most common genera for an area.  It's not impossible -- it's
> just never been done before.
>

You could feed the sequences into your calculator and do an instant
parsimony analysis. At 1 byte per cell of the data matrix, and about 4
times as many bytes per tree as there are sequences, you could store 30
sequences of 800 bases, and 50 trees resulting from the analysis, in about
30k. Figures are based on my own programming work, but with 4-8 times more
packing of the data matrix to keep the storage down, at the price of
slight slowness. You could also pack the trees still tighter if you wanted
to, with no speed penalty. The source text of the whole parsimony program
currently takes about 150k, but assuming the sequencer knows how to
behave, error checking could be cut, and let's fix the options to some
reasonable value. Code space could then be reduced to less than 80k ...
Allowing space for simple graphics as well, you only have to get a 64k
upgrade for your machine! Well, unless you want your sequences aligned.
Make it a 128k upgrade, why not.

Has anyone ever done anything like this? Suddenly I am quite excited.
Though anyone who has a sequencer can also afford a desktop computer ...
and by the time sequencers hit the 9.95 low, calculators will come with
2G RAM as standard. Oh well, the experiment might still be fun.


Daniel Barker,
Institute of Cell and Molecular Biology,
University of Edinburgh,
Daniel Rutherford Building,
King's Buildings,
Mayfield Road,
Edinburgh
EH9 3JR