Tuesday, March 22, 2011

What's On Your Cheat Sheet?

After years of scribbling on a motley collection of pads, during my time at Infinity I've been nearly rigorous about using a single notebook for my notes -- seminar notes, phone numbers, to do reminders, random thoughts (even blog ideas).  The book itself is a cheap permanently bound notebook from the local drugstore; I think they are less than $1 each.
The inside back cover of my notebook is titled "Useful Information", but I don't find very much there.  Mostly it is a lot of conversion factors, but primarily for Imperial units that nobody every uses: gills, hogsheads, penny-weights, rods, scruples and such.  Also such routinely accessed information such as the weight of a bushel of potatoes (60 pounds) or 1 barrel of flour (196 pounds) Other information include a 12x12 multiplication table, which was drilled into me over 30 years ago.  For the metric system, about a third of the page is taken up giving the same series of prefixes with each unit.  Another section has some Imperial to metric conversions.
It's interesting to think about what is curiously absent from the page.  For example, the common measurements for kitchen work, tablespoons and teaspoons, are absent.  Nowhere does a carat appear, nor conversion factors for the three different kinds of ounces (avoirdupois, troy and apothecary, for any European readers blissfully unaware of Imperial units).  I've also missed a "stone", which is a unit of weight that shows up in historical novels -- perhaps it doesn't have precise definition.  The weight of water is given in terms of a cubic ft being 2.48 gallons and weighing 62.425 pounds, rather than the usual "a pint's a pound the world around".
There are two odd values on that page given all this, but that's because I wrote them there.  It is a handy place to stash info, so I have written down that 1 human genome = 6 pg of DNA (checking that in Wikipedia, apparently it is really closer to 7: 6.95 & 6.8 for female and male respectively) .  The other odd value is 1 bp = 660 daltons.
Now, if I'm going to scribble in a few, why not add a bunch?  Indeed, while Google will happily tell me there are 8 furlongs in a mile, it won't directly answer how much a human genome weighs.  Nor will WolframAlpha -- it gave me information on human body weight in pounds.  So, what else could I need there -- and if I were printing up a bunch what would I put there.
Some of the more useful molecular biology reagent catalogs have whole sections of such information.  That is one challenge in designing such a information table; to be really useful it must be packed with information but at a density allowing high readability.  Plus, while the catalogs use many pages, I'm trying to cram it into 1 or maybe a few (the inside cover has an equally useless class schedule grid, useless to me that is).  Should I only put in what I truly can't remember, or also the things I don't have nailed so well that I can reproduce them quickly and confidently?
So, here are my current candidates, some for me and some if I were going to try to make a generally useful one.  Of course, a lot of what is valuable for ready reference depends on what you are doing.  At Codon I had a sheet taped by my desk with the sites for the restriction enzymes I used the most.  If you have a favorite vector, the polylinker map is a useful reference.  On the other hand, Planck's constant is a really important number, but one I've never needed to use in biology.  So I wouldn't bother using space on it.

  • IUPAC ambiguity codes for nucleotides.  Most I know by heart (or figure out quickly; the codes for 3 nucleotides are near the one letter they leave out), but M & K have always been a challenge.  As part of cramming for this post, I now have a mneumonic that works for me: M is Methyl, for A and C, which are capable of being methylated (I think the mnemonic is supposed to be on the native structure, but I don't know that well enough).  K is now the other two.
  • Amino acid single letter codes.  I don't need this, but for a mass produced one it would make sense.
  • The genetic code -- without trying, I have actually memorized this, but I'm not very fast working purely from memory nor am I always confident (which is why I'm not fast)
  • SI prefixes in order.  Again, I know most of these until you get to the two extremes, but usually have to rattle them off in order (milli=-3, micro=-6, nano=-9, pico=-12, etc).  
  • Powers of 2.  For up to 2^12, I can rattle these out.  Higher sometimes comes in handy.
  • Tm calculation estimation using G+C and A+T counts.  I don't use this often & don't really trust it, but for ballparking a Tm it might be worth having around
  • 1 mm^3 = 1 uL and 1000 um^3=1 pL.  Useful little conversions I found when I was exploring emPCR stuff (should I also put the formula for volume of a sphere in there, since I initially wrote it out incorrectly in that post?)
.That doesn't seem like nearly enough to fill up the page, but perhaps that's a good thing.  I probably don't know what else it would be useful to have there, so blank space to scribble more isn't a bad idea.


no said...

I think there may be a market for a cafepress mug with such conversion tables on it!

incidentally - a 'stone' is 14 lbs (English). I believe it's in continuing use, but only for measuring the mass of human beings.

such.ire said...

I keep some useful logs on my sheet that I can't always remember off the top of my head: log_10(2), ln(2), log_2(10), etc.

Chris said...

I posted this over at biostar, because I think it's a great question for the community. You might be interested in seeing what kind of answers trickle in over there as the day goes on: