Posted by: thediygeochemist | August 31, 2010


As I’ve mentioned before, my first foray into research was as SL’s very first student. He was very good at explaining things to me; I picked up the techniques right away. It helped that I took lots of notes, of course.

SL also recruited a freshman, Gabe. Gabe was very smart, but he didn’t really have the scientific background to understand what we were doing yet. SL gave him the initial introduction to the theory, but then put me in charge of training him. Since Gabe couldn’t seem to remember how we were supposed to do things (I imagine it would be hard to remember, without fully understanding the theoretical basis of the work), he kept asking me what to do again and again.

I knew that there was no way he’d be comfortable with the techniques before I left, certainly not fluent enough to train my replacement. So I wrote up a document, which I facetiously titled the “New Student Installation Guide.” This included things like how to find protein structures and import them into the software, how to run a molecular dynamics simulation, and what analysis scripts (in which order) to run on the output. I also tacked on some useful appendices: non-standard PERL commands that were very useful in writing MD analysis scripts, how to use bioinformatics tools like BLAST, etc.

When SL saw the first draft, he was ecstatic. “WOW! Do you know what you’ve done here?” he asked. Of course I knew–sort of–though I don’t think I realized how big of a help it would be. (I saw SL over winter break, by which point he’d “installed” two new students into his lab using my guide. He said it worked like a dream.)

Fast forward a few months. I had signed on to Dr. Hand-Waver’s lab, to do a project which was the natural extension of former student A’s work. The only student left in lab was T, about to graduate, who had done work in a similar field, but using different techniques. T had helped A with his field work (and vice versa), so he was somewhat familiar with the methodology, but he didn’t understand nuances like how to fine-tune the instrumentation (not to mention how to fix it if it broke).

I did, of course, correspond with A via email. But he was a busy guy–a postdoc in an environmental field, in the middle of field season. So I would often wait 3+ days for a response to any question I had.

I was frustrated. I wished I had learned from the master. I spent days, weeks even, trying to recreate things A had done for his dissertation research. Of course, I couldn’t change this situation but I decided that I could do something for future students: write another lab guide.

So whenever I am not in lab, I find myself writing about things like how to change the column in the GC-MS, how to process samples, how to run an incubation. Eventually I will get to the point where major procedures have all been covered, and then I will write about minutiae–“The tubing around the peristaltic pump must be Tygon, but all the other tubing is 1/16″ OD PEEK. All the fittings come from Upchurch Scientific.” Things like this sound trivial, but it’s taken me several hours of research to figure them out.

I figure that if I can save future labmates a bit of trouble in the future, my efforts will not have been in vain.

Closing note: when I mentioned this to my sister Chrissy (a prof with a very busy lab), she was shocked: “What? You don’t already have a document with lab procedures?” So, just out of curiosity, what’s it like in other labs out there? Do you or don’t you have a reference document like the one I’m writing?


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