My personal experience with biological repositories
When I started out as a graduate student, in the dark distant past, I chose to work on a protein that we didn’t yet have in our lab. One of my first goals was to acquire the gene and clone it into our expression system. After reading some literature, I found one group who had mentioned getting the gene from another, and so I thought I had my opportunity. I emailed the group who is on record as having supplied it and asked for the gene. They replied “sure, no problem”; I waited. Months. Occasionally I would send off another email, but I didn’t want to seem too pushy. They were doing me a favor, right? In the meantime I worked with the mouse version of the gene.
Finally, the envelope came with the gene. They didn’t provide any real information, but I went ahead and designed my PCR primers and got to work cloning it. For months. For some reason, my cloning reactions just weren’t working really well. I struggled with PCR, digestions, ligations; it seemed like every step of the way was bogged down for some reason. Eventually I managed to wrangle the gene into a vector and get a good sequence read. At this point it became abundantly clear why I had been having so much trouble - the end of the gene was missing. It turns out the lab I had gotten it from had used an enzyme in their own cloning that clipped the sequence short.
In retrospect, I probably should have figured this out much sooner. The clues were all there, but as a young graduate student I was sure that an established lab would send me the proper gene, and I was just doing something wrong.
It turns out that around this time, another graduate student mentioned that they had bought the gene for their protein for something like $80 (the fee for this particular repository has since been raised to $120), which is just about as close to free as you could hope for. It turned out that the same place carried my gene. Of course I bought it, and within weeks my cloning was successful.
When people like John Wilbanks talk about developing these repositories, this is the type of situation they are looking to improve. The old system, of asking a “favor”, little to no verification, and no real motivation for expediency or quality control is really shockingly bad. It’s amazing to me that it’s taken this long to sort of start generating significant interest in validated, standardized, open repositories. The clones, cell lines, mice, etc that we generate in great quantities need a better method of sharing and distribution than some antiquated version of quid pro quo.
May 13th, 2008 at 11:21 pm
The old system, of asking a “favor”
This gets my goat. It’s not a favor: if you’ve taken NIH funding to develop the reagent in question, or published it in most journals, you are REQUIRED to provide it to fellow researchers at nominal cost. It’s part of your job, a contractual obligation. Anyone who doesn’t do this (or does it in a sloppy fashion, deliberately or because they’re simply a lousy scientist) is failing in their professional duties.
It’s amazing to me that it’s taken this long to sort of start generating significant interest in validated, standardized, open repositories
Try this exercise: wherever you work, try to put together a plasmid repository, or a list of antibodies that are on hand. Note that this is far, far simpler than developing an actual repository of the physical reagents.
If you don’t get zero uptake, plus some egregious hostility and whining (”why would I make it easier for people to ask me for stuff?”; “what if someone takes advantage of all my work?”), then I want to work where you work.
There used to be a web app for reagent sharing, called BioRoot; it had a fully-featured database back end, security, Excel upload, the works; I wrote about it here. When I tried to get my colleagues to use it, I got the response I described; as far as I can tell, it’s now dead from lack of use. It seems that everyone is just too damn busy with their own Big Important Stuff, and too damn poisoned by our hypercompetitive environment, to bother with something that might benefit someone else.
Feh. What gives me enough hope to keep pushing these ideas is grad students like you, who have not yet been beaten hollow and filled back up with cynicism and spite.
May 14th, 2008 at 7:20 am
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