So, here is my half-baked idea:
Why not have a special week where new online collaboration tools are promoted to scientists globally ?
Similar to the way local Linux user groups sometimes run “installfests” to install Linux for users, (just to get them over the initial interia), why not have a global “signup-fest” for the core set of online tools useful for scientific collaboration ? In each local area / University / Institute, a few Web2.0 savvy scientists could promote the event and hand-hold new users through the signup process, and help with basic usage and integration of tools. Ideally, lab groups could signup together in the same room, and make an event of it. Or in places with Wifi … a “bring your laptop” signup lunchtime event. I think you get the idea.
Continue reading ‘A “Web2.0 for Scientists Week”: signup-fest ?’
I recently needed to make a simple, two dimensional figure of a beta-barrel membrane protein. I went hunting for programs that might take a sequence and/or structure and produce a pretty looking diagram to save me constructing everything by hand. Here are two I found and tried.
Continue reading ‘Software review: producing two dimensional diagrams of membrane proteins’
David Baker’s lab and friends, have recently released a new ‘experiment’ in protein folding called FoldIt. Essentially, individuals or teams can compete online to manually fold protein structures, guided by the internal energy function within the game (it very likely uses code from the impressive ab initio folding software Rosetta under the hood). The interface is designed as a game to make it accessible to everyone, not just experts in protein folding. While it’s pretty simplified compared with your average molecular structure editing software, I think designers of scientific software (often scientists themselves) should take note; a good clean interface can really assist getting a specific job done painlessly. I haven’t played enough with it yet, but I get the feeling that FoldIt could be a nice way to introduce some protein structure concepts to undergraduates too.
There were the usual complaints on Slashdot that FoldIt doesn’t have a Linux version. Well, I’m happy to report that it seems to run alright using Wine (on Ubuntu Hardy Heron). I couldn’t log in to try the competitive puzzles, but I suspect the server is just in the midst of a Slashdotting. I’ll try later.
From the FoldIt FAQ:
Can humans really help computers fold proteins?
We’re collecting data to find out if humans’ pattern-recognition and puzzle-solving abilities make them more efficient than existing computer programs at pattern-folding tasks. If this turns out to be true, we can then teach human strategies to computers and fold proteins faster than ever!
Not sure where I saw it, but I remember reading an argument that the future of crowdsourcing would be to not just blindly trust the whole crowd, but also identify experts in the crowd and weight their predictions more strongly. I’d say this is will be the case with ‘manual’ protein folding – just like some players become l33t at first-person-shooters (like my favorite, RTCW: Enemy Territory which depsite enjoying, I’m not so l33t at), and could beat any AI player that doesn’t cheat… some people will probably become pretty good at folding up proteins. Maybe FoldIt will identify them, and they can make their gaming skills useful, and teach their tricks to software to automate the process. Or maybe it will just remain a fun-ish puzzle game 
I see Lars Juhl Jensen has come up with a fun tag cloud of recently popular buzzwords in the biosciences. He calls it a BuzzCloud. The buzzword from the cloud I’ve noticed most lately is “Quantative Proteomics” … quantitation is a good goal for the field of proteomics to aim for, since IMHO it doesn’t really deserve the -omics prefix. “Omics” tends to imply the possibility of global proteome coverage, which proteomic studies rarely, if ever, achieve. But enough of the side-rants.
The way Lars’ BuzzCloud is constructed by extracting phrases ending in -ics, -ology, -omy, -phy, -chemistry, -medicine, or -sciences etc reminded me of a stupid little CGI application I wrote a few years back … the Biotech company name generator. When you take common prefixes like “Gene-”, “Pept-” or “Chemi-” and suffixes like “-omics” or “-agen” etc, it’s amazing how often Googling the name turns up a real honest-to-goodness biotech company.
Feel free to comment on any “biotechie” suffixes and prefixes that I should add … the hardcoded list in the script isn’t that long.
Occasionally impoverished University labs and early career researchers go looking for bargain priced lab equipment on Ebay … sometimes hard to get but still very useful equipment also comes up. A colleague of mine found this entertaining auction for a P20 Gilson Pipette, much of it written from the pipettes perspective. Here’s a quote:
For the purposes of full disclosure, this pipette has NOT resulted in data that has made it into Nature or Science (and in hindsight then the Cell paper may be considered to be a fluke). However, we choose to believe that that is the fault of both the editorial staff of these journals, and many a short-sighted peer-reviewer, rather than the pipette itself. Nonetheless, you may want to calibrate the pipette upon its arrival.
Fluke or not, a sentient pipette that produces Cell papers has got to be worth more than the mere $48 it’s currently sitting at ! Sadly (or maybe happily for them), it looks like the seller is leaving bench science and selling up their gear. I’ve no idea who it is, but they live in the same suburb as me, so there’s a good chance this is a fairly well-published senior scientist that I’ve crossed paths with at some stage. Also, don’t miss the (*) footnote at the bottom of the auction info about impact factors …
