Project ideas for BioCurious?

[Tristan Eversole]

As I might have mentioned at some point, I'm one of the volunteer staffers at BioCurious, one of the two hackerspaces devoted to biology. (The other one is GenSpace, in New York.) We're essentially a community laboratory with an emphasis on molecular biology. On Nov. 10th, we're going to have a big brainstorming session to think up interesting projects that could be done at BioCurious.

Now, most of the people there are more into molecular biology or software than they are into conservation, ecology, evolution, or organismal biology-- understandably, because BioCurious has been pitched in terms of 'biohacking'. And BioCurious really is oriented towards molecular biology, because the facility itself essentially IS a molecular biology lab (or an embryonic one) and wouldn't work well for, say, veterinary medicine. However, as a de facto ambassador from the other realms of biology-- my own interests lie in macroevolution-- I thought I'd ask the members of this list whether they have any ideas for projects referencing ecology, evolution, or especially conservation that could be accomplished at a community molecular biology lab.

--DNA barcoding is an easy one. I thought I'd go after dandelions, myself, although the method doesn't work too well for plants yet. There's no particularly good reason for me to pick dandelions beyond the fact that I like them and think collecting samples would be easy. One could easily go after fish instead; apparently, quite a lot of fish served at restaurants are mislabeled--

> Americans spent $80.2 billion on seafood last year, $5 billion more than in 2009, but they aren't always buying what they think they are. More than one-fifth of 190 pieces of seafood we bought at retail stores and restaurants in New York, New Jersey, and Connecticut were mislabeled as different species of fish, incompletely labeled, or misidentified by employees.

(http://www.consumerreports.org/cro/magazine-archive/2011/december/food/fake-fish/overview/index.htm )

--probably because our fisheries are in such serious trouble and there's a lot of illegal fishing going on.

--With the publication of the Daphnia pulex genome, I've thought about trying to get nuclear (not mitochondrial) sequences out of species like those of the genus Triops. Triops, known by the common name tadpole shrimp, are easy to order, but haven't been very well studied; all the genetic information we have on them so far is mitochondrial. I thought it'd be fun to try to do a rudimentary phylogeny for Triops-- not exactly publishable, but fun.

--Some of the tools of molecular ecology don't require a great degree of technical sophistication. Getting microsatellite regions can't possibly be as hard as quantitative PCR! So it's reasonable to bet that at least some molecular ecology should be possible with the resources at BioCurious. Personally, I keep thinking about tracking gene flow between bedbug populations, but that's probably rather silly...

I have a lot of other things in my head, like automated species identification via artificial neural networks or morphometrics, spaced-repitiion flashcards for taxonomy (http://en.wikipedia.org/wiki/Spaced_repetition ), or cellphone-ish telemetry for studying urban wildlife (http://scholar.lib.vt.edu/theses/available/etd-05052005-081716/ ), but it's late, and I'm tired, so I'm not going to write about them right now.

Let me know if you have any ideas.

--Tristan

[LUKE APPLETON]

Tristan, I'd also joined the WAMAD to try to learn some Java coding and I don't have a strong programming background but I noticed android and figtree both use Java so for awhile I was playing with the idea of a mobile app that lets you access one of the bioinformatics databases online or something like that... I'm more of a microbiology background but I did pretty well in genetics and am dabbling as a novice in comp bio... --- On Wed, 11/9/11, Tristan Eversole <custome...@trioptimum.com> wrote:

[LUKE APPLETON]

Perhaps a slightly dumbed down mobile phylogenetic mapper application for when people are out on the field which could fit the limited constraints of smartphones as the platform?

--- On Wed, 11/9/11, Tristan Eversole <custome...@trioptimum.com> wrote:

From: Tristan Eversole <custome...@trioptimum.com> Subject: Project ideas for BioCurious? To: biodiver...@googlegroups.com Date: Wednesday, November 9, 2011, 3:18 AM

[Tristan Eversole]

Well, the two resources I can think of that would be the easiest to hook into would be the Global Biodiversity Information Facility (GBIF) and the Encyclopedia of Life (EoL). The Encyclopedia of Life is actually a clever integration of a bunch of different databases, including the GBIF, but at the moment it's not that easy to use, and I don't know whether it has a great API for talking to, say, a smartphone. Presumably we could use the GBIF information, coupled with GPS information from the smartphone, to tell someone about what species to look for wherever they happen to be, which would be one major improvement over existing field guides. Gathering information from the EoL would provide a far more sophisticated view of natural history than that represented in a traditional field guide, although the EoL is very much incomplete and not all that simple to use. Interactive dichotomous keys could also be really handy for identifying whatever it is that you find in the wild. I know that there are some Audubon guides for the iPhone, but I doubt they incorporate this kind of functionality.

The point is that I *will* be talking to some people with some very strong programming backgrounds tomorrow, and I want to have something interesting to tell them. So I thought I'd write the Biodiversity Club and see what you guys have in mind...

--Tristan

[LUKE APPLETON]

Yeah, I was thinking as things move more toward a data cloud maybe it was about time there were some more serious apps for people who were workminded.  I do feel like there's a general dearth of science software and a glut of oh,- games and things to buy movie tickets or find restaurants or go shopping. :-P It may be an underutilized or undertapped niche. Hey, that's not half bad. Field guides and keying tools...