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oGEM: An iGEM Story

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Thursday last week, the Waterloo iGem team had a online conference over Skype with the iGem teams of Toronto and Ottawa. Also present was Andrew Hessel– the seeder of Canadian iGEM teams… It was pretty extensive, so I’ll just discuss the parts that ended up being immediate goals for the Waterloo team.

oGEM Meeting Over Skype

oGEM Meeting Over Skype

The objective is to end up making an Ontario federation in synthetic biology under the iGEM scaffold a reality; we would eventually expand out of iGEM and cover synthetic biology across Canada, but — plan small, think big.

There must also be incentives for being part of such a federation– an obvious answer is a network of distributed services which are greater as oGEM than the sum of its parts.

Plan Small, Think Big

One of the first things we can experiment on is the idea of a social engineering application. This feature is being investigated by the Waterloo team– Arianne has created a mock-up using Elgg. The objective is to allow individuals across oGEM to know what expertise exists in the network, and to contact appropriate users for collaboration or help based on the interests or skills listed by each user.

Sigma is for Summation

Incentive services for oGEM are being tackled by our team. Andre wants to introduce a federated database of strains and cultures (codenamed BioMortar)– whereas iGEM offers clonable biobricks, the issue remains that cellular transformation is not deterministic. It may work some of the time, or most of the time– for some teams, certain bricks just aren’t successfully cloned. This federation would allow the cataloging of living frozen strains in freezers across oGEM and if users are willing, all synthetic open-source strains. Eventually, someone seeking a strain they’ve had issues with would message someone with a working copy as it were, and request it be shipped.

Caveats

We expect caveats to emerge– first of which is dedication. In our meeting, it is clear that working groups must emerge to take over tasks– working groups that are passionate about their own objectives. I suppose UWiGEM represents two working groups each operating on one of the above steps. Ottawa has volunteered to look at the legal caveats– how oGEM identifies itself as a legal entity as well as its level of permitted activity while still being a part of iGEM and synthetic biology across the nation is all very vague. It’s good that someone has an idea of how to investigate this feature of the problem terrain!

Group Photo

Attending the meeting on the Waterloo side…

oGEM Chat - Waterloo Side

oGEM Chat - Waterloo Side

Left to right in the above photo: Danielle, Andre, John, Leah.

OGem – Ontario iGem Mini-Conference

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Teams from the Southern Ontario University iGem teams came together on May 29th for a miniature conference at the University of Waterloo. We had members from Guelph, Toronto, Mississauga (U of T’s West Campus), Queen’s and Ottawa. The basic trend of the show was finding the fun and profit from synthetic biology. I could only stay for the morning and early afternoon segment– but I really would have loved to stay for dinner.

Dave Johnston — our very own team leader from last year at Guelph showed up with Brendan. It was kind of neat to see them again, and more so since they didn’t know I had betrayed them and joined the Waterloo team this year (amicably of course).

Meeting with like-minded individuals is a bit of a relief. It is good to need to argue, convince and learn from others in science– and out of science… but when it comes to something as difficult for outsiders to enjoy as synthetic biology, sometimes it’s a nice break to just discuss the facets within the discipline, rather than abstractly and vaguely defending it against misunderstandings. Actually, one of the standing objectives we discussed was improving public image.

Along with the theme of the fun and profit of the beast came the odd realization that what we’re studying now is likely to become obsolete within the decade– however, with that risk comes the potential for each of us attending to contribute something truly worthwhile in short notice.

One key idea that stuck with me was the development and deployment of nanometre-scale sensors to detect the changes of magnetic flux while molecules are moved within a single cell. I’d imagine that one would need to be well versed with trigonometry and calculus to write software to solve the diffraction patterns of the fields in real time. It might look something like a dynamic/real-time x-ray crystallographic analysis. Another key idea is the 1Mbp/1hr/$100 device. If DNA can be printed at the rate of one million base pairs for each hour at the price of a hundred bucks– it wouldn’t matter what currency that’s in, it would win.

Culture was something else I noticed about the group. There was the ever present odd scientist humour. We managed to have running jokes about the phrase “Killer App”, as soon as it was accidentally introduced to refer to engineered microbes.

All in all, it was a good conference.

Something that I’ll need to follow up on is the idea of doing a group / mass booking for a tour bus from Southern Ontario down to Boston come iGem conference time. This along with a group / mass hotel booking would solve a lot the travel and accomodation fragmentation everyone experienced last year.

Eddie Ma

June 1st, 2009 at 1:01 am