Ed's Big Plans

Brief: Cara and I will be married on August 1st 2009; the ceremony ends at 4pm–
I’m going to put everything else on freeze as of twelve noon today until roughly Tuesday next week.
I’ll let the countdown script do the rest…

Countdown Done– wow, that was actually very enjoyable.

Countdown script from Hashemian.com; thanks Robert!

Brief: I forgot all about sqkillall.py! It’s a convenience script for killing all of the SharcNet jobs belonging to you! (More about it; Source code).

Brief: Approaching final duties– Need to get a letter from the Chair (Dr. Stacey) and an official undergraduate (not graduate) transcript, both for Waterloo.

Brief: Met with Chris last week. Chris finished with the convergence tests and some cross validation sets on his descriptors and recommended his own design for 80/20 prediction tests… Meanwhile, I’ve updated the InChI grammar used for the NGN to work with the new data, and have set up experiments to run convergence tests using the SMILES-NGN and InChI-NGN on the eight possible QSAR datasets on SharcNet (16 processes total)… Next on the list– create a script to evaluate his preliminary cross validation experiments (based on Neural Network predicted vs. target values) and provide instructions for running the convergence tests with my NGN software… Will need to pull up an old nugget.py to wrap the convergence test (current one doesn’t halt and always runs 100 trials).

Soon: Port everything to Ubuntu Linux so that we can maintain compatibility without further porting care of Sun Virtualbox VM… Meeting again tomorrow…

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

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

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

Brief: I got my T.A. assignment from Waterloo– I’m going to do tutorials for 208: Analytical Methods in Molecular Biology!