Ed's Big Plans

Computing for Science and Awesome

Archive for the ‘Danielle Nash’ tag

oGEM: An iGEM Story

without comments

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.


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.

Meeting with Danielle

without comments

Met with Danielle Nash, coordinator at iGEM Waterloo today. There are three branches of projects this year, first the completion of last year’s project and the introduction of one new project in two parts.

Last year’s project consists of a delivery system, wherein one introduces bacteria that have been modified so that all genomic DNA is lost. The bacteria thus function as subcellular-sized vehicles that are broken down, so that some arbitrary payload is released into a patient. The focus of the team working on this subproject is its completion; elucidation and final characterization of the system behaviour.

This year’s project consists first of a “foundational advance” submission which formally defines a consistent means to create cassettes for the exchange of genetic material between some vector and a target bacterial chromosome. This involves the definition of a new mutant strain with the homologous recombination sites, suitable for the integrase used; a well defined and consistent cassette, which one would use to enclose the biobricks or other genes of interest; and a short integrase plasmid, likely with just the gene and a promoter of some arbitrary strength. The second is an extension to this project, which defines a different chasis (target organism); this time a plant, likely arabidopsis.

David Monje Johnston immediately comes to mind; he oversaw iGem Guelph last year, in his plant agriculture lab. His advice could likely benefit the team.

What am I doing?

Well, I’ve contacted Andre Masella who currently lives and reigns at Laurier. He’s the head of modeling this year for Waterloo and has summarized the objectives as the creation of some software that will anticipate the best sequence of sites needed to ensure the highest probability of consistent exchange between the cassette and the chasis chromosome.

We’ve all settled on the idea that I would be assisting Andre, with the likelihood of coaching an undergraduate in bioinformatics software design, deployment and utility all the while.

I’m very interested in seeing the background work on this, since I have little idea of what the problem constraints are. What makes a given sequence a good sequence (high in stability, high in predictability), what makes a given sequence bad (high in variance, low likelihood of working)? I’ve written back to ask about related papers he’s worked with, seen or written.

This should be a BLAST.

Eddie Ma

May 15th, 2009 at 9:14 am