# Ed's Big Plans

## The Computational Bio & Chem Group (SOLVER Revisited)

A Revisitation

In the beginnings of the Winter semester, I had an idea to start up a undergraduate/graduate student group that would provide a scaffold for faster, computer assisted research.

The semester was simply too full for me to try and get it running at that time. I’m tempted to do some work on it later this semester, after I’ve gotten more of my thesis done.

The basic idea is as follows. Faculty and graduate students in the biology and chemistry departments often have the need to analyze data with some elegant computing. Whether this be as commonplace as hacking together an excel sheet to do work or learning some existing toolbox, or something slightly more in depth such as analysis in R, Python or PERL. Unfortunately, these research problems often fall by the wayside as the time commitment to learn a new software package or programming language is not trivial without a stronger computing background. Undergraduate students who are raised in the computer science environment, particularly with a bioinformatics interest have some knowledge of the research problem semantics as well as some knowledge of how to do the above analysis by using and coding software.

The “SOLVER” group would fill the gap by performing a matchmaking and coaching service. In my vision, SOLVER creates working teams of three to four– (1) one or two graduate students or faculty with a research problem, (2) one or two undergraduate students with some knowledge in bio / chem and some talent in computing, (3) an experienced coach that can recommend best practices so that the team has a good shot of solve the problem in a reasonable amount of time. In the end, the researcher gets help and a good chance at a working solution– they might even learn some programming; educational / professional / social connections are made; and the student gets an item to add to their resume. In reality, a particular research step would be executed as week-long blocks– whether this means one block or four blocks (one month) depends on the complexity of the task.

To do…

One stretch of work that I have to do is to determine the needs of the department. I wanted to do this in the middle of Winter semester but didn’t find it a priority. For this group to work, there must be research problems. Similarly, I need to determine the capabilities of potential undergraduate students. I’m learning quickly that the key here is to start small and think big (i.e. start with one group, then two, then learn about the administrative logistics, then deploy some progress tracking mechanism, then four groups and onward).

Retuning the image

The almost idealized description above suffers from a few logistical issues. First, I will now address the issue of publication credits. Because researchers must attribute tangible work (including written code and analyses), some graduate students may be hesitant to participate in the program. I don’t know if this will actually become a barrier however as a “tangible contributor” would never be the first nor the last name on a paper (this is true in all CS, Bio and Chem). Furthermore, a paper with more than one author demonstrates the ability to collaborate in a team, and fostering the experience of another student is part of our culture (e.g. co-op students etc.). That brings me to a second major issue. One of the frames that this group could find itself in is a means to circumvent or short-circuit the co-op student appointment process– a frame that I readily reject. In fact, I should hope that this group becomes a means to introduce new putative co-op students to their future advisers which may otherwise be overlooked for their differing background. Finally, there is the problem of attrition, whereby a group dwindles in size as members drop out. The only contract-based perks or penalties I can think of is really ties to the group itself (e.g. unsatisfactory work naturally results in a time out or withdrawal from the program). It is really the only tangible leverage we can offer at the outset– unsteady leverage at best (difficult to assume a reputation when none has yet been built).

Going forward

More research has to be done in terms of polling and documenting the needs of the department. Furthermore, a deeper understanding about the kinds of students we’d attract and want to appoint is needed– this allows us to understand what time commitment is reasonable (both the lower and upper limits need definition). Finally, the group must from the outset be understood as something beneficial to all parties involved. The solutions named above must be deployed at launch time to ensure minimal friction, and maximum return. First steps were made last year by introducing this idea at the BIC-iGEM meeting– BIC students are excited with this idea, wherein an entire room of a dozen students raised their hands. Furthermore, there are no other groups on campus that attempt this activity, so that SOLVER would provide a unique non-conflicted service.

Of course– this all depends on the amount of work I get done on my own thesis in the first half of the semester.

Making friends

As an aside Isabelle Lam, a student I TA’d last semester in Biol-241 (microbio) has been planning on starting a job / volunteer / coop mine for science students. I should go and bother her and see how far she’s gotten. Her project is called “SPORE”. Last I checked, her team was registering a subdomain with the university.

EDIT: I previously confused Isabelle with Lisa– this has been corrected.

Written by Eddie Ma

April 20th, 2010 at 10:08 am

## You win again, mystery prankster! Re: QR Codes on Campus

Brief: Posters have been appearing all over campus with QR-codes on them– Since I didn’t readily have software on my cellphone that could handle decoding them, I snapped a photo and proceeded to search for software online. The photo is an example of one of the posters stuck up at the William G. Davis Computer Research Centre (DC) at U Waterloo– particularly, this one was stuck on a doorway that leads to Chemistry II on the third floor.

The posters feature a QR (“Quick Response”) Code with an explanation below in the form of a URL to a wiki page for anyone who doesn’t know what a QR code is. The specifications are owned by Denso of Japan– but the company has decided to let anyone use it without any kind of fee… in order to actually view the specification however, a fee must be paid to ISO.

A QR code can encode a variable number of characters with some redundancy to allow for dirt, corruption and other artifacts, this particular shot was decoded with the Java project, Open Source QR Code Library hosted by source forge… After copying the image to Tin from my cell phone, I did this…

Tin:qrcode eddiema$java -cp classes:lib/qrcode.jar\ example.QRCodeDecoderCUIExample res/Photo0347.jpg [Success] res/Photo0347.jpg Processed 1 images in 914ms (914 images/sec) OK: 1 NG: 0 Tin:qrcode eddiema$

And lo and beharold, I was treated to a surprise… what could that URL possibly be? More clues to a longer treasure hunt? Some strange political protest? No, no– the mystery pranksters had something better in store for me.

Yes, I’ve been had. A belated April Fools no doubt

Cheers, Mystery Prankster. I tip my hat to you.

Matt says...

It’s a rickroll, isn’t it? *Checking Google, please wait* …ahaha it totally is!

Nice find. Nerd pranks make me all warm and fuzzy inside. (On the other hand, if it were a strange political protest it would have been SO MUCH AWESOME.)

Eddie Ma says...

Matt! You weren’t supposed to actually say what it was– that kills the effect Incidentally, I never noticed the error in the calculated number of images processed per second by the Open Source QR code… 1 image in 914ms is roughly one image per second … yikes.

Mat says...

Whoops, my bad. The best part is I didn’t even click through to the video, because I’m too accustomed to use the highlight-right-click-search-in-google feature in Firefox so I just got a bunch results about… that thing which I have already spoiled but will endeavour not to ruin doubly by repeating here.

I hadn’t noticed that bug either, but now that you mention it, that’s quite odd. It probably has a one line fix, assuming someone just mixed up variable names. And a one second delay for QR’s not too bad, but if you want to do something involving realtime tracking, that’s what ARToolkit is for.

PS: On second thought, who am I kidding? Of course I want to ruin your rickroll, you darn rickrolling rickroller.

Written by Eddie Ma

April 7th, 2010 at 2:27 pm

## oGEM: An iGEM Story

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.

Written by Eddie Ma

July 27th, 2009 at 12:16 am