Why computers and biology make good bedfellows

There will come a time in the near future when most, if not all, biologists will need to understand computer code — and two Concordia University students are helping their fellow classmates get ahead of the curve.

Biology graduate students Alex Vallerand and Damien Biot-Pelletier have put together a seven-week extracurricular introductory training course on computational biology called Python for Scientific Concordians.

In short, computational biology moves certain elements of lab work to computers, where algorithms are able to process vast quantities of data, which in turn allows for a single scientist to perform more experiments than they’d ever dream of doing manually.

“We’ve built a curriculum that will take you from zero knowledge in computer programming to being able to do analyses in your field,” says Vallerand.

Computational biology helps take science out of the lab and give it real-world applications, a trend already evidenced by new biotech startups popping up.

Biot-Pelletier is almost done his PhD in biology at Concordia, after which he hopes to start his own company. “Lots of us want to have an impact. That’s why we went into science,” he says.

Biot-Pelletier and Vallerand are both working on yeast-related projects in Vincent Martin’s lab. Martin is the Concordia University Research Chair in Microbial Engineering and Synthetic Biology.

Vallerand is working on engineering yeast to use methanol as an energy source, while Biot-Pelletier is looking at identifying more sustainable sources of sugar for yeast to feed on rather than food crops,

Software for solving problems

Both students began teaching themselves how to code in order to more rapidly advance their work. Relying on software and equation libraries has limited impact, Biot-Pelletier says: “Sometimes you need to solve a problem that no one before you has solved, in which case you’ll need to write your own software.”

That’s where Python for Scientific Concordians comes in.

The workshop series begins May 16 with guest lecturer Darren Platt, head of data science at American biotechnology firm Amyris, who will shed light on why computers and biology make good bedfellows.

A natural programmer who kept computer science as a backup plan in case biology didn’t work out, Platt says he didn’t have the patience for academia and lab work. “I really like building things that people use, and I can point to the impact,” he says.

Amyris makes malaria medication, industrial lubricants, renewable jet fuel and materials used in cosmetics — namely squalene, historically cultivated from shark livers and now a plant-derived, biodegradable ingredient. “Anything nature can make you can make in yeast if you engineer it,” Platt says.

Engineered yeast holds a lot of biomedical and biotechnological promise, but it requires intensive computing, Platt says — first, to design the desired yeast, and then to test it and collect resulting data. This is where Platt, who is also a trained biologist, shines.

Strong interest so far

If registrations are a marker of interest, the seven-week workshop is bound to make waves: More than 100 people have already registered, which is free thanks to funding from the Concordia School of Graduate Studies. Platt’s introductory lecture — which is open to the public — will help set the context and make the case for computational biology. The subsequent weekly sessions will be taught by different professors from Concordia, McGill and Génome Québec.

“I hope that with this workshop and the fact that we’ve had 100 subscriptions in 10 days, the university realizes this is something people are interested in and hopefully it can become a program in the future for students to take,” Vallerand says.

Darren Platt’s lecture, “The Future of Computation in Biology,” on May 16 from 1:30 p.m. to 2:30 p.m. at the Centre for Structural and Functional Genomics (GE-110) on Loyola Campus, is free and open to the public. Subsequent workshops are on a registration basis.