BCB Project

BCB330Y1- Special Project in Bioinformatics and Computational Biology

What is it?
  • BCB330 is an opportunity for specialized individual research in bioinformatics and computational biology by arrangement with the course coordinator and a supervisor. This opportunity for students to actively participate in the research process – in the discovery and dissemination of new knowledge – may be continued with BCB430 (Advanced Special Project). Students frame the questions that will guide their research, design and conduct the research to find answers, and communicate the results of their work, drawing on skills and experience that they have previously acquired. Significant background in both life science and computer science courses is required.
  • The final decision whether a BCB330 project proposal fulfills the academic objectives is up to the Course Coordinator.
  • The original research project requires the prior consent of a faculty member to supervise the project. The topic is to be one mutually agreed upon by the student and supervisor and accepted by the course coordinator. The expectation is that the student, aided and advised by the supervisor, will read the literature, and plan, execute, analyse, and report on experimental or descriptive investigations on an appropriate topic. A literature review alone is not sufficient.
Who is it for?
This course is open to Third-Year Bioinformatics and Computational Biology Undergraduate Specialist Program students with adequate background.
Who is participating?
Faculty who have offered to supervise BCB330 projects include:

  • Gary Bader
  • Anne Bassett
  • Michael Brudno
  • Belinda Chang
  • Darrell Desveaux
  • Nahuel Fittipaldi
  • Marie-Josee Fortin
  • Leon French
  • Brendan Frey (Deep Genomics Inc.)
  • Anna Goldenberg
  • David Guttman
  • Michael Hoffman
  • Igor Jurisica
  • Gustavo Mallo
  • Daniele Merico (Deep Genomics Inc.)
  • Alan Moses
  • Quaid Morris
  • Nicholas Provart
  • John Parkinson
  • Jüri Reimand
  • Hannes Röst
  • Arneet Saltzman
  • Steve Scherer
  • Jared Simpson
  • Boris Steipe
  • Mark Sun (Deep Genomics Inc.)
  • John Vincent
  • Zhaolei Zhang

For detailed contact information, please follow the links on the People page of bioinformatics.utoronto.ca.

What is the time commitment?
Faculty members estimate that students spend 10-12 hours per week on their independent research project. Some students spend more time as they become immersed in their project.
When is offered?
  • BCB330Y projects are taken during the normal academic year.
  • BCB330Y projects may also be carried out in the summer semester, with the aggregate time spent on the project equivalent to that for projects running during the academic year.
How are students evaluated?
  • Evaluation consists of a substantive written report, a written proposal 3-5 pages in length, oral or poster presentation (which will be determined by the supervisor), and quality of the project work.
  • The proposal is due to your supervisor (and the course coordinator) one month after the last date to add a course and will be worth 15%.
  • The supervisor and student will jointly determine the components that will comprise the calculation of the final grade and how much each is worth; in addition to the written proposal (15%), written report, and oral or poster presentation, these may include quality of work, statistical analysis of data, and participation in lab meetings.
  • The final written report and presentation combined must be worth a minimum of 50% of the final grade, with the presentation worth 20%.
  • The expectations for an acceptable length for the written report will be communicated to the student by the supervisor. Written reports by past students have been approximately 10-15 double-spaced pages and are often written in the format of a manuscript to be submitted for publication to a journal. The submission date for the final report will be determined by the supervisor; usually this is close to the presentation date, but no later than 10 days after the last day of classes, as grades must be submitted by the supervisor to the course coordinator by then.
  • The oral or poster presentation will take place during the Study Week in April (or an equivalent time in the summer session).
  • The supervisor must submit a final grade and a brief (approximately one-two paragraph) critique of the student’s work, outlining the strengths and weaknesses of the work, and a rationale for the mark assigned. A copy of the critique will be given to the student on request. The course coordinator will submit the final grade to the Undergraduate Office in the Department of Biochemistry for posting on ACORN.
  • Note: the University of Toronto’s Code of Behaviour on Academic Matters applies to work produced for this course! This means proper referencing and citing of materials must be followed!
How to enrol?
  • The project course registration form (see bottom of this page for a downloadable Word document) must be submitted to the course coordinator no later than the last weekday to add a course (i.e., if the last day to add a course is a Sunday, forms must be submitted no later than 4 p.m. the Friday before). This is a signed agreement (note: the deadline to register for an academic session may be earlier than this deadline). Once received and approved by the course coordinator,the Undergraduate Office will enrol the student in the course on ACORN. (Students cannot enrol themselves on ACORN in BCB330Y1.)
  • A resumé and complete ACORN transcript must be submitted along with your registration form to the course coordinator by the date specified on the form.
  • Prior to beginning the project, the student and supervisor agree upon the time when the lab work is performed, place, and the provision of any materials. Once the details are agreed upon, a registration form (see bottom of page) must be completed.
Important dates
  • Contact potential supervisor – do this about a month before (at least!) the start of the academic session. A list of potential supervisors is available above. This list is not exhaustive. Consider contacting a potential supervisor in person.
  • Registration form (see bottom of this page) due to the course coordinator no later than the last weekday to add a course.
  • Proposal (3-5 pages) handed in to your supervisor one month after the last date to add a course.
  • Meet with supervisor no later than the last date to drop a course to discuss the progress to date and assess the expectations for successful completion.
  • Presentation will take place during the Study Week (or an equivalent week in summer session).
  • Written report due shortly after the date of the presentation date (exact date determined by supervisor).
  • Supervisor submits grade and written critique to the course coordinator no later than 10 days after the last day of classes.
Tips on finding a supervisor, and contacts for further information

Getting the BCB330Y/BCB430Y project of your dreams is quite similar to any application for a position.

1. Research the landscape:
You are free to do your BCB330/BCB430 project with any laboratory at U of T (not just those supervisors listed above), in the hospitals, in the research institutes, in industry, and even abroad. The only requirement is that you have to convince the BCB330/430 Course Coordinator that your project is academically valuable and fits the goals of the course. Don’t let this freedom overwhelm you – take it as an opportunity to figure out what you enjoy about the field, and how you can pursue it.

2. Figure out what the research is about and what life in your chosen lab is like:
Once you have narrowed it down to a handful of target projects, find out more about the lab. Read their publications. Read the publications of their competitors. Try your best to understand the high-level goals of the work and how the lab approaches it. Explain it to a good friend, to make sure you understand.

Then try to get in touch with a graduate student, postdoc, or TA in the lab, and figure out what life there is like. Treat them to a coffee and chat. Are there regular lab-meetings? When? (You need to attend, otherwise you are working in an unhealthy vacuum. You should at least have regular meetings with the PI…) What programming languages do they use? (If you don’t speak R, Python, C++ or whatever, you’ll need a plan how to catch up.) What technologies (Not familiar with what AWS, Docker, Github are … time to catch up.) Get a feeling of whether work with this group will be fun. And see whether they have advice about alternatives if your application don’t work out.

3. Write a specific application:
Only then is it worth your time to write an application. Contact the PI (Principal investigator) and state your goals clearly. What would you like to learn, what motivates you to work in their laboratory? Be humble – don’t assume you will be able to make a significant contribution to their work, but emphasize your motivation to learn. Do mention what you can bring to the project, from prior exposure, and how you plan to address any deficiencies of preparation and blemishes on your transcript.

Finally …

4. Ask for an interview, not a position:
It would be premature to expect someone to take you aboard as a team member based on an email application. So the next step will be an interview. Likely, the PI you are applying to will find it easier to grant you half an hour to discuss how your plans fit with the lab, than to make an immediate decision whether your application should go ahead.

Contacts

Prof. Nicholas Provart
Tel: 416-978-7141
Email:nicholas.provart@utoronto.ca
BCB330Y Course Coordinator
Department of Cell and Systems Biology
University of Toronto
25 Willcocks St., Rm 3072
Toronto, Ontario M5S 3B2
Fax: 416-978-5878
http://csb.utoronto.ca/faculty/nicholas-provart/

Jennifer Haughton
Tel: 416-978-2700
Email:jennifer.haughton@utoronto.ca
Undergraduate Administrator
Department of Biochemistry
University of Toronto
1 King’s College Circle, Rm. 5207
Toronto, Ontario M5S 1A8
Fax: 416-978-8548
www.biochemistry.utoronto.ca

 

  Last update: 11 July 2018

 

Enrollment Limit

None

Additional Notes and Resources

BCB330Y Registration Form
Official registration form for BCB330Y

Last Updated 11 July 2018