The town-hall meeting was attended by 4 graduate students currently in the program (Cheryl Wolting, Martin Hyrcza, Ryan Austin and Anthony Joshua.), as well as interested and current faculty - Peter Lewis, Boris Steipe, Tim Hughes, Elisabeth Tillier, Quaid Morris, Jeremy Squire, Andrew Emili, Gary Bader, John Parkinson, Alan Davidson, Daphne Goring (Chair designate, Cell and Systems Biology), Malcolm Campbell, N.N. and the program assistant, Rob Reedijk. The discussion topics are listed below, and details of each discussion are within each section under that. Summarized by Nicholas Provart, 28 May 2006.


Student and faculty benefits

  • sense of community
  • students receive the CGPPB designation on their degree
  • training across disciplines → rotations outside of home department?
  • potential of scholarships (Apple, IBM, Affymetrix, Microsoft, CIHR)
  • yearly retreat
  • joint seminar series with CCBR/CAGEF → sense of community
  • student recruitment

The perceived benefit by some members of the computer science department of having the CGPPB designation does not outweigh the costs associated with the program, in current form. Some CS members think that rotations/traineeships, if in the first year of the CS PhD program, would be doable. Having a scholarship for students to pay for the traineeship period is highly desirable, otherwise perceived cost to professor too high. It was pointed out that the traineeships are not required to be in a contiguous 4 month block, but can rather be spaced out. In addition, the traineeship is intended to further the student's PhD project, see the current CGPPB Policies.

Rotations versus traineeships

  • Traineeships perceived to be onerous, especially by departments with a rotation system or with a large number of course requirements
  • Idea: Permit an outside rotation, instead of a traineeship, in a CGPPB faculty member’s lab. This would be a unique feature of the Program.
  • Make traineeship less onerous by relaxing requirement – make it more like having a member from the CGPPB on the graduate student’s committee, with whom the student has some contact and does work towards PhD project?

The issue of rotations versus collaborative traineeships is of importance to departments like Molecular and Medical Genetics that have a rotation system, and Computer Science that has a large number of required courses. Most students are admitted at the MSc level, so it was pointed out that in order to allow students the possibility of rotating with a collaborative member, direct entry at the MSc level would be required. It might be possible to allow students conditional acceptance into the program so that they could rotate outside of e.g. Molecular and Medical Genetics. This change would presumably require no approval by U of T governance of the current administrative framework.

Name Change

The Program was called Proteomics and Bioinformatics in part for historical reasons. Might be perceived as being exclusionary to those researchers carrying out transcriptomics or other high-throughput sysbio methods that require the use of bioinformatics w.r.t. data analysis

  • Genome Biology and Bioinformatics
  • Genome and Computational Biology
  • Integrative and Computational Biology
  • ...

The name of the program was somewhat contentious. Most attendees however agreed that Genome Biology and Bioinformatics, or Genome and Computational Biology were acceptable. I will send around a survey to all CGPPB members shortly. Note that a name change would require Governance and OCGS approval.

New CGPPB Department Members and Current Membership

  • Computer Science

Issue: Meshing CS degree requirements w. CGPPB requirements a challenge, as CS requires 9 half courses. If there is a traineeship requirement, best carried out in 1st year.

  • Current Faculty Members

The issue of 'deadwood' was mentioned w.r.t. current faculty members, and that a selection mechanism should be established to remove non-participating members. For instance, if members refuse to accept students for traineeships or would not lecture in one of the core course, they should be dropped from the program. Deadwood on the other hand might not be an issue, as long as the members are willing to take on students for traineeships. Members should also be willing to have students in the collaborative program.

Alternate course requirements for the program

Program requirements (above individual departmental requirements)

  • JTB2010 - Proteomics and Functional Genomics
  • JTB2020 - Applied Bioinformatics

Some students coming from a more computational background might benefit from alternate courses on e.g. machine learning or statistical computation offered by faculty members in CS. These could be elective requirements, as an alternate to JTB2020. Amending the current requirements would only require Governance approval.

Master's component to the Program

  • requires a new application, to be approved by Governance and OCGS
  • JTB2010 could be a requirement for the M.Sc., plus graduate committee membership of another CGPPB member?

Note that a new MSc component would require a completely new application to be approved by Governance and OCGS. Mingyao Liu (outgoing Associate Dean, School of Graduate Studies) has recommended on concentrating on growing the PhD program before introducing changes. It seems like allowing conditional entry into the CGPPB might be an easier solution w.r.t. the Rotation/Traineeship issue above.

Improved website and sense of community

  • Boris Steipe has recently set up the site as a Wiki
  • Create an attractive home page
  • Also, outreach to students in 4th year considering graduate studies, and who have just started their PhD

Several of the students mentioned the lack of a sense of community for the CGPPB. Currently we have no representative from the students to liase with the Program committee. To replace the defunct Bioinformatics Developer's Network, it was suggested to have a biweekly or monthly Progress Seminar for Students, perhaps alternating with Faculty speakers. Pizza could be served. I will contact the students to ask them to help organize this for September. It was also suggested to have conference scholarships for CGPPB students, to be able to attend conferences that supervisors would not normally pay for. In addition, perhaps the Program could organize training sessions through, free for the students (a $1500 value). This would be a concrete benefit for being part of the Program.

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