Advancement to Ph.D. Candidacy

Upon completion of formal course requirements, each student will be required to take a written and oral qualifying examination. It is often known as “major proposition” or “Senate Qualifying” or “Advancement to Candidacy” exam. Prior to this examination, each student, in consultation with his or her faculty advisors, will establish a dissertation committee of five faculty members. One advisor should have a primarily computational research focus, the other a primarily experimental research focus. One of the two advisors will function as chair of the committee. The Doctoral Committee for students in the Bioinformatics and Systems Biology program should comprise a minimum of five members and of these, at least three must be members of the BISB program. If all members are from the program, then two must have a different home department than the Committee Chair, and one of these two must be tenured. The dissertation advisors will have the major responsibility for the student's research and dissertation.

At UCSD, the University “Candidacy/Senate” Examination is a requirement for a Graduate Student to complete satisfactorily once a dissertation project has been decided upon. It is strongly recommended except in special circumstances that the student complete this examination prior to the end of the first 3 years in the Program to comply with the Pre-Candidacy Time Limit (PCTL). Students will not be permitted to continue in doctoral status if they have not advanced to candidacy before the expiration of the pre-candidacy time limit. Satisfactory completion of the exam will admit the student to the candidacy of the PhD Program.

The format for this examination is consistent with the highest standards held by peer Universities. The Student must write a 12-15 page candidacy report generally following an NIH grant proposal format. The report must be submitted at least one week prior to the oral exam. Specifically, the report must contain

  • Specific Aims: A one page description of the proposed research, with specific aims supporting the thesis.
  • Research design and methods: For each of the aims, the student must provide background, rationale, and preliminary data in support of their aims. The work must be interdisciplinary in terms of computation and biology, and should have input from both dissertation advisors.
  • Proposed work, and timeline: The student must describe the research that remains to be done, and a rough timeline for accomplishing the remaining work.
  • The student must also include a bibliography or related work, and include as attachments, any publications/supplementary material. These do not count towards the 12-15 pages.

Finally, the student must defend their thesis proposal to their committee in an oral exam (“Advancement to Candidacy Examination”). Students may schedule their exam between quarters (including summer) to accommodate their PhD committee members’ schedules, but, in order for any academic event to be recorded, a student must be registered. This means that an advancement can only be posted to the academic record during a quarter of registration. It is also expected that the student will meet at least annually with the Committee to update the members on his/her progress.