The requirements for year 2 in the BCMB program focus on three important areas: a quantitative biology course, the Admission to Candidacy Exam and thesis research in the student’s chosen lab.
Courses
Quantitative Understanding in Biology (qBio)
Beginning in Fall 2015, all students enrolled in PhD programs within the Weill Graduate School of Biomedical Sciences are required to complete a one quarter course in Biostatistics. For BCMB students, this course will be taken during Quarter I of their second year in the program.
The qBio course will prepare students to apply quantitative techniques to the analysis of experimental data and the modeling of biological systems. To emphasize both practical and theoretical skills, the material will be presented whenever possible in a hands-on workshop style, and the completion of several projects by the students will be required. Topics include: practical aspects of data formatting and management; communication of quantitative concepts (verbal, graphical and mathematical); a review of statistics, with emphasis on the selection of appropriate statistical tests; the use of modern software packages; the interpretation of results; the formulation, evaluation and analysis of mathematical models of biological function, with an emphasis on linear and non-linear regression, determination of model parameters; and the critical comparison of alternative models with regard to over-parameterization. The formal components will introduce (and demystify) ordinary and partial differential equations and basic principles of non-linear dynamics, in order to enable quantitative modeling in biological arenas such as neural function, enzyme kinetics, cardiac dynamics and signaling pathways. Additional special topics will also be presented (e.g., control theory, machine learning, information theory, and image analysis) and their application will be illustrated with ongoing research in the laboratories of participating faculty.
Admission to Doctoral Candidacy Examination (ACE)
ACE description
The Admission to Doctoral Candidacy Examination (ACE) is composed of two components, a written component (a research proposal) and an oral examination in which the student defends the proposal. Both components develop critical skills necessary for a successful Ph.D. student.
A student must be in good academic standing to take the ACE. For the written exam, the student prepares a research proposal on a topic selected by the student and approved by the ACE Committee. The ACE Committee consists of several faculty members whose membership on the committee rotates. The written proposal is reviewed by the ACE Committee and returned to the student with a written critique. The oral exam tests the student's ability to respond to comments in the critique, as well as the student's general knowledge. The Examining Committee for the oral consists of five faculty members: the Special Committee (i.e. the research mentor and two additional faculty members), a chair, and one additional member. At least one of the five members is also a member of the ACE Committee. Before taking the ACE, students must have completed the core sequence of courses; however, they need not have completed their elective courses. The ACE is taken during the Spring of the second year. The official description of the requirements and procedures for the ACE is contained in a separate document that will be provided to students upon completion of their first year requirements.
No later than six months after completion of the ACE, each student is required to convene her/his first Special Committee meeting (see below for composition of the Special Committee). In addition, the student is required to prepare a written document outlining the thesis hypothesis, some background information, and a brief description of the experimental approach (i.e., rationale and anticipated and possible unanticipated results, etc.). This document should be no longer than 5 pages, excluding illustrations and references. It must be submitted to the Special Committee members at least one week in advance of this meeting. At the meeting, the student should be prepared to discuss in depth the background (general and specific) of the project, approaches that will be taken, and what has already been accomplished. This meeting will serve as a mechanism to ensure that the Thesis Project is outlined and that the student has considered the biological relevance of the project. It will also serve to familiarize the Committee with the student's project and to allow the committee to provide constructive comments. The 5 page document must be approved by the committee. A brief report will be completed by one of the committee members (not the thesis mentor) and returned to the Program Coordinator, along with a copy of the document, for forwarding to the Program Directors. Completion of the post-ACE first Special Committee meeting is required to remain in good academic standing.
ACE topic choice
The topic is up to the student, with the following advisory considerations: It is the student's privilege to have flexibility and latitude in choice of the ACE topic. However, it is the student's responsibility to convincingly demonstrate independence of thought. The closer the ACE topic is to research projects previously conceived by the student's mentor or already being conducted in the host laboratory, the more difficult it may be to establish the independence of the student's thinking. However, it is often the case that the ACE is taken at a point when the thesis topic is not defined or the thesis topic that was initially chosen does not pan out. An independently-conceived ACE topic may give shape to or even become a thesis topic; this is welcomed.
The only restriction on topic choice is that all portions of the document must be written entirely independently from the student's mentor. While the student is encouraged to build on work previously conducted in the host laboratory, direct incorporation of specific aims, hypotheses or conclusions from a previously written grant application from the mentor (or anyone else) is not allowed. The mentor must certify that the specific aims were developed and written independently, and that the content of the ACE proposal was not "lifted" from a pre-existing research plan. The student will be held responsible for all ideas expressed in the proposal, and will be expected to explain, justify and defend all concepts described in the written document.
A suitable topic is one that incorporates experimentally testable models or hypotheses, is amenable to rational experimental design, and results in more than one predictable outcome for the experiments. Research topics that are seen as "fishing expeditions" or are not hypothesis-driven will generally not be approved.
As noted above, the lab head will be given the proposed aims and the completed written exam. For the student to proceed, the lab head must attest that the aims were prepared independently and that they reflect the original work of the student.
Special Committee
Once a thesis mentor has been agreed upon (which should occur by July 1), the student, in consultation with the mentor, forms a Special Committee composed of the thesis mentor and two additional faculty members. This committee acts to evaluate a student's research and should also serve as an informational resource to the student. Special Committee forms are available from the graduate office (Cornell A -131) or on the Graduate School Website.
A Program Director must sign these forms, which are then returned to Program Coordinator, who files them with the Dean's office. Any subsequent changes must be approved by a student's mentor and the appropriate Program Director, and be indicated on the form on file in the Dean's office.
The Special Committee must meet at least once per year from year 2 through graduation. Annual special committee meetings are a requirement for remaining in good academic standing. For each Special Committee meeting (following the one that occurs within 6 months of completing the ACE), the student should prepare a 1-2 page written outline of progress and future goals. This must be submitted to all committee members prior to the meeting.
Thesis research
During the second year in the program, the student will begin work on a thesis project under the guidance of the Thesis mentor/Major Sponsor. Preparation and defense of the ACE will be invaluable for setting the course of the thesis work over the next 4 years.
Formal presentations of scientific data
The ability to accurately and effectively present scientific data in a formal setting is vital to a productive scientific career. To encourage students to gain such experience, all students upon completion of their ACE must annually present original data at a formal scientific venue. This requirement can be fulfilled by presenting a Talk or Poster at the annual Vincent Du Vigneaud Memorial Symposium hosted by the Weill Cornell Graduate School, the annual BCMB Program Retreat held every Fall, various Departmental Seminar Series or at any National or International Scientific meeting. Fulfillment of this requirement must be verified at the student's annual special committee meeting. The student is required to submit to the special committee the abstract of the presentation.