Introduction

Systems biology aims to explain how higher level properties of complex biological systems arise from the interactions among their parts. This new field requires a fusion of concepts from many disciplines, including biology, computer science, applied mathematics, physics and engineering. Students with backgrounds in any of these disciplines are encouraged to apply.

Through coursework and collaborative research, we aim to enable students to combine experimental and theoretical approaches to develop physical and quantitative models of biological processes. The Program aims to introduce students to the tools that are now available, and to help them select important unsolved problems in biology that may now be possible to address using quantitative and theoretical approaches.

This is a small and friendly Program with many opportunities to meet and interact with faculty. Program activities include seminars, a retreat, and a weekly discussion session known as Theory Lunch.

How the program works

Incoming students are assigned to two advisors, generally from different disciplines, who are available to help plan the student’s initial program of graduate study. The course requirements are minimal; because the backgrounds of entering students are varied, the coursework required by an individual student is unpredictable. The Program Faculty has instead identified a list of core competencies that each student should make progress towards in the course of their graduate career.

After the first year a student will either choose a single faculty member as their dissertation advisor, or initiate a collaboration between two or more labs. Students may choose dissertation advisors from any science department at Harvard, including the research departments of the 11 Harvard-affiliated teaching hospitals. The research topic chosen may be entirely theoretical, or entirely experimental, or anything in between.

Coursework

Students are required to take SB300 Introduction to Systems Biology, MedSci300 Conduct of Science, and four additional courses chosen in consultation with their faculty advisor. These courses must be passed with a B- or better.

The Program offers an informal summer course (in August) that introduces a range of experimental techniques (basic molecular biology, biochemistry, tissue culture, microscopy) and theoretical/computational tools (a mathematics refresher, and introductions to programming languages such as Perl and MATLAB). Attendance is not required, but is encouraged. The summer course uses a “buddy” system in which students pair up with another student with a different background.

Six formal courses are currently offered by Program Faculty. In addition, a wide variety of courses taught at Harvard and MIT are available. For course descriptions, see the Harvard Faculty of Arts and Sciences Course Catalog at http://www.registrar.fas.harvard.edu/Courses/ or the MIT Course Catalogue at http://web.mit.edu/catalogue/.

1. Systems Cell Biology SB102 An exploration of modern basic cell biology and cutting edge research approaches that used chemical, physical or computational tools to address important problems.
2. A Systems Approach to Biology SB200 Introduces theoretical tools and computational approaches from mathematics, physics, computer science and engineering in the context of biological problems and situations.
3. Seminar in Systems Biology SB 201 This course examines concepts and methods in Systems Biology, and follows the development of the field and current thinking through primary reading of classic and modern papers.
4. Introduction to Systems Biology Research SB300 Introductory lectures by Systems Biology Program members. Weekly one and a half hour lectures will introduce the research areas of faculty performing research in systems biology.
5. Special Topics in Systems Biology SB301 An exploration of new directions for the field of systems biology. This course will identify major unsolved questions in biology and discuss the possible new approaches to these questions offered by systems biology.
6. Biologists at the Computer SB302 This course provides an introduction to the field of computer science for biology students.

Rotations

Students in the program are expected to take 2-4 laboratory rotations before selecting a dissertation project. This is to allow the student to explore different research areas, identify potential collaborators, and experience the environment in different research groups (both experimental and theoretical), not to accomplish a research project. The program does not set time limits on rotations, but most rotations are expected to be 4-12 weeks long. Every rotation should include a presentation by the student to the research advisor on the background of their project, and what they learned.

Teaching

Students are required to act as teaching fellows in at least one course. Most students will fulfill this requirement by participating in a core course offered by the Program. Students who choose to be teaching fellows in a Systems Biology course will be paid in addition to receiving credit. If students teach in other departments, their compensation will be determined by that department. We recommend that students complete this requirement by the end of the second year if possible.

Preliminary Qualifying Examination

Students will be expected to complete the Preliminary Qualifying Exam by the end of their second year. The examination is divided into two parts:

Part 1 of the PQE must be completed no later than June 15 of the first year. Students will formulate a question related to any problem in biology (on any scale) and develop a simple set of equations and/or a computer program designed to address the question in a quantitative way. Students are encouraged to discuss possible questions and models with each other and with faculty in preparing for the exam, but the final project should be their own original work.

Students will prepare a short written summary and an oral presentation on their project. The examination committee (3 faculty) may ask questions about the project itself, or about background information. The committee may also ask about the courses taken by the student and/or their rotation projects. These general questions will help the faculty committee assess if they are adequately prepared to undertake a PhD project.

Part 2 of the PQE must be completed no later than March 31 of the student’s second year. Students will prepare and defend an original research proposal derived from the student’s proposed dissertation research. The proposal should define the important questions to be addressed, provide adequate background and describe some details of experiments, computation and/or theoretical work to be undertaken.

Dissertation

After completing the Qualifying Exam, students will be required to meet once a year with a Dissertation Advisory Committee (DAC) consisting of their advisor(s) and three additional faculty. The DAC and the student will meet and discuss the proposal, and the student will receive feedback, advice and suggestions from Committee members. This should help refine the student’s ideas about their dissertation project and define the scope, direction and overall soundness of the idea.

Acceptable modes of dissertation research will include experiment-based research, theoretical research, and combinations of the two. We do not attempt to constrain students to dissertation research in the traditional formats of systems biology’s parent disciplines. We encourage collaborative research, and especially situations in which the student is bringing a new question or a new tool to their dissertation lab(s).

A completed dissertation will ordinarily include at least three chapters comprising original research, of which at least two could be (or have been) submitted for peer-reviewed publication. Alternative forms of publication (for example, a useful computer program or a Website/database that required significant original research and intellectual input) may be acceptable. The Dissertation Examination will involve a public seminar describing the dissertation research, followed by an oral examination by the DAC. We expect that students will complete their dissertation by their fifth or sixth year of study.