Neurobiology 306qc – MATLAB bootcamp in MAY
Intensive January course covering theoretical foundations in population genetics, genetic drift versus selection, identifying selection in genomes, advances in laboratory evolution experiments, with applications to key questions in systems biology and evolution.
Synthetic biology is a new discipline that seeks to enable the predictable engineering of biological systems. According to one conception of synthetic biology, proteins and genetic regulatory elements are modular and can be combined in a predictable manner. In practice however, assembled genetic devices do not function as expected. The purpose of the course is to go beyond the textbook, first-pass description of molecular mechanisms and focus on details that are specifically relevant to engineering biological systems.
We will examine how the some of the key requirements of living systems are implemented and how quantitative experimental methods and mathematical analysis can help us understand them. The mathematical techniques will be introduced along the way, to the level that will help students understand current papers in systems biology.
Lecture 1: Stochastic chemical events
•When are stochastic events relevant?
•Memory-lacking exponential step
•Formulate Markov processes (Master Equations)
Lecture 2: Exact simulation algorithms
•The Doob-Gillespie algorithm
•Exact stochastic-deterministic hybrid methods
•Integrating Master Equations
•Simulating rare events
Series of lectures to introduce the research areas of current program faculty in systems biology.
A course focusing on the rational design, construction and applications of nucleic acid and protein-based synthetic molecular and cellular machinery and systems. Students are mentored to produce substantial term projects, which are tailored to each student's strengths and interests.
Rigorous introduction to (i) dynamical systems theory as a tool to understand molecular and cellular biology (ii) stochastic processes in single cells, using tools from statistical physics and information theory.
Students will work collaboratively with faculty and one another on critical science communication skills including crafting graphics, writing fellowships, and giving oral presentations.