This page contains the class material for the '11 Synthetic Biology and Modeling (SBM) MSc course. General information about the postgraduate programme can be found here.

Coursework is due Oct 31 4pm (end of the class), marks will be given Nov 3.

See the course timetable.

As an introduction to the lively subject of synthetic biology, check out this interesting article Biotechnology: The falling cost of equipment capable of manipulating DNA is opening up a new field of biohacking to enthusiasts. Check also this special Nature issue. In particular, read this great piece on 5 hard truths for synthetic biology. And this really good summary tinkering with life.
One of the nice things about synthetic biology is that it is very new and particularly friendly to students thanks to the IGEM competition. Under the supervision of Chris French and Alistair Elfick, Edinburgh has had a wonderful series of succesful IGEM projects. We will have a guest lecture from this year's IGEM'11 team, and, time permitting, a more detailed lecture on the modeling aspects of the 2010 IGEM project, which has won the "best model prize" in Oct 2010 using some of the methods we will learn in this class.

Sep 19, Sep 23: no class.

Sep 26: Introduction to synthetic biology with additional material on the synthetic biology of protein networks (after W. Lim et al.) slides. An example of a sophisticated molecular machine, to be looked at with the eye of an engineer, bacterial chemosensors.

Sep 29: Bio-Bricks and IGEM Chris French, IGEM guest lecture from the Edinburgh '11 team on their biorefineries project.

Oct 3-6-10-13: Spatial positioning of chemosensors after Wingreen et al. Notes (revised Oct 17).

Oct 17: Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen

Oct 20: Modeling exercise

Oct 24-27-31: Petri nets: invariants, stochastic semantics, equilibrium and entropy slides.

We move to a weekly 2 hours class, Thursdays 10am IF2.46.

Nov 3: Rule-based modelling: Mapk cascades (slides), and course notes; Refinement and two control motifs

Nov 10: Rule-based Bio-Bricks after Ty Thomson, and extensions after Elaine Murphy.

Nov 17: Rewiring signalling networks ; Rewiring in space (shared CSB course).

Nov 24: Advanced rule-based modelling: Energy-based modeling and allostery slides; Random protein networks

Dec 1: Cellular Potts model slides, notes.

Additional material: Model-driven engineering of transcriptional circuits: slides after J. Collins et al. Combinatorial promoters after Elowitz et al. Thermodynamic models of transcriptional regulation: slides and course notes - after Bintu et al. Advanced rule-based modelling: Information carriers in Biomolecular networks slides.

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