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.
Informatics Forum, 10 Crichton Street, Edinburgh, EH8 9AB, Scotland, UK
Tel: +44 131 651 5661, Fax: +44 131 651 1426, E-mail: school-office@inf.ed.ac.uk Please contact our webadmin with any comments or corrections. Logging and Cookies Unless explicitly stated otherwise, all material is copyright © The University of Edinburgh |