Toronto Networking Seminar


Organized by Department of Computer Science and Department of Electrical and Computer Engineering, University of Toronto







Designing Synthetic Biological Networks





Desmond Lun


Computational Biologist


The Broad Institute of MIT and Harvard




Date:  Friday, January  11,  2pm

Location: BA 1220 



Abstract:




The engineering of simple living organisms such as microbes in a
well-defined, systematic manner---in much the same way as computer
systems or communication systems are engineered---has recently emerged
as an exciting, realizable prospect.  Such engineering, which is often
referred to as synthetic biology, promises new, improved ways of
producing drugs and fuels as well as to serve functions that are yet to
be imagined.  But, as with all engineering, synthetic biology requires
design, and, at present, few design tools or principles exist for
synthetic biology.


In this talk, we discuss how mathematical optimization can be used to
aid the design of synthetic microbes.  In particular, we focus on the
problem of engineering E. coli to produce biofuel and discuss a network
optimization problem that arises in this context.  We outline a
local-search heuristic that we have implemented to tackle this problem,
and we discuss potential areas for improvement as well as general future
directions in the nascent field of analytical design for synthetic
biology.




Bio:



Desmond Lun is a Computational Biologist at the Broad Institute of MIT
and Harvard and a Research Fellow in Genetics at Harvard Medical School.
Prior to his present position, he was a Postdoctoral Research Associate
in the Coordinated Science Laboratory at the University of Illinois at
Urbana-Champaign.  He received bachelor's degrees in mathematics and
computer engineering from the University of Melbourne, Australia in
2001, and S.M. and Ph.D. degrees in electrical engineering and computer
science from MIT in 2002 and 2006, respectively.


Dr. Lun's research interests are in networking and in synthetic and
systems biology.  He is co-author, with Tracey Ho, of "Network Coding:
An Introduction," forthcoming from Cambridge University Press.




Host of the talk



Peter Marbach (marbach@cs.toronto.edu)