CHE.496/2008/Schedule/Systems biology and synthetic biology: Difference between revisions
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*'''Systems biology as a foundation for genome-scale synthetic biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=709071&_coverDate=10%2F31%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=7a316893fbee50cab2742cc3b6de73b4 link] | *'''Systems biology as a foundation for genome-scale synthetic biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=709071&_coverDate=10%2F31%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=7a316893fbee50cab2742cc3b6de73b4 link] | ||
**This article discusses the connection between systems biology and synthetic biology, specifically how modern advances in systems biology aid the development of the nascent field of synthetic biology | |||
**One current approach taken by systems biologists is to 'reconstruct' a system | |||
***This is done by first incorporating every relevant reaction into a stoichiometric matrix | |||
***From this, a set of parameters can be identified | |||
***By applying 'flux balance analysis' to this model, a concrete model that accurately predicts temporal evolution of the system can be achieved | |||
***Requires many parameters to be defined as well as a 'demand reaction' to drive the system, which is unknown in most cases outside of exponential growth | |||
**Much of the software developed for systems biology will be useful in the pursuit of computational analysis in synthetic biology | |||
**In order to deal with unknown parameters, synthetic biologists can use directed evolution to make a system conform to known parameters; in short, make the system imitate the model | |||
**New experimental techniques are always improving parameter estimation and system reconstruction, and these will clearly benefit both systems and synthetic biologists | |||
**Maybe we can use some of these techniques in our own work? | |||
***Developing our own 'reconstruction' seems unlikely to be feasible, although if we're working with a known system, we may be able to use others' results | |||
***The OptStrain strategy may be feasible if we do metabolic engineering, but I doubt we'll be doing a qualitatively new pathway, so this is likely unnecessary | |||
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*'''Modular approaches to expanding the functions of living matter [http://www.nature.com/nchembio/journal/v2/n6/abs/nchembio789.html link] | *'''Modular approaches to expanding the functions of living matter [http://www.nature.com/nchembio/journal/v2/n6/abs/nchembio789.html link] | ||
Revision as of 12:48, 2 April 2008
Systems biology and synthetic biology
- Discussion leader: George W.
- Systems biology as a foundation for genome-scale synthetic biology link
- This article discusses the connection between systems biology and synthetic biology, specifically how modern advances in systems biology aid the development of the nascent field of synthetic biology
- One current approach taken by systems biologists is to 'reconstruct' a system
- This is done by first incorporating every relevant reaction into a stoichiometric matrix
- From this, a set of parameters can be identified
- By applying 'flux balance analysis' to this model, a concrete model that accurately predicts temporal evolution of the system can be achieved
- Requires many parameters to be defined as well as a 'demand reaction' to drive the system, which is unknown in most cases outside of exponential growth
- Much of the software developed for systems biology will be useful in the pursuit of computational analysis in synthetic biology
- In order to deal with unknown parameters, synthetic biologists can use directed evolution to make a system conform to known parameters; in short, make the system imitate the model
- New experimental techniques are always improving parameter estimation and system reconstruction, and these will clearly benefit both systems and synthetic biologists
- Maybe we can use some of these techniques in our own work?
- Developing our own 'reconstruction' seems unlikely to be feasible, although if we're working with a known system, we may be able to use others' results
- The OptStrain strategy may be feasible if we do metabolic engineering, but I doubt we'll be doing a qualitatively new pathway, so this is likely unnecessary
- Modular approaches to expanding the functions of living matter link
