Computational Design in Synthetic Biology
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One of the most ambitious goals in biological engineering is the ability to computationally design an organism using unsupervised algorithms. We discuss the development of new automatic methodologies to design biological parts and devices using computational design. Some of them rely on the appropriate characterisation of single genetic elements into SBML models and their posterior assembly to generate the final transcriptional network with targeted behaviour (such as an oscillatory dynamics). This modular construction approach allows implementing a successful modelling-construction-characterization cycle. Currently, it is not clear what role is played by cellular context, and to which extent it is possible to fruitfully use such a modular approach, but the perspectives of a model-based design of biological networks overwhelms the corresponding risk.
KeywordsSynthetic Biology Genetic Network Biological Part Genetic Circuit Synthetic Biologist
This work was supported by the Spanish Ministry of Education and Science (ref. TIN 2006-12860), the Structural Funds of the European Regional Development Fund (ERDF), the EU grants BioModularH2 (FP6-NEST contract 043340) and EMERGENCE (FP6-NEST contract 043338) and the ATIGE Genopole/UEVE CR-A3405. GR acknowledges a graduate fellowship from the Conselleria d’Educacio de la Generalitat Valenciana (ref. BFPI 2007/160) and an EMBO Short-term fellowship (ref. ASTF-343.00-2007).
- Carrera J, Rodrigo G, Jaramillo A (2009b) Towards the automated engineering of a synthetic genome. Mol Biosyst DOI: 10.1039/b904400k.Google Scholar
- Genbank (2008) National center for biotechnology information. A USA national resource of molecular biology information. http://www.ncbi.nlm.nih.gov/Genbank/index.html. Data taken 20th November, 2008.
- Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, Dechancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS and Baker D (2008) Kemp elimination catalysts by computational enzyme design. Nature 9: 1–6.Google Scholar
- Suarez M, Tortosa P and Jaramillo A (2009) PROTDES: CHARMM toolbox for computational protein design. Systems and Synthetic Biology.Google Scholar