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Briefings in Bioinformatics Advance Access published online on November 11, 2009
Briefings in Bioinformatics, doi:10.1093/bib/bbp054
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© The Author 2009. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms

Gil Alterovitz, Taro Muso and Marco F. Ramoni

Corresponding author. Taro Muso. E-mail: muso{at}alum.mit.edu

The field of synthetic biology holds an inspiring vision for the future; it integrates computational analysis, biological data and the systems engineering paradigm in the design of new biological machines and systems. These biological machines are built from basic biomolecular components analogous to electrical devices, and the information flow among these components requires the augmentation of biological insight with the power of a formal approach to information management. Here we review the informatics challenges in synthetic biology along three dimensions: in silico, in vitro and in vivo. First, we describe state of the art of the in silico support of synthetic biology, from the specific data exchange formats, to the most popular software platforms and algorithms. Next, we cast in vitro synthetic biology in terms of information flow, and discuss genetic fidelity in DNA manipulation, development strategies of biological parts and the regulation of biomolecular networks. Finally, we explore how the engineering chassis can manipulate biological circuitries in vivo to give rise to future artificial organisms.

Keywords: informatics, synthetic biology, systems biology, networks

Submitted: August 5, 2009. Accepted: September 23, 2009.


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