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

@article{citeulike:6100886, abstract = {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. 10.1093/bib/bbp054}, author = {Alterovitz, Gil and Muso, Taro and Ramoni, Marco F.}, booktitle = {Brief Bioinform}, citeulike-article-id = {6100886}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bib/bbp054}, citeulike-linkout-1 = {http://bib.oxfordjournals.org/content/bbp054v1/.abstract}, citeulike-linkout-2 = {http://bib.oxfordjournals.org/content/bbp054v1/.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19906839}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19906839}, day = {11}, doi = {10.1093/bib/bbp054}, issn = {1477-4054}, journal = {Briefings in bioinformatics}, keywords = {synthetic\_biology}, month = {November}, pages = {bbp054+}, posted-at = {2009-11-12 08:23:35}, priority = {2}, title = {The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms}, url = {http://dx.doi.org/10.1093/bib/bbp054}, year = {2009} }

TY - JOUR ID - citeulike:6100886 L3 - citeulike-article-id:6100886 N2 - 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. 10.1093/bib/bbp054 JF - Briefings in bioinformatics SN - 1477-4054 TI - The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms T2 - Brief Bioinform SP - bbp054 KW - synthetic_biology AU - Alterovitz, Gil AU - Muso, Taro AU - Ramoni, Marco PY - 2009/11/11/ UR - http://dx.doi.org/10.1093/bib/bbp054 ER -