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Computational tools for metabolic engineering.
Copeland WB, Bartley BA, Chandran D, Galdzicki M, Kim KH, Sleight SC, Maranas CD, Sauro HM. Copeland WB, et al. Metab Eng. 2012 May;14(3):270-80. doi: 10.1016/j.ymben.2012.03.001. Metab Eng. 2012. PMID: 22629572 Free PMC article. Review.
SBOL Visual: A Graphical Language for Genetic Designs.
Quinn JY, Cox RS 3rd, Adler A, Beal J, Bhatia S, Cai Y, Chen J, Clancy K, Galdzicki M, Hillson NJ, Le Novère N, Maheshwari AJ, McLaughlin JA, Myers CJ, P U, Pocock M, Rodriguez C, Soldatova L, Stan GB, Swainston N, Wipat A, Sauro HM. Quinn JY, et al. PLoS Biol. 2015 Dec 3;13(12):e1002310. doi: 10.1371/journal.pbio.1002310. eCollection 2015 Dec. PLoS Biol. 2015. PMID: 26633141 Free PMC article.
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.
Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Grünberg R, Hallinan J, Hillson NJ, Johnson JD, Kuchinsky A, Lux M, Misirli G, Peccoud J, Plahar HA, Sirin E, Stan GB, Villalobos A, Wipat A, Gennari JH, Myers CJ, Sauro HM. Galdzicki M, et al. Nat Biotechnol. 2014 Jun;32(6):545-50. doi: 10.1038/nbt.2891. Epub 2014 Jun 6. Nat Biotechnol. 2014. PMID: 24911500
A reappraisal of how to build modular, reusable models of biological systems.
Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL, Gennari JH. Neal ML, et al. PLoS Comput Biol. 2014 Oct 2;10(10):e1003849. doi: 10.1371/journal.pcbi.1003849. eCollection 2014 Oct. PLoS Comput Biol. 2014. PMID: 25275523 Free PMC article. No abstract available.