Literature DB >> 22132053

Programming languages for synthetic biology.

P Umesh, F Naveen, Chanchala Uma Maheswara Rao, Achuthsankar S Nair.   

Abstract

In the backdrop of accelerated efforts for creating synthetic organisms, the nature and scope of an ideal programming language for scripting synthetic organism in-silico has been receiving increasing attention. A few programming languages for synthetic biology capable of defining, constructing, networking, editing and delivering genome scale models of cellular processes have been recently attempted. All these represent important points in a spectrum of possibilities. This paper introduces Kera, a state of the art programming language for synthetic biology which is arguably ahead of similar languages or tools such as GEC, Antimony and GenoCAD. Kera is a full-fledged object oriented programming language which is tempered by biopart rule library named Samhita which captures the knowledge regarding the interaction of genome components and catalytic molecules. Prominent feature of the language are demonstrated through a toy example and the road map for the future development of Kera is also presented.

Entities:  

Keywords:  Computational biology; Design and construction of organisms; Programming language; Synthetic biology

Year:  2011        PMID: 22132053      PMCID: PMC3065592          DOI: 10.1007/s11693-011-9070-y

Source DB:  PubMed          Journal:  Syst Synth Biol        ISSN: 1872-5325


  15 in total

1.  Construction of a genetic toggle switch in Escherichia coli.

Authors:  T S Gardner; C R Cantor; J J Collins
Journal:  Nature       Date:  2000-01-20       Impact factor: 49.962

2.  A synthetic oscillatory network of transcriptional regulators.

Authors:  M B Elowitz; S Leibler
Journal:  Nature       Date:  2000-01-20       Impact factor: 49.962

3.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal:  Bioinformatics       Date:  2003-03-01       Impact factor: 6.937

Review 4.  The second wave of synthetic biology: from modules to systems.

Authors:  Priscilla E M Purnick; Ron Weiss
Journal:  Nat Rev Mol Cell Biol       Date:  2009-06       Impact factor: 94.444

5.  Towards programming languages for genetic engineering of living cells.

Authors:  Michael Pedersen; Andrew Phillips
Journal:  J R Soc Interface       Date:  2009-04-15       Impact factor: 4.118

Review 6.  Computational design tools for synthetic biology.

Authors:  Mario A Marchisio; Jörg Stelling
Journal:  Curr Opin Biotechnol       Date:  2009-09-14       Impact factor: 9.740

7.  A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts.

Authors:  Yizhi Cai; Brian Hartnett; Claes Gustafsson; Jean Peccoud
Journal:  Bioinformatics       Date:  2007-09-05       Impact factor: 6.937

Review 8.  Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems.

Authors:  Caleb J Bashor; Andrew A Horwitz; Sergio G Peisajovich; Wendell A Lim
Journal:  Annu Rev Biophys       Date:  2010       Impact factor: 12.981

9.  TinkerCell: modular CAD tool for synthetic biology.

Authors:  Deepak Chandran; Frank T Bergmann; Herbert M Sauro
Journal:  J Biol Eng       Date:  2009-10-29       Impact factor: 4.355

10.  Writing DNA with GenoCAD.

Authors:  Michael J Czar; Yizhi Cai; Jean Peccoud
Journal:  Nucleic Acids Res       Date:  2009-05-08       Impact factor: 16.971

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  3 in total

1.  Towards a behavioral-matching based compilation of synthetic biology functions.

Authors:  Adrien Basso-Blandin; Franck Delaplace
Journal:  Acta Biotheor       Date:  2015-07-05       Impact factor: 1.774

2.  2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts.

Authors:  Mariana Leguia; Jennifer An Brophy; Douglas Densmore; Angel Asante; J Christopher Anderson
Journal:  J Biol Eng       Date:  2013-01-10       Impact factor: 4.355

3.  A novel sequence and context based method for promoter recognition.

Authors:  Umesh P; Jitendra Kumar Dubey; Karthika Rv; Betsy Sheena Cherian; Gopakumar Gopalakrishnan; Achuthsankar Sukumaran Nair
Journal:  Bioinformation       Date:  2014-04-23
  3 in total

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