Literature DB >> 19628507

iBioSim: a tool for the analysis and design of genetic circuits.

Chris J Myers1, Nathan Barker, Kevin Jones, Hiroyuki Kuwahara, Curtis Madsen, Nam-Phuong D Nguyen.   

Abstract

SUMMARY: iBioSim is a tool that supports learning of genetic circuit models, efficient abstraction-based analysis of these models and the design of synthetic genetic circuits. iBioSim includes project management features and a graphical user interface that facilitate the development and maintenance of genetic circuit models as well as both experimental and simulation data records. AVAILABILITY: iBioSim is available for download for Windows, Linux, and MacOS at http://www.async.ece.utah.edu/iBioSim/ CONTACT: myers@ece.utah.edu.

Mesh：

Year:  2009        PMID： 19628507     DOI： 10.1093/bioinformatics/btp457

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  21 in total

1.  Stochastic steady state gain in a gene expression process with mRNA degradation control.

Authors:  Hiroyuki Kuwahara; Russell Schwartz
Journal:  J R Soc Interface       Date:  2012-01-11       Impact factor: 4.118

Review 2.  Genetic design automation: engineering fantasy or scientific renewal?

Authors:  Matthew W Lux; Brian W Bramlett; David A Ball; Jean Peccoud
Journal:  Trends Biotechnol       Date:  2011-10-14       Impact factor: 19.536

3.  libRoadRunner: a high performance SBML simulation and analysis library.

Authors:  Endre T Somogyi; Jean-Marie Bouteiller; James A Glazier; Matthias König; J Kyle Medley; Maciej H Swat; Herbert M Sauro
Journal:  Bioinformatics       Date:  2015-06-17       Impact factor: 6.937

Review 4.  Design Automation in Synthetic Biology.

Authors:  Evan Appleton; Curtis Madsen; Nicholas Roehner; Douglas Densmore
Journal:  Cold Spring Harb Perspect Biol       Date:  2017-04-03       Impact factor: 10.005

5.  The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Authors:  Michal Galdzicki; Kevin P Clancy; Ernst Oberortner; Matthew Pocock; Jacqueline Y Quinn; Cesar A Rodriguez; Nicholas Roehner; Mandy L Wilson; Laura Adam; J Christopher Anderson; Bryan A Bartley; Jacob Beal; Deepak Chandran; Joanna Chen; Douglas Densmore; Drew Endy; Raik Grünberg; Jennifer Hallinan; Nathan J Hillson; Jeffrey D Johnson; Allan Kuchinsky; Matthew Lux; Goksel Misirli; Jean Peccoud; Hector A Plahar; Evren Sirin; Guy-Bart Stan; Alan Villalobos; Anil Wipat; John H Gennari; Chris J Myers; Herbert M Sauro
Journal:  Nat Biotechnol       Date:  2014-06-06       Impact factor: 54.908

6.  Bayesian design of synthetic biological systems.

Authors:  Chris P Barnes; Daniel Silk; Xia Sheng; Michael P H Stumpf
Journal:  Proc Natl Acad Sci U S A       Date:  2011-08-29       Impact factor: 11.205

Review 7.  Quantitative and logic modelling of molecular and gene networks.

Authors:  Nicolas Le Novère
Journal:  Nat Rev Genet       Date:  2015-02-03       Impact factor: 53.242

8.  Towards the rational design of synthetic cells with prescribed population dynamics.

Authors:  Neil Dalchau; Matthew J Smith; Samuel Martin; James R Brown; Stephen Emmott; Andrew Phillips
Journal:  J R Soc Interface       Date:  2012-06-08       Impact factor: 4.118

9.  Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE).

Authors:  Nicolas Le Novère; Michael Hucka; Nadia Anwar; Gary D Bader; Emek Demir; Stuart Moodie; Anatoly Sorokin
Journal:  Stand Genomic Sci       Date:  2011-11-30

10.  Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits.

Authors:  Mario Andrea Marchisio; Moreno Colaiacovo; Ellis Whitehead; Jörg Stelling
Journal:  BMC Syst Biol       Date:  2013-05-27
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