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Volumn 6, Issue 8, 2017, Pages 1496-1508

A New Improved and Extended Version of the Multicell Bacterial Simulator gro

Author keywords

bioCAD tools; cell cell interactions; cell shoving algorithm; gro; individual based model; intercellular communication; multicellular biocircuits; synthetic biology; synthetic microbial consortia

Indexed keywords

BACTERIAL PHENOMENA AND FUNCTIONS; CELL COMMUNICATION; CELL PROLIFERATION; COMPUTER LANGUAGE; GENE EXPRESSION REGULATION; MICROBIAL CONSORTIUM; ORGANISMAL INTERACTION; PHYSIOLOGY; SOFTWARE;

EID: 85027548145     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.7b00003     Document Type: Article
Times cited : (42)

References (73)
  • 1
    • 84861342483 scopus 로고    scopus 로고
    • Distributed computation: The new wave of synthetic biology devices
    • Macía, J., Posas, F., and Solé, R. V. (2012) Distributed computation: the new wave of synthetic biology devices Trends Biotechnol. 30, 342-349 10.1016/j.tibtech.2012.03.006
    • (2012) Trends Biotechnol. , vol.30 , pp. 342-349
    • Macía, J.1    Posas, F.2    Solé, R.V.3
  • 2
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie, D. T. (1977) Exact stochastic simulation of coupled chemical reactions J. Phys. Chem. 81, 2340-2361 10.1021/j100540a008
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 3
    • 52649087274 scopus 로고    scopus 로고
    • Modelling and analysis of gene regulatory networks
    • Karlebach, G. and Shamir, R. (2008) Modelling and analysis of gene regulatory networks Nat. Rev. Mol. Cell Biol. 9, 770-780 10.1038/nrm2503
    • (2008) Nat. Rev. Mol. Cell Biol. , vol.9 , pp. 770-780
    • Karlebach, G.1    Shamir, R.2
  • 5
    • 85013413953 scopus 로고    scopus 로고
    • Agent-based modelling in synthetic biology
    • Gorochowski, T. E. (2016) Agent-based modelling in synthetic biology Essays Biochem. 60, 325-336 10.1042/EBC20160037
    • (2016) Essays Biochem. , vol.60 , pp. 325-336
    • Gorochowski, T.E.1
  • 7
    • 84868261037 scopus 로고    scopus 로고
    • Computational Modeling of Synthetic Microbial Biofilms
    • Rudge, T. J., Steiner, P. J., Phillips, A., and Haseloff, J. (2012) Computational Modeling of Synthetic Microbial Biofilms ACS Synth. Biol. 1, 345-352 10.1021/sb300031n
    • (2012) ACS Synth. Biol. , vol.1 , pp. 345-352
    • Rudge, T.J.1    Steiner, P.J.2    Phillips, A.3    Haseloff, J.4
  • 9
    • 84911403647 scopus 로고    scopus 로고
    • Biocellion: Accelerating Computer Simulation of Multicellular Biological System Models
    • Kang, S., Kahan, S., McDermott, J., Flann, N., and Shmulevich, I. (2014) Biocellion: Accelerating Computer Simulation of Multicellular Biological System Models Bioinformatics 30, 3101-3108 10.1093/bioinformatics/btu498
    • (2014) Bioinformatics , vol.30 , pp. 3101-3108
    • Kang, S.1    Kahan, S.2    McDermott, J.3    Flann, N.4    Shmulevich, I.5
  • 10
    • 85027569358 scopus 로고    scopus 로고
    • Georgiev Lab. CeCe. Accessed March 21
    • Georgiev Lab. CeCe. https://github.com/GeorgievLab/CeCe/, Accessed March 21, 2017.
    • (2017)
  • 11
    • 84868233914 scopus 로고    scopus 로고
    • Specification and Simulation of Synthetic Multicelled Behaviors
    • Jang, S. S., Oishi, K. T., Egbert, R. G., and Klavins, E. (2012) Specification and Simulation of Synthetic Multicelled Behaviors ACS Synth. Biol. 1, 365-374 10.1021/sb300034m
    • (2012) ACS Synth. Biol. , vol.1 , pp. 365-374
    • Jang, S.S.1    Oishi, K.T.2    Egbert, R.G.3    Klavins, E.4
  • 14
    • 34547868946 scopus 로고    scopus 로고
    • Modelling the spatial dynamics of plasmid transfer and persistence
    • Krone, S. M., Lu, R., Fox, R., Suzuki, H., and Top, E. M. (2007) Modelling the spatial dynamics of plasmid transfer and persistence Microbiology 153, 2803-16 10.1099/mic.0.2006/004531-0
    • (2007) Microbiology , vol.153 , pp. 2803-2816
    • Krone, S.M.1    Lu, R.2    Fox, R.3    Suzuki, H.4    Top, E.M.5
  • 15
    • 84901273253 scopus 로고    scopus 로고
    • Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics
    • Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A. H., Bonilla, G., Kar, A., Leiby, N., and Mehta, P. et al. 2014, Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics Cell Rep. 7, 1104-1115 10.1016/j.celrep.2014.03.070
    • (2014) Cell Rep. , vol.7 , pp. 1104-1115
    • Harcombe, W.R.1    Riehl, W.J.2    Dukovski, I.3    Granger, B.R.4    Betts, A.5    Lang, A.H.6    Bonilla, G.7    Kar, A.8    Leiby, N.9    Mehta, P.10
  • 16
    • 84879255427 scopus 로고    scopus 로고
    • Multicellular computing using conjugation for wiring
    • Goni-Moreno, A., Amos, M., and de la Cruz, F. (2013) Multicellular computing using conjugation for wiring PLoS One 8, e65986 10.1371/journal.pone.0065986
    • (2013) PLoS One , vol.8 , pp. e65986
    • Goni-Moreno, A.1    Amos, M.2    De La Cruz, F.3
  • 17
    • 84889000190 scopus 로고    scopus 로고
    • Repast: An extensible framework for agent simulation
    • Collier, N. (2003) Repast: An extensible framework for agent simulation Univ. Chicago's Soc. Sci. Res. 36, 2003
    • (2003) Univ. Chicago's Soc. Sci. Res. , vol.36 , pp. 2003
    • Collier, N.1
  • 21
    • 85027559583 scopus 로고    scopus 로고
    • GRO Github. Accessed March 21
    • Klavins, E. GRO Github. https://github.com/klavinslab/gro, Accessed March 21, 2017.
    • (2017)
    • Klavins, E.1
  • 24
    • 85027542324 scopus 로고    scopus 로고
    • GRO simulation after five days. Accessed March 21
    • Klavins, E. GRO simulation after five days. https://www.youtube.com/watch?v=P0ykJZhcOwI, Accessed March 21, 2017.
    • (2017)
    • Klavins, E.1
  • 25
    • 85027585908 scopus 로고    scopus 로고
    • Howling Moon Software. (2011) Chipmunk. Accessed March 21
    • Lembcke, S., and Howling Moon Software. (2011) Chipmunk. Chipmunk 2D Phys. https://chipmunk-physics.net/, Accessed March 21, 2017.
    • (2017) Chipmunk 2D Phys.
    • Lembcke, S.1
  • 26
    • 3042649845 scopus 로고    scopus 로고
    • A language for modeling and programming cooperative control systems
    • Klavins, E. (2004) A language for modeling and programming cooperative control systems IEEE International Conference on Robotics and Automation 3403-3410 10.1109/ROBOT.2004.1308780
    • (2004) IEEE International Conference on Robotics and Automation , pp. 3403-3410
    • Klavins, E.1
  • 30
    • 0002439750 scopus 로고
    • An efficient program for many-body simulation
    • Appel, A. W. (1985) An efficient program for many-body simulation SIAM J. Sci. Stat. Comput. 6, 85-103 10.1137/0906008
    • (1985) SIAM J. Sci. Stat. Comput. , vol.6 , pp. 85-103
    • Appel, A.W.1
  • 31
    • 85021630072 scopus 로고    scopus 로고
    • D-VASim: An interactive virtual laboratory environment for the simulation and analysis of genetic circuits
    • Baig, H. and Madsen, J. (2017) D-VASim: an interactive virtual laboratory environment for the simulation and analysis of genetic circuits Bioinformatics 33, 297-299 10.1093/bioinformatics/btw592
    • (2017) Bioinformatics , vol.33 , pp. 297-299
    • Baig, H.1    Madsen, J.2
  • 32
    • 83655164994 scopus 로고    scopus 로고
    • Ultra-small block-codes for binary discrete memoryless channels
    • Chen, P.-N., Lin, H.-Y., and Moser, S. M. (2011) Ultra-small block-codes for binary discrete memoryless channels IEEE Information Theory Workshop 175-179 10.1109/ITW.2011.6089371
    • (2011) IEEE Information Theory Workshop , pp. 175-179
    • Chen, P.-N.1    Lin, H.-Y.2    Moser, S.M.3
  • 33
    • 27244433119 scopus 로고    scopus 로고
    • An introduction to probabilistic automata
    • Stoelinga, M. (2002) An introduction to probabilistic automata Bull. EATCS 78, 176-198
    • (2002) Bull. EATCS , vol.78 , pp. 176-198
    • Stoelinga, M.1
  • 34
    • 0037036274 scopus 로고    scopus 로고
    • Automatic verification of real-time systems with discrete probability distributions
    • Kwiatkowska, M., Norman, G., Segala, R., and Sproston, J. (2002) Automatic verification of real-time systems with discrete probability distributions Theor. Comput. Sci. 282, 101-150 10.1016/S0304-3975(01)00046-9
    • (2002) Theor. Comput. Sci. , vol.282 , pp. 101-150
    • Kwiatkowska, M.1    Norman, G.2    Segala, R.3    Sproston, J.4
  • 38
    • 0001639179 scopus 로고
    • The growth of bacterial cultures
    • Monod, J. (1949) The growth of bacterial cultures Annu. Rev. Microbiol. 3, 371-394 10.1146/annurev.mi.03.100149.002103
    • (1949) Annu. Rev. Microbiol. , vol.3 , pp. 371-394
    • Monod, J.1
  • 39
    • 0014083610 scopus 로고
    • A kinetic study of the mode of growth of surface colonies of bacteria and fungi
    • Pirt, S. (1967) A kinetic study of the mode of growth of surface colonies of bacteria and fungi J. Gen. Microbiol. 47, 181-197 10.1099/00221287-47-2-181
    • (1967) J. Gen. Microbiol. , vol.47 , pp. 181-197
    • Pirt, S.1
  • 41
    • 0019419796 scopus 로고
    • The influence of nutrition and temperature on the growth of colonies of Escherichia coli K12
    • Lewis, M. W. and Wimpenny, J. W. (1981) The influence of nutrition and temperature on the growth of colonies of Escherichia coli K12 Can. J. Microbiol. 27, 679-684 10.1139/m81-105
    • (1981) Can. J. Microbiol. , vol.27 , pp. 679-684
    • Lewis, M.W.1    Wimpenny, J.W.2
  • 42
    • 84885804295 scopus 로고    scopus 로고
    • Mechanically driven growth of quasi-two-dimensional microbial colonies
    • Farrell, F. D. C., Hallatschek, O., Marenduzzo, D., and Waclaw, B. (2013) Mechanically driven growth of quasi-two-dimensional microbial colonies Phys. Rev. Lett. 111, 168101 10.1103/PhysRevLett.111.168101
    • (2013) Phys. Rev. Lett. , vol.111 , pp. 168101
    • Farrell, F.D.C.1    Hallatschek, O.2    Marenduzzo, D.3    Waclaw, B.4
  • 44
    • 0035675837 scopus 로고    scopus 로고
    • Regulation of gene expression by cell-to-cell communication: Acyl-homoserine lactone quorum sensing
    • Fuqua, C., Parsek, M. R., and Greenberg, E. P. (2001) Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing Annu. Rev. Genet. 35, 439-468 10.1146/annurev.genet.35.102401.090913
    • (2001) Annu. Rev. Genet. , vol.35 , pp. 439-468
    • Fuqua, C.1    Parsek, M.R.2    Greenberg, E.P.3
  • 45
    • 0034770056 scopus 로고    scopus 로고
    • Quorum sensing in bacteria
    • Miller, M. B. and Bassler, B. L. (2001) Quorum sensing in bacteria Annu. Rev. Microbiol. 55, 165-199 10.1146/annurev.micro.55.1.165
    • (2001) Annu. Rev. Microbiol. , vol.55 , pp. 165-199
    • Miller, M.B.1    Bassler, B.L.2
  • 46
    • 27944442272 scopus 로고    scopus 로고
    • Quorum sensing: Cell-to-cell communication in bacteria
    • Waters, C. M. and Bassler, B. L. (2005) Quorum sensing: cell-to-cell communication in bacteria Annu. Rev. Cell Dev. Biol. 21, 319-346 10.1146/annurev.cellbio.21.012704.131001
    • (2005) Annu. Rev. Cell Dev. Biol. , vol.21 , pp. 319-346
    • Waters, C.M.1    Bassler, B.L.2
  • 48
    • 17844374314 scopus 로고    scopus 로고
    • A synthetic multicellular system for programmed pattern formation
    • Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H., and Weiss, R. (2005) A synthetic multicellular system for programmed pattern formation Nature 434, 1130-1134 10.1038/nature03461
    • (2005) Nature , vol.434 , pp. 1130-1134
    • Basu, S.1    Gerchman, Y.2    Collins, C.H.3    Arnold, F.H.4    Weiss, R.5
  • 49
    • 1942467023 scopus 로고    scopus 로고
    • Programmed population control by cell-cell communication and regulated killing
    • You, L., Cox, R. S., Weiss, R., and Arnold, F. H. (2004) Programmed population control by cell-cell communication and regulated killing Nature 428, 868-871 10.1038/nature02491
    • (2004) Nature , vol.428 , pp. 868-871
    • You, L.1    Cox, R.S.2    Weiss, R.3    Arnold, F.H.4
  • 51
    • 78651397316 scopus 로고    scopus 로고
    • Robust multicellular computing using genetically encoded NOR gates and chemical "wires
    • Tamsir, A., Tabor, J. J., and Voigt, C. A. (2011) Robust multicellular computing using genetically encoded NOR gates and chemical "wires Nature 469, 212-5 10.1038/nature09565
    • (2011) Nature , vol.469 , pp. 212-215
    • Tamsir, A.1    Tabor, J.J.2    Voigt, C.A.3
  • 52
    • 0001235787 scopus 로고
    • Numerical methods for convection-dominated diffusion problems based on combining the method of characteristics with finite element or finite difference procedures
    • Douglas, J. J. and Russell, T. F. (1982) Numerical methods for convection-dominated diffusion problems based on combining the method of characteristics with finite element or finite difference procedures SIAM J. Numer. Anal. 19, 871-885 10.1137/0719063
    • (1982) SIAM J. Numer. Anal. , vol.19 , pp. 871-885
    • Douglas, J.J.1    Russell, T.F.2
  • 53
    • 84865815764 scopus 로고    scopus 로고
    • Engineered cell-cell communication via DNA messaging
    • Ortiz, M. E. and Endy, D. (2012) Engineered cell-cell communication via DNA messaging J. Biol. Eng. 6, 16 10.1186/1754-1611-6-16
    • (2012) J. Biol. Eng. , vol.6 , pp. 16
    • Ortiz, M.E.1    Endy, D.2
  • 55
    • 44649093274 scopus 로고    scopus 로고
    • Why is entry exclusion an essential feature of conjugative plasmids?
    • Garcillán-Barcia, M. P. and de la Cruz, F. (2008) Why is entry exclusion an essential feature of conjugative plasmids? Plasmid 60, 1-18 10.1016/j.plasmid.2008.03.002
    • (2008) Plasmid , vol.60 , pp. 1-18
    • Garcillán-Barcia, M.P.1    De La Cruz, F.2
  • 56
    • 0942301205 scopus 로고    scopus 로고
    • Kinetics of plasmid segregation in Escherichia coli
    • Gordon, S., Rech, J., Lane, D., and Wright, A. (2004) Kinetics of plasmid segregation in Escherichia coli Mol. Microbiol. 51, 461-469 10.1046/j.1365-2958.2003.03837.x
    • (2004) Mol. Microbiol. , vol.51 , pp. 461-469
    • Gordon, S.1    Rech, J.2    Lane, D.3    Wright, A.4
  • 57
    • 82055165427 scopus 로고    scopus 로고
    • On the meaning and estimation of plasmid transfer rates for surface-associated and well-mixed bacterial populations
    • Zhong, X., Droesch, J., Fox, R., Top, E. M., and Krone, S. M. (2012) On the meaning and estimation of plasmid transfer rates for surface-associated and well-mixed bacterial populations J. Theor. Biol. 294, 144-152 10.1016/j.jtbi.2011.10.034
    • (2012) J. Theor. Biol. , vol.294 , pp. 144-152
    • Zhong, X.1    Droesch, J.2    Fox, R.3    Top, E.M.4    Krone, S.M.5
  • 58
    • 84896115316 scopus 로고    scopus 로고
    • Susceptible-infectious-recovered models revisited: From the individual level to the population level
    • Magal, P. and Ruan, S. (2014) Susceptible-infectious-recovered models revisited: From the individual level to the population level Math. Biosci. 250, 26-40 10.1016/j.mbs.2014.02.001
    • (2014) Math. Biosci. , vol.250 , pp. 26-40
    • Magal, P.1    Ruan, S.2
  • 59
    • 84879045964 scopus 로고    scopus 로고
    • Strong inter-population cooperation leads to partner intermixing in microbial communities
    • Momeni, B., Brileya, K. A., Fields, M. W., and Shou, W. (2013) Strong inter-population cooperation leads to partner intermixing in microbial communities eLife 2, e00230 10.7554/eLife.00230
    • (2013) ELife , vol.2 , pp. e00230
    • Momeni, B.1    Brileya, K.A.2    Fields, M.W.3    Shou, W.4
  • 60
    • 84941626864 scopus 로고    scopus 로고
    • Bacterial social interactions drive the emergence of differential spatial colony structures
    • Blanchard, A. E. and Lu, T. (2015) Bacterial social interactions drive the emergence of differential spatial colony structures BMC Syst. Biol. 9, 59 10.1186/s12918-015-0188-5
    • (2015) BMC Syst. Biol. , vol.9 , pp. 59
    • Blanchard, A.E.1    Lu, T.2
  • 61
    • 34548305141 scopus 로고    scopus 로고
    • Mobility promotes and jeopardizes biodiversity in rock-paper-scissors games
    • Reichenbach, T., Mobilia, M., and Frey, E. (2007) Mobility promotes and jeopardizes biodiversity in rock-paper-scissors games Nature 448, 1046-1049 10.1038/nature06095
    • (2007) Nature , vol.448 , pp. 1046-1049
    • Reichenbach, T.1    Mobilia, M.2    Frey, E.3
  • 62
    • 84961904331 scopus 로고    scopus 로고
    • Challenges in microbial ecology: Building predictive understand- ing of community function and dynamics
    • Widder, S., Allen, R. J., Pfeiffer, T., Curtis, T. P., Wiuf, C., Sloan, W. T., Cordero, O. X., Brown, S. P., Momeni, B., and Shou, W. et al. 2016, Challenges in microbial ecology: building predictive understand- ing of community function and dynamics ISME J. 10, 2557-2568 10.1038/ismej.2016.45
    • (2016) ISME J. , vol.10 , pp. 2557-2568
    • Widder, S.1    Allen, R.J.2    Pfeiffer, T.3    Curtis, T.P.4    Wiuf, C.5    Sloan, W.T.6    Cordero, O.X.7    Brown, S.P.8    Momeni, B.9    Shou, W.10
  • 64
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Elowitz, M. B. and Leibler, S. (2000) A synthetic oscillatory network of transcriptional regulators Nature 403, 335-338 10.1038/35002125
    • (2000) Nature , vol.403 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 65
    • 23444461901 scopus 로고    scopus 로고
    • Advances in synthetic biology: On the path from prototypes to applications
    • McDaniel, R. and Weiss, R. (2005) Advances in synthetic biology: on the path from prototypes to applications Curr. Opin. Biotechnol. 16, 476-483 10.1016/j.copbio.2005.07.002
    • (2005) Curr. Opin. Biotechnol. , vol.16 , pp. 476-483
    • McDaniel, R.1    Weiss, R.2
  • 66
    • 84956857435 scopus 로고    scopus 로고
    • Engineering Synthetic Gene Circuits in Living Cells with CRISPR Technology
    • Jusiak, B., Cleto, S., Perez-Pinera, P., and Lu, T. K. (2016) Engineering Synthetic Gene Circuits in Living Cells with CRISPR Technology Trends Biotechnol. 34, 535-547 10.1016/j.tibtech.2015.12.014
    • (2016) Trends Biotechnol. , vol.34 , pp. 535-547
    • Jusiak, B.1    Cleto, S.2    Perez-Pinera, P.3    Lu, T.K.4
  • 67
    • 84909963314 scopus 로고    scopus 로고
    • Resource Toehold Switches: De-Novo-Designed Regulators of Gene Expression
    • Green, A. a, Silver, P. a, Collins, J. J., and Yin, P. (2014) Resource Toehold Switches: De-Novo-Designed Regulators of Gene Expression Cell 159, 925-939 10.1016/j.cell.2014.10.002
    • (2014) Cell , vol.159 , pp. 925-939
    • Green, A.A.1    Silver, P.A.2    Collins, J.J.3    Yin, P.4
  • 68
    • 0032644351 scopus 로고    scopus 로고
    • Fully implicit finite differences methods for two-dimensional diffusion with a non-local boundary condition
    • Dehghan, M. (1999) Fully implicit finite differences methods for two-dimensional diffusion with a non-local boundary condition J. Compuational Appl. Math. 106, 255-269 10.1016/S0377-0427(99)00065-5
    • (1999) J. Compuational Appl. Math. , vol.106 , pp. 255-269
    • Dehghan, M.1
  • 70
    • 84949293235 scopus 로고    scopus 로고
    • At-risk" places: Inequities in the distribution of environmental stressors and prescription rates of mental health medications in Glasgow, Scotland
    • Maantay, J. and Maroko, A. (2015) At-risk" places: inequities in the distribution of environmental stressors and prescription rates of mental health medications in Glasgow, Scotland Environ. Res. Lett. 10, 115003 10.1088/1748-9326/10/11/115003
    • (2015) Environ. Res. Lett. , vol.10 , pp. 115003
    • Maantay, J.1    Maroko, A.2
  • 72
    • 33645055465 scopus 로고    scopus 로고
    • Spatial statistics for urban analysis: A review of techniques with examples
    • Páez, A. and Scott, D. M. (2005) Spatial statistics for urban analysis: a review of techniques with examples GeoJournal 61, 53-67 10.1007/s10708-005-0877-5
    • (2005) GeoJournal , vol.61 , pp. 53-67
    • Páez, A.1    Scott, D.M.2
  • 73
    • 0001182393 scopus 로고    scopus 로고
    • Islands of decay in seas of renewal: Housing policy and the resurgence of gentrification
    • Wyly, E. K. and Hammel, D. J. (1999) Islands of decay in seas of renewal: Housing policy and the resurgence of gentrification Hous. Policy Debate 10, 711-771
    • (1999) Hous. Policy Debate , vol.10 , pp. 711-771
    • Wyly, E.K.1    Hammel, D.J.2


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