Skip to main content

Computational Modeling in Systems Biology

  • Protocol
  • First Online:
Systems Biology in Drug Discovery and Development

Part of the book series: Methods in Molecular Biology ((MIMB,volume 662))

Abstract

Interactions among cellular constituents play a crucial role in overall cellular function and organization. These interactions can be viewed as being complementary to the usual “parts list” of genes and proteins and, in conjunction with the expression states of these parts, are key to a systems level understanding of the cell. Here, we review computational approaches to the understanding of the functional roles of cellular networks, ranging from “static” models of network topology to dynamical and stochastic simulations.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Kitano H (2002) Systems biology: a brief overview. Science 295:1662–1664

    Article  CAS  PubMed  Google Scholar 

  2. Ekins R, Chu FW (1999) Microarrays: their origins and applications. Trends Biotechnol 17(6):217–218

    Article  CAS  PubMed  Google Scholar 

  3. Brown PO, Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet 21:33–37

    Article  CAS  PubMed  Google Scholar 

  4. DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680–686

    Article  CAS  PubMed  Google Scholar 

  5. Nadon R, Shoemaker J (2003) Statistical issues with microarrays: processing and delays. Trends Genet 18:265–271

    Article  Google Scholar 

  6. Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet 32:496–501

    Article  CAS  PubMed  Google Scholar 

  7. Leung YF, Cavalieri D (2003) Fundamentals of cDNA microarray data analysis. Trends Genet 19:649–659

    Article  CAS  PubMed  Google Scholar 

  8. Allison DB, Cui X, Page GP, Sabripour M (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7:55–65

    Article  CAS  PubMed  Google Scholar 

  9. Marshall E (2004) Getting the noise out of gene arrays. Science 306:630–631

    Article  CAS  PubMed  Google Scholar 

  10. Troyanskaya O, Cantor M, Sherlock G, Brown PO, Hastie T et al (2001) Missing value estimation methods of DNA microarrays. Bioinformatics 17:520–525

    Article  CAS  PubMed  Google Scholar 

  11. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95(25):14863–14868

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Quackenbush J (2001) Computational analysis of microarray data. Nat Rev Genet 2:418–427

    Article  CAS  PubMed  Google Scholar 

  13. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complimentary DNA microarray. Science 270(5235):467–470

    Article  CAS  PubMed  Google Scholar 

  14. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM (1999) Expression profiling using cDNA microarrays. Nat Genet 21:10–14

    Article  CAS  PubMed  Google Scholar 

  15. Hacia JG (1999) Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet 21:42–47

    Article  CAS  PubMed  Google Scholar 

  16. Haab BB, Dunham MJ, Brown PO (2001) Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol 2:1–13

    Article  Google Scholar 

  17. Debouck C, Goodfellow PN (1999) DNA microarrays in drug discovery and development. Nat Genet 21:48–50

    Article  CAS  PubMed  Google Scholar 

  18. DeRisi JL, Penland L, Brown PO, Bittner ML, Meltzer PS et al (1996) Use of a cDNA microarray to analyze gene expression patterns in human cancer. Nat Genet 14:457–460

    Article  CAS  PubMed  Google Scholar 

  19. Michiels S, Koscielny S, Hill C (2005) Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 365:488–492

    Article  CAS  PubMed  Google Scholar 

  20. Ma J, Ptashne M (1988) Converting a eukaryotic transcriptional inhibitor into an activator. Cell 55:443–446

    Article  CAS  PubMed  Google Scholar 

  21. Fields S, Song OK (1989) A novel genetic system to detect protein–protein interactions. Nature 40:245–246

    Article  Google Scholar 

  22. Phizicky EM, Fields S (1995) Protein–protein interactions: methods for detection and analysis. Microbiol Rev 59:94–123

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Puig O et al (2001) The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24:218–229

    Article  CAS  PubMed  Google Scholar 

  24. Solomon MJ, Varshavsky A (1985) Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. Proc Natl Acad Sci USA 82:6470–74

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Tong AH et al (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294:2364–2368

    Article  CAS  PubMed  Google Scholar 

  26. Tong AH et al (2004) Global mapping of the yeast genetic interaction network. Science 303:808

    Article  CAS  PubMed  Google Scholar 

  27. Schuldiner M, Collins SR, Weissman JS, Krogan NJ (2006) Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions. Methods 40:344–352

    Article  CAS  PubMed  Google Scholar 

  28. Huang H, Jedynak BM, Bader JS (2007) Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Comput Biol 3:e214

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Deeds EJ, Ashenberg O, Shakhnovich EI (2006) A simple physical model for scaling in protein–protein interaction networks. Proc Natl Acad Sci USA 103:311–316

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Przulj N, Higham DJ (2006) Modeling protein–protein interaction networks via a stickiness index. J R Soc Interface 3:711–716

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. D’haeseleer P, Church GM (2004) Estimating and improving protein interaction error rates. Proc IEEE Comput Syst Bioinform Conf, 216–223

    Google Scholar 

  32. Hart GT, Ramani AK, Marcotte EM (2006) How complete are current yeast and human protein-interaction networks? Genome Biol 7:120

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Huang H, Bader JS (2009) Precision and recall estimates for two-hybrid screens. Bioinformatics 25:372–378

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. van Someren EP, Wessels LF, Backer E, Reinders MJ (2002) Genetic network modeling. Pharmacogenomics 3:507–525

    Article  PubMed  Google Scholar 

  35. Margolin AA, Califano A (2007) Theory and limitations of genetic network inference from microarray data. Ann N Y Acad Sci 1115:51–72

    Article  CAS  PubMed  Google Scholar 

  36. Liang S, Fuhrman S, Somogyi R (1998) Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac Symp Biocomput 1998:18–29

    Google Scholar 

  37. Murphy K, Mian S (1999) Modeling gene expression data using dynamic Bayesian networks. Technical report. University of California, Berkeley

    Google Scholar 

  38. Perrin B-E, Ralaivola L, Mazurie A, Bottani S, Mallet J, d’Alche Buc F (2003) Gene networks inference using dynamic Bayesian networks. Bioinformatics 19:S138–S148

    Article  Google Scholar 

  39. Rangel C, Angus J, Ghahramani Z, Lioumi M, Sotheran E, Gaiba A, Wild DL, Falciani F (2004) Modelling T-cell activation using gene expression profiling and state space models. Bioinformatics 20:1361–1372

    Article  CAS  PubMed  Google Scholar 

  40. Beal MJ, Falciani F, Ghahramani Z, Rangel C, Wild DL (2005) A Bayesian approach to reconstructing genetic regulatory networks with hidden factors. Bioinformatics 21:349–356

    Article  CAS  PubMed  Google Scholar 

  41. Zou M, Conzen SD (2005) A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data. Bioinformatics 21:71–79

    Article  CAS  PubMed  Google Scholar 

  42. Skrabanek L, Saini HK, Bader GD, Enright EJ (2008) Computational prediction of protein–protein interactions. Mol Biotechnol 38:1–17

    Article  CAS  PubMed  Google Scholar 

  43. Liu Y, Kim I, Zhao H (2008) Protein interaction predictions from diverse sources. Drug Discov Today 13:409–416

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ et al (2003) A Bayesian networks approach for predicting protein–protein interactions from genomic data. Science 302:449–453

    Article  CAS  PubMed  Google Scholar 

  45. Lin N, Wu B, Jansen R, Gerstein M, Zhao H (2004) Information assessment on predicting protein–protein interactions. BMC Bioinform 5:154

    Article  CAS  Google Scholar 

  46. Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S et al (2005) Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci USA 102:1974–1979

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Qi Y, Bar-Joseph Z, Klein-Seetharaman J (2006) Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins 63:490–500

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Deng M, Mehta S, Sun F, Chen T (2002) Inferring domain-domain interactions from protein–protein interactions. Genome Res 12:1504–1508

    Article  CAS  Google Scholar 

  49. Kim I, Liu Y, Zhao H (2007) Bayesian methods for predicting interacting protein pairs using domain information. Biometrics 63:824–833

    Article  CAS  PubMed  Google Scholar 

  50. Segrè D, DeLuna A, Church GM, Kishony R (2004) Modular epistasis in yeast metabolism. Nat Genet 37:77–83

    PubMed  Google Scholar 

  51. Kelley R, Ideker T (2005) Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 23:561–566

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Wong SL, Zhang LV, Tong AHY, Li Z, Goldberg D et al (2004) Combining biological networks to predict genetic interactions. Proc Natl Acad Sci USA 101:15682–15687

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Paladugu SR, Zhao S, Ray A, Raval A (2008) Mining protein networks for synthetic genetic interactions. BMC Bioinform 9:426

    Article  CAS  Google Scholar 

  54. Albert R, Jeong H, Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406:378–382

    Article  CAS  PubMed  Google Scholar 

  55. Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF et al (2004) Evidence for dynamically organized modularity in the yeast protein–protein interaction network. Nature 430:88–93

    Article  CAS  PubMed  Google Scholar 

  56. Jin G, Zhang S, Zhang XS, Chen L (2007) Hubs with network motifs organize modularity dynamically in the protein–protein interaction network of yeast. PLoS One 2:e1207

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  57. Batada NN, Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ et al (2006) Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol 4:1720–1731

    Article  CAS  Google Scholar 

  58. Batada NN, Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ et al (2007) Still stratus not altocumulus: further evidence against the date/party hub distinction. PLoS Biol 5:e154

    Article  PubMed  PubMed Central  Google Scholar 

  59. Bertin N, Simonis N, Dupuy D, Cusick ME, Han JDJ et al (2007) Confirmation of organized modularity in the yeast interactome. PLoS Biol 5:e153

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  60. Vallabhajosyula RR, Chakravarti D, Lutfeali S, Ray A, Raval A (2009) Identifying hubs in protein interaction networks. PLoS One 4:e5344

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  61. Hartwell LH, Hopfield JJ, Liebler S, Murray AW (1999) From molecular to modular cell biology. Nature 402:C47–C52

    Article  CAS  PubMed  Google Scholar 

  62. Lauffenberger DA (2000) Cell signaling pathways as control modules: complexity for simplicity? Proc Natl Acad Sci USA 97:5031–5033

    Article  Google Scholar 

  63. Rao CV, Arkin AP (2001) Control motifs for intracellular regulatory networks. Annu Rev Biomed Eng 3:391–419

    Article  CAS  PubMed  Google Scholar 

  64. Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N (2002) Revealing modular organization in the yeast transcriptional network. Nat Genet 31:370–377

    CAS  PubMed  Google Scholar 

  65. Segal E, Shapira M, Regev A, Pe’er D, Botstein D et al (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34:166–176

    Article  CAS  PubMed  Google Scholar 

  66. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM (1999) Systematic determination of genetic network architecture. Nat Genet 22:281–285

    Article  CAS  PubMed  Google Scholar 

  67. Rives AW, Galitski T (2003) Modular organization of cellular networks. Proc Natl Acad Sci USA 100:1128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL (2002) Hierarchical organization of modularity in metabolic networks. Science 297:1551–1555

    Article  CAS  PubMed  Google Scholar 

  69. Newman MEJ, Girvan M (2004) Finding and evaluating community structure in networks. Phys Rev E Stat Nonlin Soft Matter Phys 69:026113

    Article  CAS  PubMed  Google Scholar 

  70. Guimera R, Amaral LAN (2005) Functional cartography of complex metabolic networks. Nature 433:895–900

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Guimera R, Sales-Pardo M, Amaral LAN (2007) A network-based method for target selection in metabolic networks. Bioinformatics 23:1616–1622

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Fernandez A (2007) Molecular basis for evolving modularity in the yeast protein in the yeast protein interaction network. PLoS Comput Biol 3:e226

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  73. Qin H, Lu HHS, Wu WB, Li W-H (2003) Evolution of the yeast protein interaction network. Proc Natl Acad Sci USA 100:12820

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Kashtan N, Alon U (2005) Spontaneous evolution of modularity and network motifs. Proc Natl Acad Sci USA 102:13773–13778

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Snel B, Huynen MA (2004) Quantifying modularity in the evolution of biomolecular systems. Genome Res 14:391–397

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB et al (2003) Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci USA 100:15428–15433

    Article  CAS  Google Scholar 

  77. von Campillos M, Mering C, Jensen LJ, Bork P (2006) Identification and analysis of evolutionary cohesive functional modules in protein networks. Genome Res 16:374–382

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Petti AA, Church GM (2005) A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae. Genome Res 15:1298–1306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Lu H, Shi B, Wu G, Zhang Y, Zhu X et al (2006) Integrated analysis of multiple data sources reveals modular structure of biological networks. Biochem Biophys Res Commun 345:302–309

    Article  CAS  PubMed  Google Scholar 

  80. Tanay A, Sharan R, Kupiec M, Shamir R (2004) Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogenous genomewide data. Proc Natl Acad Sci USA 101:2981–2986

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Barabasi AL (2004) Network biology: understanding the cell’s functional organization. Nat Rev Genet 5:101–113

    Article  CAS  PubMed  Google Scholar 

  82. Kholodenko BN (2006) Cell-signalling dynamics in time and space. Nat Rev Mol Cell Biol 7:165–176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Schoeberl B, Eichler-Jonsson C, Gilles ED, Muller G (2002) Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol 20:370–375

    Article  PubMed  Google Scholar 

  84. Wiley SH, Shvartsman Y, Lauffenburger DA (2003) Computational modeling of the EGF-receptor system: a paradigm for systems biology. Trends Cell Biol 13:43–50

    Article  CAS  PubMed  Google Scholar 

  85. Chickarmane V, Troein C, Nuber UA, Sauro HM, Peterson C (2006) Transcriptional dynamics of the embryonic stem cell switch. PLoS Comput Biol 2(9):1080–1092

    Article  CAS  Google Scholar 

  86. Le Nov`ere N, Bornstein B, Broicher A, Courtot M, Donizelli M (2006) BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 34:689–691

    Article  CAS  Google Scholar 

  87. Segel IH (1975) Enzyme kinetics. Wiley, New York

    Google Scholar 

  88. Cornish-Bowden A (1979) Fundamentals of enzyme kinetics. Butterworths, London and Boston

    Google Scholar 

  89. Mendes P, Kell D (1998) Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14:869–883

    Article  CAS  PubMed  Google Scholar 

  90. Ko CL, Voit EO, Wang FS (2009) Estimating parameters for generalized mass action models with connectivity information. BMC Bioinform 10:140

    Article  Google Scholar 

  91. Moles CG, Mendes P, Banga JR (2003) Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res 13:2467–2474

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Fell DA (1992) Metabolic control analysis: a survey of its theoretical and experimental development. Biochem J 286(2):313–330

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Cascante M, Boros LG, Comin-Anduix B, Atauri P, Centelles JJ, Lee PWN (2002) Metabolic control analysis in drug discovery and disease. Nat Biotechnol 20:243–249

    Article  CAS  PubMed  Google Scholar 

  94. Wu L, Wang W, van Winden WA, van Gulik WM, Heinjen JJ (2004) A new framework for the estimation of control parameters in metabolic pathways using lin-log kinetics. FEBS J 271:3348–3359

    Article  CAS  Google Scholar 

  95. Bergmann F, Sauro HM (2006) SBW – a modular framework for systems biology. In: Proceedings of the 38th conference on Winter simulation, Monterey, CA, USA, 1637–1645

    Google Scholar 

  96. Olivier BG, Rohwer JM, Hofmeyr HS (2005) Modeling cellular systems with PySCeS. Bioinformatics 21:560–561

    Article  CAS  PubMed  Google Scholar 

  97. Hoops S, Sahle S, Gauges R, Lee C, Pahle J et al (2006) COPASI – a COmplex PAthway SImulator. Bioinformatics 22:3067–3074

    Article  CAS  PubMed  Google Scholar 

  98. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC et al (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4):524–531

    Article  CAS  PubMed  Google Scholar 

  99. Bergmann F, Sauro HM (2008) Comparing simulation results of SBML capable simulators. Bioinformatics 24:1963–1965

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Vallabhajosyula RR, Sauro HM (2006) Complexity reduction in biochemical networks. In: Proceedings of the 38th conference on Winter simulation, Monterey, CA, USA, 1690–1697

    Google Scholar 

  101. Surovtsova I, Sable S, Pahle J, Kummer U (2006) Approaches to complexity reduction in a Systems Biology Research Environment. In: Proceedings of the 38th conference on Winter simulation, Monterey, CA, USA, 1683–1689

    Google Scholar 

  102. Sauro HM, Ingalls B (2004) Conservation analysis in biochemical networks: computational issues for software writers. Biophys Chem 109(1):1–15

    Article  CAS  PubMed  Google Scholar 

  103. Vallabhajosyula RR, Chickarmane V, Sauro HM (2006) Conservation analysis of large biochemical networks. Bioinformatics 22:346–353

    Article  CAS  PubMed  Google Scholar 

  104. Chickarmane V, Paladugu SR, Bergmann F, Sauro HM (2005) Bifurcation discovery tool. Bioinformatics 21(18):3688–3690

    Article  CAS  PubMed  Google Scholar 

  105. Bergmann F, Vallabhajosyula RR, Sauro HM (2006) Computational tools for modeling protein networks. Curr Proteomics 3(3):181–197

    Article  CAS  Google Scholar 

  106. Varma A, Palsson BO (1994) Metabolic flux balancing: basic concepts, scientific and practical use. Nat Biotechnol 12:994–998

    Article  CAS  Google Scholar 

  107. Raman K, Chandra N (2009) Flux balance analysis of biological systems: applications and challenges. Brief Bioinform 10:435–449

    Article  CAS  PubMed  Google Scholar 

  108. Segrè D, Vitkup D, Church GM (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 99:15112–15117

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  109. Shlomi T, Berkman O, Ruppin E (2005) Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci USA 102:7695–7700

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Kell D (2006) Systems biology, metabolic modeling and metabolomics in drug discovery and development. Drug Discov Today 11:1085–1092

    Article  CAS  PubMed  Google Scholar 

  111. Sweetlove LJ, Last RL, Fernie AR (2003) Predictive metabolic engineering: a goal for systems biology. Plant Physiol 132:420–425

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Ballarini P, Guido R, Mazza T, Prandi D (2009) Taming the complexity of biological pathways through parallel computing. Brief Bioinform 10(3):278–288

    Article  CAS  PubMed  Google Scholar 

  113. Arkin AP, Ross J, McAdams HH (1998) Stochastic kinetic analysis of developmental pathway bifurcation in Phage λ-infected Escherichia coli cells. Genetics 149:1633–1648

    CAS  PubMed  PubMed Central  Google Scholar 

  114. Gillespie DT (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical species. J Comput Phys 22:403–434

    Article  CAS  Google Scholar 

  115. Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340–2361

    Article  CAS  Google Scholar 

  116. van Kampen NG (1992) Stochastic processes in physics and chemistry. NHPL, Elsevier Science

    Google Scholar 

  117. Wilkinson DJ (2006) Stochastic modelling for systems biology. Chapman and Hall, CRC Press, Boca Raton, Florida, USA

    Google Scholar 

  118. Meng TC, Somani S, Dhar P (2004) Modeling and simulation of biological systems with stochasticity. In Silico Biol 4:293–309

    CAS  PubMed  Google Scholar 

  119. Adalsteinsson D, McMillen D, Elston TC (2004) Biochemical network stochastic simulator (BioNetS): software for stochastic modeling of biochemical networks. BMC Bioinform 5:24

    Article  Google Scholar 

  120. Li H, Cao Y, Petzold LR, Gillespie DT (2008) Algorithms and software for stochastic simulation of biochemical reacting systems. Biotechnol Prog 24(1):56–61

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  121. Ramsey S, Orrell D, Bolouri H (2005) Dizzy: stochastic simulation of large-scale genetic regulatory networks. J Bioinform Comput Biol 13:49

    Google Scholar 

  122. Ullah M, Schmidt H, Cho K-H, Wolkenhauer O (2006) Deterministic modeling and stochastic simulation of biochemical pathways using MATLAB. Syst Biol 153:53–60

    Article  CAS  Google Scholar 

  123. Vallabhajosyula RR, Sauro HM (2007) A stochastic simulation GUI for biochemical networks. Bioinformatics 23:1859–1861

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors would like to acknowledge support provided by the US National Science Foundation grant FIBR 0527023.

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Vallabhajosyula, R.R., Raval, A. (2010). Computational Modeling in Systems Biology. In: Yan, Q. (eds) Systems Biology in Drug Discovery and Development. Methods in Molecular Biology, vol 662. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-800-3_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-60761-800-3_5

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-799-0

  • Online ISBN: 978-1-60761-800-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics