DOTcvpSB: a Matlab Toolbox for Dynamic Optimization in Systems ...

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CHAPTER 6Importing SBML modelsThe DOTcvpSB toolbox provides the function for the transformation of SBML [18; 20] models (Systems BiologyMarkup Language) into the toolbox. The transformation process is based on several key questions by followingwhich the toolbox m-file is generated. At the end of this transformation it is necessary to check if all parameterswere transformed correctly. This transformation can be checked by the simulation module, as it is shown later. Ifthe simulation passes without any problem, then it is possible to choose some decision variables and accede to theoptimization.6.1 ILLUSTRATIVE SYSTEM BIOLOGY EXAMPLEDOTcvpSB: dotcvp_sbml2dotcvpsb.mFor the testing purposes, the problem from [33] was chosen and transformed to the DOTcvpSB toolbox.The problem marked as BIOMD0000000005, Tyson1991_CellCycle_6var, 1831270 can be downloaded as f.e.’.xml’ file suitable for the function from the following web page: http://www.ebi.ac.uk/biomodels/. Thebox below shows the transformation process from SBML to DOTcvpSB toolbox.1 ______________________________________________________________23 DOTcvpSB: Dynamic Optimization Toolbox with CVP approach for4 handling continuous and MIDO problems in Systems Biology56 Main author: Tomas Hirmajer, thirmajer@gmail.com7 Coauthors: Eva Balsa-Canto and Julio R. Banga8 Web page: http://www.iim.csic.es/~dotcvpsb/9 Core version: DOTcvp_R2010_E310 _______________________________________________________________1112 _______________________________________________________________1314 DOTcvpSB - a Module for Import of SBML Models to DOTcvpSB (.xml)15 Note: this module requires the installation of SBML and libSBML.16 _______________________________________________________________1718 Do you want to print all the import information on the screen? [y|n]: y1920 Name: Tyson1991_CellCycle_6var21 ID: Tyson1991CellModel_622 SBML_level: 223 SBML_version: 124 Time_symbol:2526 --- Getting information from model functions ------------------27 1. parameter from the model : k6 (k6_Reaction1) = 1.000000 (1.000000)28 2. parameter from the model : k8notP (k8notP_Reaction2) = 1000000.000000 (1000000.000000)29 3. parameter from the model : k9 (k9_Reaction3) = 1000.000000 (1000.000000)30 4. parameter from the model : k3 (k3_Reaction4) = 200.000000 (200.000000)31 5. parameter from the model : k5notP (k5notP_Reaction5) = 0.000000 (0.000000)32 6. parameter from the model : k1aa (k1aa_Reaction6) = 0.015000 (0.015000)33 7. parameter from the model : k2 (k2_Reaction7) = 0.000000 (0.000000)34 8. parameter from the model : k7 (k7_Reaction8) = 0.600000 (0.600000)35 9. parameter from the model : k4 (k4_Reaction9) = 180.000000 (180.000000)36 10. parameter from the model : k4prime (k4prime_Reaction9) = 0.018000 (0.018000)3738 --- Getting information from reaction functions ---------------39 1. parameter for reaction( 1) : k6 (k6_Reaction1) = 1.000000 (1.000000)
DOTcvpSB: a Matlab Toolbox for Dynamic Optimization in Systems Biology40 2. parameter for reaction( 2) : k8notP (k8notP_Reaction2) = 1000000.000000 (1000000.000000)41 3. parameter for reaction( 3) : k9 (k9_Reaction3) = 1000.000000 (1000.000000)42 4. parameter for reaction( 4) : k3 (k3_Reaction4) = 200.000000 (200.000000)43 5. parameter for reaction( 5) : k5notP (k5notP_Reaction5) = 0.000000 (0.000000)44 6. parameter for reaction( 6) : k1aa (k1aa_Reaction6) = 0.015000 (0.015000)45 7. parameter for reaction( 7) : k2 (k2_Reaction7) = 0.000000 (0.000000)46 8. parameter for reaction( 8) : k7 (k7_Reaction8) = 0.600000 (0.600000)47 9. parameter for reaction( 9) : k4 (k4_Reaction9) = 180.000000 (180.000000)48 10. parameter for reaction( 9) : k4prime (k4prime_Reaction9) = 0.018000 (0.018000)4950 --- Determine species role in reaction ------------------------51 1. species( 1) reaction( 1) : [0]52 2. species( 1) reaction( 2) : [0]53 3. species( 1) reaction( 3) : [0]54 4. species( 1) reaction( 4) : [0]55 5. species( 1) reaction( 5) : [0]56 6. species( 1) reaction( 6) : [0 1 0 0 1]57 7. species( 1) reaction( 7) : [1 0 0 1 0]58 8. species( 1) reaction( 8) : [1 0 0 1 0]59 9. species( 1) reaction( 9) : [0]60 10. species( 2) reaction( 1) : [1 0 0 1 0]61 11. species( 2) reaction( 2) : [0 1 0 0 1]62 12. species( 2) reaction( 3) : [1 0 0 1 0]63 13. species( 2) reaction( 4) : [0]64 14. species( 2) reaction( 5) : [0]65 15. species( 2) reaction( 6) : [0]66 16. species( 2) reaction( 7) : [0]67 17. species( 2) reaction( 8) : [0]68 18. species( 2) reaction( 9) : [0]69 19. species( 3) reaction( 1) : [0]70 20. species( 3) reaction( 2) : [1 0 0 1 0]71 21. species( 3) reaction( 3) : [0 1 0 0 1]72 22. species( 3) reaction( 4) : [0 1 0 0 1]73 23. species( 3) reaction( 5) : [0]74 24. species( 3) reaction( 6) : [0]75 25. species( 3) reaction( 7) : [0]76 26. species( 3) reaction( 8) : [0]77 27. species( 3) reaction( 9) : [0]78 28. species( 4) reaction( 1) : [0 1 0 0 1]79 29. species( 4) reaction( 2) : [0]80 30. species( 4) reaction( 3) : [0]81 31. species( 4) reaction( 4) : [0]82 32. species( 4) reaction( 5) : [0 1 0 0 1]83 33. species( 4) reaction( 6) : [0]84 34. species( 4) reaction( 7) : [0]85 35. species( 4) reaction( 8) : [0]86 36. species( 4) reaction( 9) : [1 0 0 1 0]87 37. species( 5) reaction( 1) : [0]88 38. species( 5) reaction( 2) : [0]89 39. species( 5) reaction( 3) : [0]90 40. species( 5) reaction( 4) : [1 0 0 1 0]91 41. species( 5) reaction( 5) : [1 0 0 1 0]92 42. species( 5) reaction( 6) : [0]93 43. species( 5) reaction( 7) : [0]94 44. species( 5) reaction( 8) : [0]95 45. species( 5) reaction( 9) : [0 1 0 0 1]96 46. species( 6) reaction( 1) : [0]97 47. species( 6) reaction( 2) : [0]98 48. species( 6) reaction( 3) : [0]99 49. species( 6) reaction( 4) : [0 1 0 0 2]100 50. species( 6) reaction( 5) : [0]101 51. species( 6) reaction( 6) : [1 0 0 1 0]102 52. species( 6) reaction( 7) : [0 1 0 0 1]103 53. species( 6) reaction( 8) : [0]104 54. species( 6) reaction( 9) : [0]105 55. species( 7) reaction( 1) : [1 0 0 2 0]106 56. species( 7) reaction( 2) : [0]107 57. species( 7) reaction( 3) : [0]108 58. species( 7) reaction( 4) : [0]109 59. species( 7) reaction( 5) : [0]110 60. species( 7) reaction( 6) : [0]111 61. species( 7) reaction( 7) : [0]112 62. species( 7) reaction( 8) : [0 1 0 0 1]113 63. species( 7) reaction( 9) : [0]114115 --- Determine stoichiometry matrix ----------------------------116 1. species( EmptySet) : 0 0 0 0 0 -1 1 1 0117 2. species( C2) : 1 -1 1 0 0 0 0 0 0118 3. species( CP) : 0 1 -1 -1 0 0 0 0 0119 4. species( M) : -1 0 0 0 -1 0 0 0 1120 5. species( pM) : 0 0 0 1 1 0 0 0 -1121 6. species( Y) : 0 0 0 -1 0 1 -1 0 0122 7. species( YP) : 1 0 0 0 0 0 0 -1 0123124 --- Determine initial concentration ---------------------------125 1. species( EmptySet) : 0.000000126 2. species( C2) : 0.000000127 3. species( CP) : 1.000000128 4. species( M) : 0.000000129 5. species( pM) : 0.300000130 6. species( Y) : 0.000000131 7. species( YP) : 0.000000132133 --- Get rate laws from reactions ------------------------------134 1. species( EmptySet) : 0135 2. species( C2) : + (k6_Reaction1*M) - (C2*k8notP_Reaction2) + (CP*k9_Reaction3)Page – 26
Page 1 and 2: TECHNICAL REPORTDOTcvpSB: a Matlab
Page 3 and 4: Main Web PageIt is possible to get
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