Software tools that facilitate kinetic modelling with large data sets: an example using growth modelling in sugarcane.
A solution to manage cumbersome data sets associated with large modelling projects is described. A kinetic model of sucrose accumulation in sugarcane is used to predict changes in sucrose metabolism with sugarcane internode maturity. This results in large amounts of output data to be analysed. Growth is simulated by reassigning maximal activity values, specific to each internode of the sugarcane plant, to parameter attributes of a model object. From a programming perspective, only one model definition file is required for the simulation software used; however, the amount of input data increases with each extra interrnode that is modelled, and likewise the amount of output data that is generated also increases. To store, manipulate and analyse these data, the modelling was performed from within a spreadsheet. This was made possible by the scripting language Python and the modelling software PySCeS through an embedded Python interpreter available in the Gnumeric spreadsheet program.
Uys
L
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Triple-J Group for Molecular Cell Physiology, Department of Biochemistry, Stellenbosch University, Private Bag X1, ZA-7602 Matieland, South Africa.
Hofmeyr
J H S
JH
Snoep
J L
JL
Rohwer
J M
JM
D000465:Algorithms; D003198:Computer Simulation; D003628:Database Management Systems; D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000379:methods; D007700:Kinetics; D008954:Models, Biological; D010940:Plant Proteins / Q000378:metabolism*; D031786:Saccharum / Q000254:growth & development* / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software
D010940:Plant Proteins