PMC:4331679 / 17164-18248 JSONTXT

{"project":"2_test","denotations":[{"id":"25707537-19619456-14870728","span":{"begin":507,"end":509},"obj":"19619456"},{"id":"25707537-22967854-14870729","span":{"begin":721,"end":722},"obj":"22967854"},{"id":"25707537-18406323-14870730","span":{"begin":726,"end":728},"obj":"18406323"}],"text":"In our study, the ODEs were solved using the standard Matlab library function ode45. This function can interpret the differential equations in the form of rate reactions. The ode45 accepts the initial values of the molecules and the time duration in the form of function parameters [20,21]. Using this procedure, we derived the rate equations and time course data for all twenty-two signalling proteins. The initial concentrations of the signalling molecules were set to dimensionless numeric value of one [22]. Some of the rate constants were taken directly from the literature. These include Casp9 \u0026 Casp3, Casp9 \u0026 XIAP, Casp8 \u0026 BID, Casp3 \u0026 XIAP, Casp3 \u0026Casp8, Casp3 \u0026 Apop, p53 \u0026 PUMA, Casp3 \u0026 Casp6 and XIAP \u0026 SMAC [4,23,24]. The remaining parameters were generated randomly but we verified them by Partial Least Square Regression (PLSR) test. We also performed sensitivity analysis of the model parameters by varying the model parameters to ensure overall robustness of the model to the small variations of parameters (see result section for PLSR test and sensitivity analysis)."}