Figure 4.

Refactoring of published models into PySB. (A) Relationships between the models examined in this paper. The ‘Albeck Group’ incorporates a series of incrementally expanded models shown in Figure 11 of Albeck et al (2008b); the ‘Shen/Howells Group’ incorporates models from three papers from the research group of Shen and colleagues (Chen et al, 2007a, Chen et al, 2007b; Cui et al, 2008) and a derivative model from Howells et al (2010); the ‘Lopez group’ includes three expanded models introduced in this paper. The arrows indicate that one model has been derived or extended from a prior model and point in the direction Base Model → Derivative Model. (B) The ‘Direct’ model from Chen et al (2007b) in its original ODE-based representation. (C) Conversion of the Chen ‘Direct’ model to a PySB module. The execution of the

chen_febs_direct

function results in rules that exactly reproduce the ODEs shown above (the molecule type

Bad

in the PySB function corresponds to the generic enabler species Ena in the original equations;

Bid

corresponds to the generic activator Act). The macro

catalyze_one_step_reversible

implements the two-reaction scheme E+S→E+P, P→S;

assemble_pore_spontaneous

implements the order-4 reaction 4 × subunit pore. The

bind_table

macro is illustrated in Figure 2C. (D) Model extension in PySB. Module Reuse (Figure 3B) was used to implement the ‘Direct’ model from Cui et al (2008) as an extension of the prior ‘Direct’ model from Chen et al (2007b) shown in Figure 4C. Invocation of the PySB function

chen_febs_direct

incorporates the elements of the original Chen et al (2007b) model; subsequent statements specify the modifications and additions required to yield the derived model from Cui et al (2008).