Representations of the Bcl‐2 interaction topology in the EARM 2 Representations of the Bcl‐2 interaction topology in the EARM 2.0‐M1b (‘Lopez Embedded’) model. Representations of the Bcl‐2 interaction topology in the EARM 2.0‐M1b (‘Lopez Embedded’) model. The Bcl‐2 interaction model consists of five basic mechanistic elements or ‘motifs’—tBid/Bax/Bcl‐xL translocation, activation of Bax and Bak by tBid, Bcl‐2 family binding, Bax/Bak auto‐activation, and pore assembly—that are highlighted in A, B, and C according to the colors in the legend. (A) PySB source code for the model, edited for brevity. (B) Simplified, manually drawn representation. (C) The full reaction network, generated from the PySB model using the PySB render_reactions tool. Rectangles represent species, circles represent reactions, lines represent reactions with the solid arrowhead representing the nominal forward direction, and the empty arrowhead (for reversible reactions only) representing the reverse direction. Catalytic reactions are depicted with a boxed arrow pointing from the catalyst to the reaction circle (species for enzyme–substrate complexes are omitted for clarity). (D) Kappa contact map, which shows the superset of all possible bonds between monomers calculated by static analysis (Danos et al, 2008). The contact map was computed using Kappa's complx tool accessed through the PySB Kappa wrapper library. Rectangles represent monomers, circles represent sites, and lines represent bonds. Carlos F Lopez et al. Mol Syst Biol 2013;9:646 © as stated in the article, figure or figure legend