**What: **Predict the behavior of cells based on the pathways investigated.
EGFR and FAS-apoptotic pathways have been simulated.

**Why: **The simulation of biochemical interactions within a living cell
is itself not a new idea. The literature is rife with various simulators and
models, focusing often on small sets of local sub-cellular processes.
While these simulations are intriguing, there is a necessity for large scale
whole cell simulation. Accounts may vary, but scientists generally put the
number of possible interactions in the hundreds of thousands. So, the
question remains: how can one feasibly simulate the biochemical evolution
of an entire cell?

Employing systems of ordinary differential equations (ODEs) to model biological
phenomena leaves much to be desired, since these techniques are inherently
deterministic and continuous - i.e., based on concentrations instead of
multiplicities of molecules. Because of this, they fail to capture the discrete
nature of actual biological situations. In contrast to ODEs, Gillespie developed
the Direct Method (DM) and the First Reaction Method (FRM) in the late seventies.

We have chosen to explore an alternative method to biochemical modeling. Our
approach draws upon the emerging field of membrane systems computing. Simply
stated, we are further developing/refining an algorithm which is (a) faster than
the Gillespie approach, and yet is (b) discrete and nondeterministic, which we
argue is more sensitive to biological situations than deterministic ordinary
differential equations. With (a) and (b), our algorithm is somewhere between
the standard ODE and Gillespie techniques.

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