bioPN-package


  bioPN is a package of C functions that can be used to simulate
  time-dependent evolution of biochemical reaction networks. The model
  is defined as a place/transition Petri Net, which is close to how
  biochemical reactions are defined. The model can be either
  deterministically solved using an explicit Runge Kutta Dormand Prince
  45 method, simulated using four highly optimized variants of the
  stochastic simulation algorithm, or as a deterministic/stochastic
  hybrid, according to the Haseltine and Rawlings' algorithm, or using
  the Partitioned Leaping Algorithm. The library has been optimized for
  speed and flexibility.<p></p><p>  bioPN has been tested only on 64 bits machines, relying on integers of
  64 bits. The behavior on 32 bits architectures is untested and not supported.
</p>

a) bioPN package


bioPN is a package suited to perform simulation of deterministic and stochastic systems of biochemical reaction
networks.
Models are defined using a subset of Petri Nets, in a way that is close at how chemical reactions
are defined.
For deterministic solutions, bioPN creates the associated system of differential equations "on the fly", and
solves it with a Runge Kutta Dormand Prince 45 explicit algorithm.
For stochastic solutions, bioPN offers variants of Gillespie algorithm, or SSA.
For hybrid deterministic/stochastic,
it employs the Haseltine and Rawlings algorithm, that partitions the system in fast and slow reactions.
bioPN algorithms are developed in C to achieve adequate performance.

a) bioPN package: Simulation of deterministic and stochastic biochemical reaction networks using Petri Nets

Description

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Details

References