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RuleWorld / nfsim

A general-purpose, stochastic, biochemical reaction simulator for large reaction networks
http://michaelsneddon.net/nfsim/
MIT License
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complex with redundant bonds causing issues in time series generation #14

Open jjtapia opened 8 years ago

jjtapia commented 8 years ago

In the attached file, nfsim and ssa/ode simulations produce different results. The cause is likely to be in the reverse reaction

B(b1!1).C(c1!1) -> B(b1) + C(c1) kr

NFSim becomes confused between

B(b1!1).C(c1!1) -> B(b1) + C(c1) kr where B and C

where C and A are not bound together and

B(b1!1).C(c1!1) -> B(b1) .C(c1) kr

Where C and A still maintain a bond. While network expansion distinguishes between the two correctly and only triggers the event specified by the user.

odevsnf.bngl.txt