Tau-leap for kappa?
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David C Sterratt
Jan 18, 2019, 8:41:18 AM1/18/19
to kappa...@googlegroups.com
Dear all,
a student is working with me to simulate molecular pathways in the
synapse. At the moment simulation speed is not an issue, but I can see
that it will become one soon. I was wondering if there had been any work
done on generating trajectories from Kappa models using a tau-leap
method in a "network-free" simulation.
I'd always thought that tau-leap and Kappa were mutually incompatible,
but I'm now wondering if it could be done by enumerating the complexes
on the LHS and RHS of each rule that were likely to be reached by the
end of a step, and then treating them as conventional complexes in a
tau-leap simulation.
I'd be grateful for any pointers or thoughts, even if those thoughts are
that it's impossible or pointless!
Best wishes,
David
--
David C Sterratt, Senior Research Associate
Institute for Adaptive and Neural Computation, School of Informatics
University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, Scotland, UK
http://homepages.inf.ed.ac.uk/sterratt - tel: +44 131 651 1739
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
a student is working with me to simulate molecular pathways in the
synapse. At the moment simulation speed is not an issue, but I can see
that it will become one soon. I was wondering if there had been any work
done on generating trajectories from Kappa models using a tau-leap
method in a "network-free" simulation.
I'd always thought that tau-leap and Kappa were mutually incompatible,
but I'm now wondering if it could be done by enumerating the complexes
on the LHS and RHS of each rule that were likely to be reached by the
end of a step, and then treating them as conventional complexes in a
tau-leap simulation.
I'd be grateful for any pointers or thoughts, even if those thoughts are
that it's impossible or pointless!
Best wishes,
David
--
David C Sterratt, Senior Research Associate
Institute for Adaptive and Neural Computation, School of Informatics
University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, Scotland, UK
http://homepages.inf.ed.ac.uk/sterratt - tel: +44 131 651 1739
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
Bill Hlavacek
Jan 18, 2019, 4:03:10 PM1/18/19
to David C Sterratt, kappa-users
BioNetGen implements a partitioned leaping algorithm (a variation of tau leaping):
The algorithm is described here:
The BioNetGen implementation is NOT "network free" but you could perhaps use it in testing
w/ increasingly more complex models to determine if a network-free version might be worth pursuing.
I'm generally skeptical about tau leaping because it's unusual for a problem to meet the requirements for this approach to be helpful.
BioNetGen uses BNGL instead of Kappa for model definition, but
there's 2-way translator that is compatible with current versions of BNGL and Kappa (called TRuML):
If anyone tries TRuML, I'd be interested in feedback.
--Bill
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