c/C++ open-source kinetics simulator
04 Sep '09 09:59
I'm trying to determine the current availability of modular c/c++ libraries for evaluating (and, related, simulating both as ode and various stochastic methods) sets of the kineticlaws from sbml.
I take it that there's a policy/design decision that such a core functionality does not belong in libsbml itself, given the diversity of possible models that include a kineticlaw as a detail.
I see copasi is active and well regarded, but it is distinctly not open-source.
There is a trace of SOSLib, which appears to be inactive, development-wise.
There are numerous packages oriented at proprietary languages like matlab and mathematica.
I'd much prefer to contribute to improving something open-source than reinventing if possible; in particular i can imagine adding the automatic calculation of analytic derivatives for use in solvers or bringing some package that's dormant up to the latest sbml spec.
Ultimately, i'm interested in the scalability and wall-clock performance of large mechanism models and possibly in transferring those calculations through appropriate code generation to GPUs and multicore processors/clusters, but we walk before we run.
Does anyone have any comments on soslib status, other packages i've overlooked/misunderstood in my examination of the huge list of packages on sbml.org, and whether they have a similar interest and might use a new (or updated) library in this area?
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