Paul Lang

At the moment SBMLToolkit converts everything that is not already an absolute quantity to an absolute quantity. So in the resulting ReactionSystem contains species in absolute quantities and rate_rules of...

@isaacsas : Yes. Just to divide the solution for a species by the volume it resides in in case the user is more interested in concentrations than absolute numbers.

In my use case, the output of `rate_cost = SymbolicUtils.simplify_fractions(rate_const)` is expected to be a functions of parameters only. To something like `convert_all_vars_to_pars(rate_const)` should fix it for me. Is there...

Thanks @yannikschaelte for getting back. I was using the Banga implementation. More specifically I used [this code](https://zenodo.org/record/1304034#.XqFfl2gzaMr) to run CeSS with some minor modifications.

> Something else? Calling Matlab from Python?

> In particular, this version probably does not yet allow gradient-based optimization using e.g. AMICI From my perspective, I have only tested eSS in combination with adjoint sensitivity analysis for...

I had a look at the `eSS_kernel.m` and `essR.R` scripts. They are about 1000 lines of code. In addition, they call a bunch of other functions that would need to...

I guess these questions would become clear when reimplementing the code. I am probably not in the position to judge what is the best way forward, but I still tried...

Thanks for thinking about that. > If you know any python package, which implements mini-batch optimizers with black-box objective functions (i.e., without assuming a neural net structure), we could try...

I heard about a parallel implementation of SSA. I think [this](https://arxiv.org/abs/2005.05295) is the paper about it. Perhaps [this paper](https://joss.theoj.org/papers/10.21105/joss.02685.pdf) is also relevant.