Vincent Wieland

Process Error when using julia in python

1

Hello together, I want to use the _DifferentialEquations_ julia module in python via PyJulia. So I tried to get julia and PyJulia running. I have installed Julia versions 1.4.1 and...

Restricting sampling of parameters

3

Hello again, I am still trying to implement particle filters for the following SDE-model: $$ \begin{cases} dS(t) = -\alpha S(t)I(t)dt+\frac{1}{\sqrt{100}}\sqrt{\alpha S(t)I(t)}dB_1(t) \\ dI(t) = \alpha S(t)I(t)-\gamma I(t)dt-\frac{1}{\sqrt{100}}\sqrt{\alpha S(t)I(t)}dB_1(t)+\frac{1}{\sqrt{100}}\sqrt{\gamma I(t)}dB_2(t) \end{cases}...

Update python support

1

As seen in #1378 petab tests are failing due to use of syntax in AMICI that is not supported in python version

I am currently trying to export the `Merkle_JAK2STAT5_PCB2016` model from the examples folder to PEtab by running the `SetupFinal.m` script to load and compile the model with the corresponding data....

Building a `SDEProblem` from a composed `SDESystems` does not work.

1

I am trying to introduce a time-varying parameter following an SDE into an `SDESystem` obtained from Catalyst.jl `ReactionSystem`. However, when I want to create an `SDEProblem` from the composed `SDESystem`,...

NaN gradient occurring in `SpecialFunctions.gamma`, when using float arguments.

2

I tried to use ForwardDiff on the upper incomplete gamma function as provided in [SpecialFunctions.jl](https://github.com/JuliaMath/SpecialFunctions.jl/blob/124915fce203925b69fa1a295a2ab3025cbe3f3c/src/gamma_inc.jl#L1099-L1113) Calling it with the first argument being an integer did work fine, but changing it...

Event assignment not working

2

Dear all, I am trying to import and convert an SBML model with 50 reactions, 29 species, 34 parameters and 17 events into a `ReactionSystem` using the following recommended code...

Sampling fails due to degenerate covariance matrix in parameter proposal step.

1

I have a model with some unidentifiabilities and want to perform sampling after optimization. Using the `AdaptiveParallelTemperingSampler` with an `AdaptiveMetropolisSampler` as an internal sampler does work for some hundred thousands...