basico
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copasi
A simplified python interface to COPASI.
I noticed parsing this sbml model: [BIOMD0000000429_url.xml](https://www.ebi.ac.uk/biomodels/services/download/get-files/MODEL1209110001/2/BIOMD0000000429_url.xml) that Basico returns expressions containing `if` statements incorrectly: In the model there is an expression for global quantity "Turgor" which Basico currently returns...
Heya Frank, I stumbled across this while trying to implement parameter estimation for shared and non-shared experiments. When I run something like: ``` fit_items = [ {'name': "Values[k_on]", 'lower': 1e05,...
Heya, hope you're well! I was wondering if simultaneous parameter estimation was possible with copasi/basico. For example, if you had two experiments you want to fit to, and of the...
Hello! I have thinking of running Basico on an HPC, but I was wondering if Basico uses threading to make use of multitasking and more CPU cores. I have run...
Hello @fbergmann , I tried to make a few changes in the function `def plot_per_dependent_variable` to create plots for the steady-state data and I would like to share the modified...
Heya Frank, I hope you're doing well! I wondered if it would be possible to add a custom, time-values argument to the to the `get_simulation_results()` function in `task_parameterestimation.py`. I often...
Heya, I don't have information and good examples at the moment as I'm still investigating it. But when I run `save_model_and_data`, open the newly created .cps file in CopasiUI, run...
Specifically, the call: df.set_index('Time') Causes an exception in Pandas, as it will find two Columns named "Time". The example SBML model attached has a model with id="s23" and name="Time". [ExampleSBML.zip](https://github.com/user-attachments/files/17295669/ExampleSBML.zip)...
A bug at biosimulators mentions, that basico does not resolve display names with nested parenthesis: https://github.com/biosimulators/Biosimulators_COPASI/issues/74
Currently the task for Lyapunov exponents is not yet exposed in basico. This should change.