William Poole
William Poole
When running code like: `data, sample_times = bscrlin.py_PropagateCells( initial_cell_states = Ncells, timepoints = timepoints, sample_times = sample_times, Model = M, safe = False)` Using a model with no birth/death/growth If...
Emcee is designed to deal with parallelization - we should make use of this!
This could be text and/or graphical [or ideally options for both]. The goal is it should help people debug the models they build.
[From Sam's Turbidostat:] The two common failure modes I saw were: Reading outside the bounds of the timepoints array when calculating a dt, and Issues when the timepoint array is...
To do a parameter sweet and to run many stochastic simulations and average the results to get a distribution.
The following is a very simple and easy way to add a noise model to Bioscrape inference so cost functions are actually probabilities. Allow two noise models, normal and log-normal...
This issue is to scope the possibility of allowing more general SBML events be incorporated into bioscrape as rules (possible called EventRules - but what might a better name be?)....
I believe this occurs due when global species are synchronized and then ssa results are merged using np.concatenate. Not sure the best fix - it doesn't always happen, so it...
Seems like in some cases a single cell state is sent (if there is only one model) instead of [LineageCellState] in a list.
Some of the wrappers must forget to call this which results in some events not working.