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Related to https://github.com/AMICI-dev/AMICI/issues/1319, i was wondering about the following:
In case of preequilibration, should the occurrence in the condition table of any parameter that someh…
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I am using a model containing PEtab priors. Therefore my `problem.objective` is an aggregated objective containing negative log likelihood + negative log prior.
At the moment, calling `importer.creat…
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Would be interesting to interface the software that Clemens sent around today: https://www.mdpi.com/2073-8994/12/3/469
their code is here
https://github.com/GemmaMasFes6/Lie-Symmetries
dlill updated
4 years ago
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- [ ] Check that data points sharing scaling and offset have the same noise parameter
- [ ] Check that selected parameters are actually offset/proportionality/sigma parameters
- [ ] Check that only …
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Most of the fields are very easy to fill. We simply need the bibtex files for the models in the respective folders and (optional) also a remark file (in case several models are described in the respec…
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The package needs a bit of love to get it to 1.0. No guarantees on when all of the below can be accomplished, but it should be written down. In addition to the below, the code just needs to be simplif…
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To be discussed at a later point
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uhm regarding `x_fixed_vals` and `x_fixed_indices`, I think it would be much cleaner if they were combined into a single dict `{x_name: value}`. Would make assignment less error prone, would avoid ind…
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This issue serves as an overview of which models already have the visualization file. During the work on each model this model's issue should be re-opened. Once all models have one this can be closed.…
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Might be helpful to add an option to pass assumptions on parameters and states during model import that might allow for better symbolic simplifications. (E.g. helpful for #1151)
Might be useful to …