Release v0.14.0 #278
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Release v0.14.0 #278
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…273) It should be acceptable to have experimental data with different time points between conditions for the same observable (as in [Raia *et al.*, 2011](https://doi.org/10.1158/0008-5472.CAN-10-2987)), but currently it is only possible to vary the time points between the observables. Here, I modified the `get_timepoint()` function to return a dictionary (`{ "condition": list(tpoints) }`) to offer more flexibility while trying not to complicate the code too much. Due to this change, I needed to alter several parts of the code including `get_timepoint()` of the example model files. I also added a replication of Raia *et al.*'s JAK-STAT model to showcase an actual use case of this feature. I would like to know what you think about changing the return type of `get_timepoint()`, because alternatively I think we can pass the condition name as one of the inputs to achieve the same effect. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Hiroaki Imoto <hiroaki.imoto@ucd.ie>
This PR makes the following two changes to how the user-defined `@rxn` reactions are handled within the code: - fixes wrong variable in `user_defined()` There was a line that incorrectly refers to `product` instead of `reactant` when handling user-defined degradation reactions (e.g., `@rxn A -> 0:...`), which led to the placeholder variable (`"0"`) being included as one of the species in the resulting model. - Adds feature to allow multiple reactants and/or products in user-defined reactions Currently, the `@rxn` reaction type only accepts single reactant and product reactions. Changes were made to allow users to describe custom reactions with multiple reactants/products by concatenating them with a `+` symbol within the Text2Model file. The implementation of this feature mimics that of the `state_transition()` function. I will attach a toy Text2Model file that I used for testing below. I would appreciate any type of comments/suggestions. Thanks in advance! ``` @rxn 0 -> A: p[kf_a] | kf_a=0.1 @rxn A -> 0: p[deg_a] * u[A] | deg_a=0.05 @rxn A + B -> AB + B: p[kf_ab] * u[A] * u[B] | kf_ab=0.1 @rxn AB + B -> 0: p[deg_ab] * u[AB] | deg_ab=0.05 @obs A: u[A] @obs B: u[B] @obs AB: u[AB] @SiM tspan:[0, 100] @SiM condition control: init[A]=1; init[B]=1 ```
himoto
approved these changes
Nov 6, 2024
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Hello @himoto!
Sorry I haven't been able to actively work on this project lately. Although the feature discussed in #274 is still under development, I though we should make the other updated features available by releasing a new version.
I hope you can take your time to review the changes and let me know if we need any further discussions, thank you!