Gabriel Miranda

### Problem Description For sparse data, even though the ml model I am using can handle them, it could be good to avoid showing them in violin or beeswarm plots...

### Issue Description I am using seaborn to plot the shap values and showing their relation with the data that was used for the prediction to avoid plotting nan values...

Analysis inside a region designated by a Binary Mask

2

Please fill in the following for any issues Your setup: 1. Operating System (Linux, MacOS, Windows): MacOS 2. Hardware type (x86, ARM..) and RAM: M1 16 gb 3. Python Version...

Getting a frequentist model from BART model

3

## Short Description Hi, I have been wordering if there is a way to connect the bart regression model with some other tree based model, like XGboost or sklearn's trees....

M2M workflow and mincom

1

Hi, I have been working with m2m to do some microbial community metabolic interaction analysis and I have stumble with and issue. When trying to run the mincom minimal_community.mincom() function...

Hi, I was working on time series analysis, specially in systems where various parameters interact to an end. I was setting the model, but I only manage to do a...

[Feature] Verbosity Option in `read_sbml_model` or similar.

1

### Checklist - [X] There are [no similar issues or pull requests](https://github.com/opencobra/cobrapy/issues) for this yet. ### Problem I been trying to work on some metagenome analysis with cobrapy. And to...

Cofactor issue

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Hello, Together with my team, we’ve been exploring the behavior of m2m during scope generation and have encountered an issue related to the degradation of cofactors. Specifically, we’ve observed that...