search

SysBioChalmers / Human-GEM

The generic genome-scale metabolic model of Homo sapiens
https://sysbiochalmers.github.io/Human-GEM-guide/
Creative Commons Attribution 4.0 International
98 stars 41 forks source link

add qualitative workflows #732

Open mihai-sysbio opened 11 months ago

mihai-sysbio commented 11 months ago

The GitHub Action workflows that are set up in the repository are informative. They have highlighted accidental mistakes and typos upon which corrective actions were decided to be followed. However, they are mostly limited to model structure and file format. Only more recently have functional checks been added, i.e., metabolic task checks.

What seems to be still missing are more diverse Action workflows around simulations. More recently, this discussed in the release review of 1.17. The way I see it, these are very important, as they would act as a mirror of the changes in the dynamic behavior the model as a result of the changes that are being introduced.

If there were a super easy way to do this, it would have already been done. My aim here is to make a first step and open the discussion, hoping to reach some actionable conclusions.

haowang-bioinfo commented 11 months ago

@mihai-sysbio thanks for bringing up this interesting topic of mirroring the resulted dynamic behavior from the changes introduced

I'm afraid this is too general to implement, could you help to further clarify what do you specifically suggest, and maybe what to begin with?

mihai-sysbio commented 11 months ago

I would start from https://github.com/SysBioChalmers/Human-GEM/pull/675 Later, it'd be more interested in running FVA with COBREXA, but for that a model extraction/contextualization method needs to be used, e.g., tINIT and the like.

haowang-bioinfo commented 11 months ago

I would start from https://github.com/SysBioChalmers/Human-GEM/pull/675

to merge #675, the error message should be somehow resolved, probably by generating more concise output?