Closed maozhitao closed 2 years ago
Before addressing your question, I will take the time to clarify some aspects that I consider important.
In this context, and addressing what you identified as a "problem", if time is a concern to you, I discourage the use of MEWPy. The parallelisation of genes essentiality computation has not yet been concluded as it is not a priority. Indeed, in the context of large optimizations, which for example might use 100 threads for a week, the few minutes required by sequential gene essentiality analysis seems meaningless.
Besides the justification identified above regarding the limited utilization of some frameworks' features, and in the particular case of COBRApy, its API is frequently altered which hinders our capacity to maintain compatibility.
Nonetheless, I expect that in the near weeks the gene essentiality task, and others, will be parallelized.
Best regards
Thank you very much for such a detailed reply.
For the GKOProblem problem, it takes too long to calculate essential genes ( for iML1515 model), so why not just use the find_essential_genes function in the COBRApy, which gets results in seconds.![image](https://user-images.githubusercontent.com/3759962/149945471-5dd52bf8-b559-43b4-be1d-3682c30287ab.png)