Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Implement biomass sampling experiments for metabolic networks in C++ #197

Merged
merged 4 commits into from
Feb 8, 2022

Conversation

TolisChal
Copy link
Member

This PR implements C++ tests for sampling from the flux space of 3 metabolic networks:

  1. e_coli
  2. iAT_PTL_636
  3. Recon1
    with respect to the exponential distribution induced by the biomass objective function of each model.

The PR adds the e_coli polytope and its objective function in a new folder metabolic_full_dim in folder tests.
The tests for 2. and 3. are commented out from CMakeLists.txt because the .ine files are too big.

One could run the test for e_coli by running:

logconcave_sampling_test -tc=e_coli_biomass

Copy link
Member

@vissarion vissarion left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for this PR!
There is an issue in CI tests for e_coli_biomass, to my understanding it shouldn't take that long to execute.

@vissarion
Copy link
Member

BTW, instead of commenting out the new tests, you could create a new test file that is not tested in CI but a user can test it on demand locally (without editing/uncommenting code in the test files).

@vissarion vissarion added the tests label Feb 3, 2022
@papachristoumarios
Copy link
Collaborator

iAT_PTL_636_biomass -> iAT_PLT_636_biomass.
@TolisChal Can you also create a test that calls the three tests? Since on gaussian sampling we have it like this, I think it should be a good idea to keep it this way for the exponential case as well.

@TolisChal TolisChal merged commit 6591ae8 into GeomScale:develop Feb 8, 2022
@TolisChal TolisChal deleted the bio_tests branch March 8, 2022 15:57
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants