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Sampling on the flux space of multiple metabolic networks #18

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Sampling on the flux space of multiple metabolic networks #18

wants to merge 65 commits into from

Commits on Jul 15, 2021

  1. unknown

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    hariszaf committed Jul 15, 2021
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  2. Revert "Create CODE_OF_CONDUCT.md" 

    This reverts commit 23639fc.
    @hariszaf
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  3. Revert "Update issue templates" 

    This reverts commit a76b4be.
    @hariszaf
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  4. Revert "unknown" 

    This reverts commit cb6005e.
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  5. Revert "Revert "Create CODE_OF_CONDUCT.md"" 

    This reverts commit 3fc3d12.
    @hariszaf
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  6. Revert "Revert "Update issue templates"" 

    This reverts commit ffd7eaf.
    @hariszaf
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Commits on Aug 15, 2021

  1. parse 2 models and build concatenated S

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  2. .mat models for species of a

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  3. .mat models for species of b

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  4. .mat models for species of c

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  5. init classes for community level

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  6. embl models in mat format

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  7. embl models in mat format

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  8. embl models in mat format

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Commits on Aug 16, 2021

  1. embl models in mat format

    @hariszaf
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  2. embl models in mat format

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  3. embl models in mat format

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  4. embl models in mat format

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  5. embl models in mat format

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  6. embl models in mat format

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  7. embl models in mat format

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  8. embl models in mat format

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  9. embl models in mat format

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  10. embl models in mat format

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  11. embl models in mat format

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  12. embl models in mat format

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  13. embl models in mat format

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  14. embl models in mat format

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  15. embl models in mat format

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  16. embl models in mat format

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  17. embl models in mat format

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  18. embl models in mat format

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  19. embl models in mat format

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  20. new function for building the community level model

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  21. new class for building community level model

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  22. fix identification error

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  23. communityMetabolicNetwork class for loading multiple files and buildi… 

    …ng S
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  24. fix typo in class name

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  25. buildConqMatrix function added

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  26. import buildConqMatrix

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  27. fix self variables

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  28. import CommunityPolytopeSampler class

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  29. building the sampling function for community; in progress

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  30. getIndividualMatrices and matrices_for_community_level functions working

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  31. sampling on the flux space of 2 models

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Commits on Aug 17, 2021

  1. remove .mat.gz from mmodels dir

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  2. merge @ dell in the /GitHub dir 

    Merge branch 'pairs' of https://github.com/hariszaf/dingo into pairs
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  3. script to build .mat models from .xml ones

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  4. ignore notebook checkpoints

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  5. test case for the community classes

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  6. modifs

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Commits on Aug 19, 2021

  1. add parameters for community models

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  2. modif in comment

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  3. add community case

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    hariszaf committed Aug 19, 2021
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  4. fix args

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    hariszaf committed Aug 19, 2021
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  5. modifs

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  6. modifs to fix main for community

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Commits on Aug 31, 2021

  1. remove .mat models; they ll be available in a zenodo repo

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  2. replace the 2 model files with a README

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  3. running from terminal example

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Commits on Sep 20, 2021

  1. one class per file; according modifs to import classes

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Commits on Sep 22, 2021

  1. replace the pair-based notion in the get_model_list for multiple spec… 

    …ies; working on the community growth function
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Commits on Sep 25, 2021

  1. notebook to set the workflow for working with polyround - hops

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  2. merge before adding jupyter notebook for hops and polyround 

    Merge branch 'pairs' of https://github.com/hariszaf/dingo into pairs
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  3. maybe mapped samples maybe not

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    hariszaf committed Sep 25, 2021
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