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Adding new environments analysis, an experiment file, and a test #205

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Adding new environments analysis, an experiment file, and a test #205

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Commits on Jun 12, 2023

  1. Fixed separate notebook to work with new implementation.

    @cyrus-bio
    cyrus-bio committed Jun 12, 2023
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  2. Small changes.

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    cyrus-bio committed Jun 12, 2023
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Commits on Jun 14, 2023

  1. New metal binding investigation notebook started.

    @cyrus-bio
    cyrus-bio committed Jun 14, 2023
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Commits on Jun 15, 2023

  1. Investigating what fraction of iron goes to which enzymes.

    @cyrus-bio
    cyrus-bio committed Jun 15, 2023
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Commits on Jun 16, 2023

  1. Almost finished protein feature metals.

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    cyrus-bio committed Jun 16, 2023
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Commits on Jun 19, 2023

  1. Finished adding protein feature metal binding. Need to merge and incl… 

    …ude in counts calculations
    @cyrus-bio
    cyrus-bio committed Jun 19, 2023
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  2. Finished adding protein feature metal binding. Need to merge and incl… 

    …ude in counts calculations
    @cyrus-bio
    cyrus-bio committed Jun 19, 2023
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Commits on Jun 22, 2023

  1. Creating new notebook to retrieve UniProt annotations since they seem… 

    … to have more accurate stoichiometry.
    @cyrus-bio
    cyrus-bio committed Jun 22, 2023
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Commits on Jun 26, 2023

  1. Small changes.

    @cyrus-bio
    cyrus-bio committed Jun 26, 2023
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  2. New folder for Tim

    @cyrus-bio
    cyrus-bio committed Jun 26, 2023
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  3. Merge branch 'master' of https://github.com/CovertLab/vivarium-ecoli … 

    …into metabolism-redux
    @cyrus-bio
    cyrus-bio committed Jun 26, 2023
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  4. Cleaned up notebook for Tim.

    @cyrus-bio
    cyrus-bio committed Jun 26, 2023
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  5. New branch for Tim

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    cyrus-bio committed Jun 26, 2023
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Commits on Jun 29, 2023

  1. Added control vs. experiment flux distinction and support for excel i… 

    …mport of environments
    @timzjing
    timzjing committed Jun 29, 2023
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  2. Add Excel with first-pass of new metabolism genes

    @timzjing
    timzjing committed Jun 29, 2023
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Commits on Jul 10, 2023

  1. Update Excel with first-pass of second set of metabolism genes

    @timzjing
    timzjing committed Jul 10, 2023
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  2. Test adding a putative L-selenocysteine synthesis pathway that is non… 

    … tRNA dependent
    @timzjing
    timzjing committed Jul 10, 2023
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Commits on Jul 12, 2023

  1. Test adding a putative Fe-S cluster synthesis pathway in a separate n… 

    …otebook
    @timzjing
    timzjing committed Jul 12, 2023
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  2. Test adding a putative Fe-S cluster synthesis pathway in a separate n… 

    …otebook
    @timzjing
    timzjing committed Jul 12, 2023
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  3. Commit for bug-finding on Fd-S pathway

    @timzjing
    timzjing committed Jul 12, 2023
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Commits on Jul 13, 2023

  1. Fixed homeostatic value estimate based on reactions where the demand … 

    …compound is the reactant
    @timzjing
    timzjing committed Jul 13, 2023
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Commits on Jul 14, 2023

  1. Fixed separate notebook to work with new implementation.

    @cyrus-bio @timzjing
    cyrus-bio authored and timzjing committed Jul 14, 2023
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  2. Small changes.

    @cyrus-bio @timzjing
    cyrus-bio authored and timzjing committed Jul 14, 2023
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  3. New metal binding investigation notebook started.

    @cyrus-bio @timzjing
    cyrus-bio authored and timzjing committed Jul 14, 2023
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  4. Investigating what fraction of iron goes to which enzymes.

    @cyrus-bio @timzjing
    cyrus-bio authored and timzjing committed Jul 14, 2023
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  5. Almost finished protein feature metals.

    @cyrus-bio @timzjing
    cyrus-bio authored and timzjing committed Jul 14, 2023
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  6. Finished adding protein feature metal binding. Need to merge and incl… 

    …ude in counts calculations
    @cyrus-bio @timzjing
    cyrus-bio authored and timzjing committed Jul 14, 2023
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  7. Finished adding protein feature metal binding. Need to merge and incl… 

    …ude in counts calculations
    @cyrus-bio @timzjing
    cyrus-bio authored and timzjing committed Jul 14, 2023
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  8. Creating new notebook to retrieve UniProt annotations since they seem… 

    … to have more accurate stoichiometry.
    @cyrus-bio @timzjing
    cyrus-bio authored and timzjing committed Jul 14, 2023
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  9. Small changes.

    @cyrus-bio @timzjing
    cyrus-bio authored and timzjing committed Jul 14, 2023
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  10. New folder for Tim

    @cyrus-bio @timzjing
    cyrus-bio authored and timzjing committed Jul 14, 2023
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  11. Cleaned up notebook for Tim.

    @cyrus-bio @timzjing
    cyrus-bio authored and timzjing committed Jul 14, 2023
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  12. New branch for Tim

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    cyrus-bio authored and timzjing committed Jul 14, 2023
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  13. Added control vs. experiment flux distinction and support for excel i… 

    …mport of environments
    @timzjing
    timzjing committed Jul 14, 2023
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  14. Add Excel with first-pass of new metabolism genes

    @timzjing
    timzjing committed Jul 14, 2023
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  15. Update Excel with first-pass of second set of metabolism genes

    @timzjing
    timzjing committed Jul 14, 2023
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  16. Test adding a putative L-selenocysteine synthesis pathway that is non… 

    … tRNA dependent
    @timzjing
    timzjing committed Jul 14, 2023
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  17. Test adding a putative Fe-S cluster synthesis pathway in a separate n… 

    …otebook
    @timzjing
    timzjing committed Jul 14, 2023
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  18. Test adding a putative Fe-S cluster synthesis pathway in a separate n… 

    …otebook
    @timzjing
    timzjing committed Jul 14, 2023
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  19. Commit for bug-finding on Fd-S pathway

    @timzjing
    timzjing committed Jul 14, 2023
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  20. Fixed homeostatic value estimate based on reactions where the demand … 

    …compound is the reactant
    @timzjing
    timzjing committed Jul 14, 2023
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Commits on Jul 18, 2023

  1. Add 4Fe-4S Pathway

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    timzjing committed Jul 18, 2023
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  2. Merge remote-tracking branch 'origin/new-environments' into new-envir… 

    …onments

# Conflicts:
#	ecoli/processes/metabolism_redux.py
#	notebooks/new_environments/Fe_S_pathway.ipynb
#	notebooks/new_environments/new_genes.xlsx
    @timzjing
    timzjing committed Jul 18, 2023
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Commits on Jul 21, 2023

  1. Adding actual experiment file for the new environments

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    timzjing committed Jul 21, 2023
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Commits on Jul 24, 2023

  1. Added a notebook for analysis of official simulation run

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    timzjing committed Jul 24, 2023
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Commits on Jul 28, 2023

  1. Added tree visualization of metabolites in analysis notebook

    @timzjing
    timzjing committed Jul 28, 2023
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  2. Added pull request test to new_environments_sim.py

    @timzjing
    timzjing committed Jul 28, 2023
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  3. Added fba_new_environments.json

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    timzjing committed Jul 28, 2023
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Commits on Jul 31, 2023

  1. Added failing test that tests division (not working correctly)

    @cyrus-bio
    cyrus-bio committed Jul 31, 2023
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  2. Fixed failing test for testing cell division and metabolism process s… 

    …wap.
    @cyrus-bio
    cyrus-bio committed Jul 31, 2023
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  3. Added todos

    @cyrus-bio
    cyrus-bio committed Jul 31, 2023
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  4. Changed solver.

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    cyrus-bio committed Jul 31, 2023
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Commits on Aug 1, 2023

  1. Added graph visualization of reaction and metabolite flux

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    timzjing committed Aug 1, 2023
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  2. Merge remote-tracking branch 'origin/new-environments' into new-envir… 

    …onments

# Conflicts:
#	ecoli/experiments/metabolism_redux_sim.py
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    timzjing committed Aug 1, 2023
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Commits on Aug 2, 2023

  1. Added directed arrows and coloring for easier graph flux analysis

    @timzjing
    timzjing committed Aug 2, 2023
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Commits on Aug 4, 2023

  1. Added visualization of metabolic networks based on specific metabolit… 

    …es and its lower order connections
    @timzjing
    timzjing committed Aug 4, 2023
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  2. Added visualization of metabolic pathways based on greatest flux-chan… 

    …ged reactions + support for specific metabolites of interest in the same script
    @timzjing
    timzjing committed Aug 4, 2023
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Commits on Aug 7, 2023

  1. Improved pathway visualization to include more reactions

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    timzjing committed Aug 7, 2023
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Commits on Aug 9, 2023

  1. Updated pathway visualization to include a threshold for plotting rea… 

    …ctions
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    timzjing committed Aug 9, 2023
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Commits on Aug 11, 2023

  1. Added script to generate a pathway heatmap based on reaction heatmap

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    timzjing committed Aug 11, 2023
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Commits on Aug 17, 2023

  1. Initial plotting of pathways as nodes

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    timzjing committed Aug 17, 2023
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