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

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timzjing wants to merge 49 commits intomasterfrom

new-environments

Commits on Jun 26, 2023

New branch for Tim
cyrus-bio
committed

Commits on Jun 29, 2023

Added control vs. experiment flux distinction and support for excel import of environments
timzjing
committed
Add Excel with first-pass of new metabolism genes
timzjing
committed

Commits on Jul 10, 2023

Update Excel with first-pass of second set of metabolism genes
timzjing
committed
Test adding a putative L-selenocysteine synthesis pathway that is non tRNA dependent
timzjing
committed

Commits on Jul 12, 2023

Commits on Jul 13, 2023

Fixed homeostatic value estimate based on reactions where the demand compound is the reactant
timzjing
committed

Commits on Jul 14, 2023

Fixed separate notebook to work with new implementation.

cyrus-bio
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timzjing
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Small changes.

cyrus-bio
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timzjing
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New metal binding investigation notebook started.

cyrus-bio
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timzjing
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Investigating what fraction of iron goes to which enzymes.

cyrus-bio
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timzjing
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Almost finished protein feature metals.

cyrus-bio
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timzjing
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Finished adding protein feature metal binding. Need to merge and include in counts calculations

cyrus-bio
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timzjing
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Finished adding protein feature metal binding. Need to merge and include in counts calculations

cyrus-bio
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timzjing
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Creating new notebook to retrieve UniProt annotations since they seem to have more accurate stoichiometry.

cyrus-bio
authored and
timzjing
committed
Small changes.

cyrus-bio
authored and
timzjing
committed
New folder for Tim

cyrus-bio
authored and
timzjing
committed
Cleaned up notebook for Tim.

cyrus-bio
authored and
timzjing
committed
New branch for Tim

cyrus-bio
authored and
timzjing
committed
Added control vs. experiment flux distinction and support for excel import of environments
timzjing
committed
Add Excel with first-pass of new metabolism genes
timzjing
committed
Update Excel with first-pass of second set of metabolism genes
timzjing
committed
Test adding a putative L-selenocysteine synthesis pathway that is non tRNA dependent
timzjing
committed
Test adding a putative Fe-S cluster synthesis pathway in a separate notebook
timzjing
committed
Test adding a putative Fe-S cluster synthesis pathway in a separate notebook
timzjing
committed
Commit for bug-finding on Fd-S pathway
timzjing
committed
Fixed homeostatic value estimate based on reactions where the demand compound is the reactant
timzjing
committed

Commits on Jul 18, 2023

Commits on Jul 21, 2023

Adding actual experiment file for the new environments
timzjing
committed

Commits on Jul 24, 2023

Added a notebook for analysis of official simulation run
timzjing
committed

Commits on Jul 28, 2023

Commits on Aug 1, 2023

Commits on Aug 2, 2023

Added directed arrows and coloring for easier graph flux analysis
timzjing
committed

Commits on Aug 4, 2023

Commits on Aug 7, 2023

Improved pathway visualization to include more reactions
timzjing
committed

Commits on Aug 9, 2023

Updated pathway visualization to include a threshold for plotting reactions
timzjing
committed

Commits on Aug 11, 2023

Added script to generate a pathway heatmap based on reaction heatmap
timzjing
committed

Commits on Aug 17, 2023

Initial plotting of pathways as nodes
timzjing
committed