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Updated Notebooks and simulations #13

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Updated Notebooks and simulations #13

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Commits on Jul 17, 2022

  1. bad_data_timesteps addition, polishing, direct CSV import/parsing

    Andrew Freiburger authored and Andrew Freiburger committed Jul 17, 2022
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Commits on Jul 18, 2022

  1. graphing update

    Andrew Freiburger authored and Andrew Freiburger committed Jul 18, 2022
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  2. copied TSV files

    Andrew Freiburger authored and Andrew Freiburger committed Jul 18, 2022
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  3. Merge remote-tracking branch 'upstream/main' into main

    Andrew Freiburger authored and Andrew Freiburger committed Jul 18, 2022
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  4. figure finalization

    Andrew Freiburger authored and Andrew Freiburger committed Jul 18, 2022
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Commits on Jul 19, 2022

  1. km logic and Notebook exploration

    Andrew Freiburger authored and Andrew Freiburger committed Jul 19, 2022
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Commits on Jul 20, 2022

  1. ReFramed code and docstrings

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  2. Add files via upload

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    freiburgermsu committed Jul 20, 2022
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Commits on Jul 22, 2022

  1. zip extraction and updated Notebooks

    Andrew Freiburger authored and Andrew Freiburger committed Jul 22, 2022
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  2. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks 

     into main
    Andrew Freiburger authored and Andrew Freiburger committed Jul 22, 2022
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Commits on Jul 25, 2022

  1. SMETANA draft

    Andrew Freiburger authored and Andrew Freiburger committed Jul 25, 2022
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  2. attempted recapitulation of the SMETANA example

    Andrew Freiburger authored and Andrew Freiburger committed Jul 25, 2022
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  3. clean SMETANA directory

    Andrew Freiburger authored and Andrew Freiburger committed Jul 25, 2022
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Commits on Jul 26, 2022

  1. partial COBRA translation of ReFramed SMETANA

    Andrew Freiburger authored and Andrew Freiburger committed Jul 26, 2022
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Commits on Jul 28, 2022

  1. debugging of SMETANA curation

    Andrew Freiburger authored and Andrew Freiburger committed Jul 28, 2022
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Commits on Aug 2, 2022

  1. standardization of experimental data and MSsmetana

    Andrew Freiburger authored and Andrew Freiburger committed Aug 2, 2022
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Commits on Aug 5, 2022

  1. MSsmetana draft and associated files/Notebooks

    Andrew Freiburger authored and Andrew Freiburger committed Aug 5, 2022
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Commits on Aug 8, 2022

  1. plotting individual phenotypes and improved concentration plots

    Andrew Freiburger authored and Andrew Freiburger committed Aug 8, 2022
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Commits on Aug 9, 2022

  1. towards automating the phenotype fluxes

    Andrew Freiburger authored and Andrew Freiburger committed Aug 9, 2022
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  2. automated phenotype fluxes, not calibrated for M9

    Andrew Freiburger authored and Andrew Freiburger committed Aug 9, 2022
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Commits on Aug 10, 2022

  1. acetate production patch and dictionary v API Optlang comparison

    Andrew Freiburger authored and Andrew Freiburger committed Aug 10, 2022
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  2. Add files via upload

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    freiburgermsu committed Aug 10, 2022
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Commits on Aug 11, 2022

  1. old edits before a merged update

    Andrew Freiburger authored and Andrew Freiburger committed Aug 11, 2022
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  2. merge conflicts

    Andrew Freiburger authored and Andrew Freiburger committed Aug 11, 2022
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Commits on Aug 12, 2022

  1. merge conflicts

    Andrew Freiburger authored and Andrew Freiburger committed Aug 12, 2022
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  2. Updated GEM fluxes in MSComFitting and MSsmetana revisions

    Andrew Freiburger authored and Andrew Freiburger committed Aug 12, 2022
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  3. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks 

     into main
    Andrew Freiburger authored and Andrew Freiburger committed Aug 12, 2022
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Commits on Aug 14, 2022

  1. SMETANA logical edits and use of leveraged functions

    Andrew Freiburger authored and Andrew Freiburger committed Aug 14, 2022
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Commits on Aug 16, 2022

  1. SMETANA, OptlangHelper, and MinimalMedia edits

    Andrew Freiburger authored and Andrew Freiburger committed Aug 16, 2022
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Commits on Aug 17, 2022

  1. SMETANA edits

    Andrew Freiburger authored and Andrew Freiburger committed Aug 17, 2022
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  2. SMETANA object creation as an abstraction of staticmethods

    Andrew Freiburger authored and Andrew Freiburger committed Aug 17, 2022
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Commits on Aug 18, 2022

  1. MSCommFitting dictionary replacement and error images

    Andrew Freiburger authored and Andrew Freiburger committed Aug 18, 2022
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Commits on Aug 23, 2022

  1. removed folder

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  2. merge conflict resolutions

    @freiburgermsu
    freiburgermsu committed Aug 23, 2022
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Commits on Aug 25, 2022

  1. commfitting dictionary development

    Andrew Freiburger authored and Andrew Freiburger committed Aug 25, 2022
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  2. simulation images

    Andrew Freiburger authored and Andrew Freiburger committed Aug 25, 2022
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  3. Delete CommunityModeling/CommFitting/C:/Users/Andrew Freiburger/Docum… 

    …ents/Argonne/cobrakbase/.matplotlib directory
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  4. Delete CommunityModeling/CommFitting/Fatimas_drafts/C:/Users/Andrew F… 

    …reiburger/Documents/Argonne/cobrakbase/.matplotlib directory
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  5. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks 

     into main
    Andrew Freiburger authored and Andrew Freiburger committed Aug 25, 2022
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Commits on Aug 26, 2022

  1. MSsmetana edits

    Andrew Freiburger authored and Andrew Freiburger committed Aug 26, 2022
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  2. MSCommFitting recursive assignment of a dictionary expression

    Andrew Freiburger authored and Andrew Freiburger committed Aug 26, 2022
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Commits on Aug 27, 2022

  1. OptlangHelper expansion with a recursive expression definition

    Andrew Freiburger authored and Andrew Freiburger committed Aug 27, 2022
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Commits on Aug 28, 2022

  1. drafts of all but SCscore

    Andrew Freiburger authored and Andrew Freiburger committed Aug 28, 2022
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Commits on Aug 29, 2022

  1. SMETANA updates and CommFitting dictionary infrastructure

    Andrew Freiburger authored and Andrew Freiburger committed Aug 29, 2022
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Commits on Aug 30, 2022

  1. SMETANA updates and Notebook development

    Andrew Freiburger authored and Andrew Freiburger committed Aug 30, 2022
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Commits on Aug 31, 2022

  1. dictionary MSCommFitting method and MSSmetana edits

    Andrew Freiburger authored and Andrew Freiburger committed Aug 31, 2022
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Commits on Sep 2, 2022

  1. MIP and MU score improvements

    Andrew Freiburger authored and Andrew Freiburger committed Sep 2, 2022
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  2. MSCommFitting loading data &parameter changes

    Andrew Freiburger authored and Andrew Freiburger committed Sep 2, 2022
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Commits on Sep 3, 2022

  1. Operational and polished MSsmetana

    Andrew Freiburger authored and Andrew Freiburger committed Sep 3, 2022
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Commits on Sep 6, 2022

  1. cleaning the directory ; SMETANA and CommFitting edits

    Andrew Freiburger authored and Andrew Freiburger committed Sep 6, 2022
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Commits on Sep 9, 2022

  1. smetana score operational draft

    Andrew Freiburger authored and Andrew Freiburger committed Sep 9, 2022
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Commits on Sep 12, 2022

  1. smetana notebook updates

    Andrew Freiburger authored and Andrew Freiburger committed Sep 12, 2022
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Commits on Sep 13, 2022

  1. mscommfitting_dict edits

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  2. mscommfitting_dict merge conflict resolutions

    @freiburgermsu
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  3. reorganized CommFitting and minimal media development

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Commits on Sep 16, 2022

  1. save open notebooks

    Andrew Freiburger authored and Andrew Freiburger committed Sep 16, 2022
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Commits on Sep 20, 2022

  1. MSCommFitting polishing ; bad timesteps

    Andrew Freiburger authored and Andrew Freiburger committed Sep 20, 2022
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Commits on Sep 21, 2022

  1. reorganize CommunityModeling directory

    @freiburgermsu
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  2. conflict resolution

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Commits on Sep 22, 2022

  1. MSCommFitting and SMETANA edits

    Andrew Freiburger authored and Andrew Freiburger committed Sep 22, 2022
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  2. conflict resolution

    Andrew Freiburger authored and Andrew Freiburger committed Sep 22, 2022
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Commits on Sep 25, 2022

  1. Michaelis-Menten logic development

    Andrew Freiburger authored and Andrew Freiburger committed Sep 25, 2022
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Commits on Sep 26, 2022

  1. Michaelis-Menten logic development & _standard()

    Andrew Freiburger authored and Andrew Freiburger committed Sep 26, 2022
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Commits on Sep 27, 2022

  1. DataStandardization package

    Andrew Freiburger authored and Andrew Freiburger committed Sep 27, 2022
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Commits on Sep 29, 2022

  1. DataStandardization completion and beginning of commfitting revisions

    Andrew Freiburger authored and Andrew Freiburger committed Sep 29, 2022
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Commits on Sep 30, 2022

  1. developing a standardized CommFitting

    Andrew Freiburger authored and Andrew Freiburger committed Sep 30, 2022
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Commits on Oct 5, 2022

  1. towards a generalized CommFitting, with associated files

    Andrew Freiburger authored and Andrew Freiburger committed Oct 5, 2022
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Commits on Oct 6, 2022

  1. near generalized CommFitting and associated files

    Andrew Freiburger authored and Andrew Freiburger committed Oct 6, 2022
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Commits on Oct 10, 2022

  1. generalized core edits ; ignore_timesteps development ; new data

    Andrew Freiburger authored and Andrew Freiburger committed Oct 10, 2022
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Commits on Oct 12, 2022

  1. generalized core correction of carbon constraints ; ignore_timesteps … 

    …development ; new data
    Andrew Freiburger authored and Andrew Freiburger committed Oct 12, 2022
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Commits on Oct 14, 2022

  1. generalized CommFitting

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  2. generalized core, sans growing PF

    Andrew Freiburger authored and Andrew Freiburger committed Oct 14, 2022
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Commits on Oct 15, 2022

  1. generalized core and updated graph arguments

    Andrew Freiburger authored and Andrew Freiburger committed Oct 15, 2022
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  2. reorganize the repository ; E.coli Acetate phenotype simulation

    Andrew Freiburger authored and Andrew Freiburger committed Oct 15, 2022
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  3. supplant the original CommFitting with the standardized CommFitting

    Andrew Freiburger authored and Andrew Freiburger committed Oct 15, 2022
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Commits on Oct 19, 2022

  1. BIOLOG standardization drafts

    Andrew Freiburger authored and Andrew Freiburger committed Oct 19, 2022
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  2. BIOLOG standardization drafts

    Andrew Freiburger authored and Andrew Freiburger committed Oct 19, 2022
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  3. BIOLOG standardization drafts

    Andrew Freiburger authored and Andrew Freiburger committed Oct 19, 2022
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Commits on Oct 20, 2022

  1. development toward simulating BIOLOG data

    Andrew Freiburger authored and Andrew Freiburger committed Oct 20, 2022
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Commits on Oct 22, 2022

  1. AIChE poster simulations, and associated edits

    Andrew Freiburger authored and Andrew Freiburger committed Oct 22, 2022
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Commits on Oct 25, 2022

  1. AIChE Figures; reorganized data; OD plateau check

    Andrew Freiburger authored and Andrew Freiburger committed Oct 25, 2022
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  2. OD plateau removal simulations

    Andrew Freiburger authored and Andrew Freiburger committed Oct 25, 2022
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  3. Acetate simulation development and edits

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Commits on Oct 29, 2022

  1. Distinguished phenotype growth rates ; Acetate media simulation

    Andrew Freiburger authored and Andrew Freiburger committed Oct 29, 2022
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Commits on Oct 31, 2022

  1. first phase of kinetic optimization draft

    Andrew Freiburger authored and Andrew Freiburger committed Oct 31, 2022
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Commits on Nov 1, 2022

  1. polishing

    Andrew Freiburger authored and Andrew Freiburger committed Nov 1, 2022
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Commits on Nov 2, 2022

  1. updated phenotype definition and simulation figures

    Andrew Freiburger authored and Andrew Freiburger committed Nov 2, 2022
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Commits on Nov 7, 2022

  1. reorganization ; simulation Notebooks and figures ; CommPhitting phen… 

    …otype draft optimization
    Andrew Freiburger authored and Andrew Freiburger committed Nov 7, 2022
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Commits on Nov 8, 2022

  1. phenotype debugging

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  2. phenotypes code draft

    Andrew Freiburger authored and Andrew Freiburger committed Nov 8, 2022
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Commits on Nov 9, 2022

  1. pre-dual-optimization phenotypes code

    Andrew Freiburger authored and Andrew Freiburger committed Nov 9, 2022
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  2. dual-optimization phenotyping draft

    Andrew Freiburger authored and Andrew Freiburger committed Nov 9, 2022
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  3. operational dual-optimization phenotyping

    Andrew Freiburger authored and Andrew Freiburger committed Nov 9, 2022
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  4. debugging dual-optimization phenotyping

    Andrew Freiburger authored and Andrew Freiburger committed Nov 9, 2022
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Commits on Nov 10, 2022

  1. drafted operational phenotyping and final AIChE simulations

    Andrew Freiburger authored and Andrew Freiburger committed Nov 10, 2022
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Commits on Nov 11, 2022

  1. generalized phenotype excretion optimization

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Commits on Nov 13, 2022

  1. recrganized the CommPhitting directory

    Andrew Freiburger authored and Andrew Freiburger committed Nov 13, 2022
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Commits on Nov 18, 2022

  1. added Ross Carlson's E.coli and P.aeruginosa data

    Andrew Freiburger authored and Andrew Freiburger committed Nov 18, 2022
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  2. remove nested repository

    Andrew Freiburger authored and Andrew Freiburger committed Nov 18, 2022
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  3. add submodule of Ross's E.coli study data

    Andrew Freiburger authored and Andrew Freiburger committed Nov 18, 2022
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Commits on Nov 22, 2022

  1. developing the fitKinetics method

    Andrew Freiburger authored and Andrew Freiburger committed Nov 22, 2022
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Commits on Nov 23, 2022

  1. BIOLOG simulations and logic simplifications

    Andrew Freiburger authored and Andrew Freiburger committed Nov 23, 2022
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Commits on Nov 24, 2022

  1. preliminary paper figures of mono- and co-cultures

    Andrew Freiburger authored and Andrew Freiburger committed Nov 24, 2022
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  2. minor CommPhitting edits

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  3. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks

    @freiburgermsu
    freiburgermsu committed Nov 24, 2022
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Commits on Nov 29, 2022

  1. kinetics optimization edits and Notebook

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  2. figure export adjustment

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  3. new additions

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  4. Delete CommunityModeling/CommFitting/C:/Users/Andrew Freiburger/Docum… 

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  5. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks 

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  1. microarray transcriptomics data simplification

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  2. BIOLOG simulations

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  3. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks

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  4. draft towards paper figures

    Andrew Freiburger authored and Andrew Freiburger committed Dec 1, 2022
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  5. conflict resolution

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  6. updated kinetics loop to share

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  1. operational kinetics optimization ; problem definition corrections ; … 

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  1. debugged simulations and refined fitting graph

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  1. Paper figure debugging and kinetics refinement

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  1. paper_figure simulations

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  1. fit_kinetics2 draft with experimental data

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  1. BIOLOG test

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  2. Notebook simulations

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  3. merge resolution

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  4. BIOLOG simulation development

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  1. Delete CommunityModeling/CommFitting/C:/Users/Andrew Freiburger/Docum… 

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  2. unknown AIChE simulation edits

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  3. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks 

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  1. Chris' kinetics formulation, initial draft

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  1. further CommPhitting refinements, with a few remaining bugs

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  1. further CommPhitting refinements, possibly correct final bioc

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  1. constrained CommPhitting bioc for all members

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  1. cFBA notebook draft for SynBio ; expanded c_ variable definitions

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  1. simulations for the preprint

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  2. merge conflict resolution

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  1. complete paper_figures simulations

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  1. BIOLOG simulation drafting

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  1. updated directory naming

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  1. BIOLOG developing and simulations ; ANME reorganization

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  1. ANME SteadyCom Notebook simulations

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  1. CommPhitting graphing updates and parsed functinoality

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  1. updated pipeline and paper_figures Notebook

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  1. CommPhitting code updates

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  2. adding the cleaned Notebook

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  1. paper_figures, ANME SMETANA, and Data parameterization for CommPhitting

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  1. ANME SMETANA Notebook

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  2. conflicts

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  1. CommPhitting updates

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  2. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks

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  1. CommPhitting examples

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  1. CommPhitting Poster simulations

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  2. overnight CommPhitting Poster simulation

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  1. CommPhitting HDF5 output ; new metabolomics data

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  1. ANME and CommPhitting updates

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  2. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks

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  1. CommPhitting updates

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  2. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks

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  3. ANME GeneID information parsing

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  4. t pushMerge branch 'main' of https://github.com/freiburgermsu/Project… 

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  1. Victoria's annotation parsing and gene->genome mapping

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  1. ANME edits

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  1. GROW files and ANME updates

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  1. ANME/SRB Gene ID corrections

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  1. ANME geneID -> GenomeID -> KBase obj mappings

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  1. updated ANME genome mappings

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  1. TMS significant compounds

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  2. KBase mapped genomes and Jeff's writing drafts

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  1. CommScores

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  2. ANME genomeID mapping updates

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  1. merge edits

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  2. Dileep's compound mapping

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  3. Update .gitignore

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  4. Update .gitignore

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  1. ANME and Mouse Microbiome files

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  2. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks

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  1. AGORA2 model processing

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  1. AGORA2 and SBI collab

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  1. SBI_collab data and CommScores interaction example

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  1. SBML3 models

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  2. update SBML3 path

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  1. CommScores parsing code and BSS bug

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  2. pull updates

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  1. ANME syntrophy simulations, CommScores paper data, and Concerto

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  2. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks

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  3. concerto simulations

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  1. ANME clade pairings

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  1. ANME and DORF maping

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  1. AGORA2 models mapping from ASV

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  1. AGORA2 ASV megaModel mapping

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  1. phenotyping updates

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  2. Notebook updates for examining AGORA2

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  3. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks

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  1. AGORA built models

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  2. SBML update and AGORA_comm Notebook

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  3. merge conflict resolution

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  1. AGORA2_comm Notebook update

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  1. AuroraGPT and illustrations

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  2. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks

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  1. AuroraGPT files

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  1. Updated compounds paragraphs

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  1. AuroraGPT updates and MSCompatibility scrubbing

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  2. merge conflict resolution

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  3. reaction paragraphs update

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  1. rxns and cpds paragraphs for round 1 training

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  1. mouse_microbiome updates

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  2. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks

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  3. minor microbiome Notebook edits

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  4. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks

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  1. Mapping metabolomics data

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  2. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks

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Commits on Nov 20, 2023

  1. Megan's models updates

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    freiburgermsu committed Nov 20, 2023
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  2. Megan's mapping updates

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    freiburgermsu committed Nov 20, 2023
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Commits on Nov 25, 2023

  1. AuroraGPT updates

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    freiburgermsu committed Nov 25, 2023
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Commits on Nov 27, 2023

  1. Notebook updates

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    freiburgermsu committed Nov 27, 2023
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Commits on Nov 28, 2023

  1. AuroraGPT level-1 tests

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    freiburgermsu committed Nov 28, 2023
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  2. Merge branch 'main' of https://github.com/freiburgermsu/ProjectNotebooks

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    freiburgermsu committed Nov 28, 2023
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  3. AuroraGPT question updates and AGORA2 files

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    freiburgermsu committed Nov 28, 2023
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Commits on Dec 15, 2023

  1. Merge pull request #5 from ModelSEED/main 

    Acquiring Chris' Phenotyping Notebooks
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    freiburgermsu committed Dec 15, 2023
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Commits on Dec 20, 2023

  1. parsed out content to dedicated repositories

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    freiburgermsu committed Dec 20, 2023
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Commits on Dec 22, 2023

  1. remove AuroraGPT content

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    freiburgermsu committed Dec 22, 2023
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Commits on Dec 23, 2023

  1. AuroraGPT data and Notebooks

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    freiburgermsu committed Dec 23, 2023
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  2. relocating living projects

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    freiburgermsu committed Dec 23, 2023
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