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Update ProtPool Calculation by Including usage_prot_ Reaction Fluxes #372

Merged
merged 12 commits into from
May 8, 2024
Merged

Update ProtPool Calculation by Including usage_prot_ Reaction Fluxes #372

merged 12 commits into from
May 8, 2024

Commits on Jul 17, 2023

  1. Merge pull request SysBioChalmers#340 from SysBioChalmers/develop 

    GECKO 3.1.1
    @edkerk
    edkerk committed Jul 17, 2023
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  2. Create version.txt

    @edkerk
    edkerk committed Jul 17, 2023
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Commits on Dec 2, 2023

  1. Merge pull request SysBioChalmers#358 from SysBioChalmers/develop 

    * fix: loadDatabases check for duplicate protIDs (SysBioChalmers#349)

* fix: prevent NaN in light ecModels (SysBioChalmers#346)

* fix: calculateFfactor if paxDB has taxID !4 chars (SysBioChalmers#347)

* fix: runDLKcat if path has spaces (SysBioChalmers#352)

* refactor: FSEOF (SysBioChalmers#356)

* fix: FSEOF to 0.9 of teorethical max prod

* refactor: switch force objetive to target

* fix: remove unnecesary function

* fix: update input arguments

* fix: temporal solution k-score

* refactor: FSEOF

* feat: add gene essentiality to FSEOF

* fix: file writing

* feat: add cutoff based on quantile

* feat: report target transport reactions

* refactor: add cutoff for essentiality

* fix: bug identifying gene essentiality

* doc: move installations instructions to wiki (SysBioChalmers#357)

* move installation instructions to wiki

* GECKOInstaller checks for latest GECKO version

* fix: prevent duplications in protein pseudometabolites

* minor fixes

* doc: update documentation

* doc: swap gitter for GitHub Discussions

* fix: correct link to upgrade instructions

* fix: synchronize STEP numbers  protocol and paper

---------

Co-authored-by: Albert Tafur Rangel <[email protected]>
    @edkerk @ae-tafur
    edkerk and ae-tafur committed Dec 2, 2023
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  2. Update version.txt

    @edkerk
    edkerk committed Dec 2, 2023
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Commits on Jan 30, 2024

  1. Merge pull request SysBioChalmers#365 from SysBioChalmers/develop 

    GECKO 3.1.3
    @mihai-sysbio
    mihai-sysbio committed Jan 30, 2024
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  2. Update version.txt

    @edkerk
    edkerk committed Jan 30, 2024
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Commits on Apr 18, 2024

  1. Update 'reportEnzymeUsage' to modify the total protein pool by summin… 

    …g up protein pool exchange and proteomics integrated, adjusting 'percUsage' accordingly.
    HossFir committed Apr 18, 2024
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  2. Update 'reportEnzymeUsage' to modify the total protein pool by summin… 

    …g up protein pool exchange and proteomics integrated, adjusting 'percUsage' accordingly.
    HossFir committed Apr 18, 2024
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Commits on Apr 28, 2024

  1. feat: enzymeUsage parses fluxes to output

    @edkerk
    edkerk committed Apr 28, 2024
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  2. feat: reportEnzymeUsage input and output 

    - use fluxes from usageData
- give protein pool in usageReport instead of printing to command window
    @edkerk
    edkerk committed Apr 28, 2024
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  3. delete empty git file

    @edkerk
    edkerk committed Apr 28, 2024
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  4. Delete version.txt

    @edkerk
    edkerk committed Apr 28, 2024
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