From cd29926c129def879bc4206f674c2283aea4f7ac Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Mon, 6 Mar 2023 00:11:29 +0100 Subject: [PATCH 1/2] Update README.rst --- README.rst | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/README.rst b/README.rst index 4d16e916f..7ea076556 100644 --- a/README.rst +++ b/README.rst @@ -3,12 +3,12 @@ |Current Version| |Tests passing| |Gitter| |Zenodo| -About GECKO +About GECKO 3 ----------- The **GECKO** toolbox is able to enhance a **G**\ enome-scale model to account for **E**\ nzyme **C**\ onstraints, using **K**\ inetics and **O**\ mics. The resulting enzyme-constrained model (**ecModel**) can be used to perform simulations where enzyme allocation is either drawn from a total protein pool, or constrained by measured protein levels from proteomics data. -**Note:** Due to significant refactoring of the code, ecModels generated with GECKO versions 1 or 2 are not compatible with GECKO 3, and *vice versa*. The latest GECKO 2 release is available `here `_, while the ``gecko2`` branch is retained. +**Note:** Regarding code and model compatibility with earlier GECKO versions (before 3.0), see `Notes on GECKO 1 and 2`_. **Citation** @@ -16,8 +16,6 @@ The **GECKO** toolbox is able to enhance a **G**\ enome-scale model to account f - For GECKO release 2, please cite `Domenzain et al. (2022) `_. - For GECKO release 1, please cite `Sánchez et al. (2017) `_. -Last update: 2023-03-05 - Required software ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -65,6 +63,18 @@ Getting started In the GECKO folder, ``protocols.m`` contains instructions on how to reconstruct and analyze an ecModel for *S. cerevisiae*. +Notes on GECKO 1 and 2 +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Due to significant refactoring of the code, GECKO version 3 is generally not backwards compatible with earlier versions. + +- Most notably, GECKO 3 ecModels have a `.ec` structure containing all enzyme and kcat information. +- In addition, enzymes are incorporated as MW/kcat in GECKO 3, while this was 1/kcat in GECKO 1 and 2. +- Most functions in GECKO 3 do not work on ecModels generated with GECKO versions 1 or 2. +- ecModels generated in GECKO 3 do not work with functions from GECKO versions 1 or 2. +- At this moment, there are no Python functions to work with GECKO 3 formatted ecModels. +- The last GECKO 2 release (2.0.3) is available `here `_. +- The ``gecko2`` branch remains available for any potential fixes. + Contributing ------------ @@ -79,3 +89,5 @@ Contributions are always welcome! Please read the `contributing guidelines Date: Mon, 6 Mar 2023 00:14:38 +0100 Subject: [PATCH 2/2] Update README.rst --- README.rst | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/README.rst b/README.rst index 7ea076556..df6317904 100644 --- a/README.rst +++ b/README.rst @@ -8,7 +8,7 @@ About GECKO 3 The **GECKO** toolbox is able to enhance a **G**\ enome-scale model to account for **E**\ nzyme **C**\ onstraints, using **K**\ inetics and **O**\ mics. The resulting enzyme-constrained model (**ecModel**) can be used to perform simulations where enzyme allocation is either drawn from a total protein pool, or constrained by measured protein levels from proteomics data. -**Note:** Regarding code and model compatibility with earlier GECKO versions (before 3.0), see `Notes on GECKO 1 and 2`_. +**Note:** Regarding code and model compatibility with earlier GECKO versions, see `GECKO 1 and 2`_. **Citation** @@ -65,10 +65,11 @@ In the GECKO folder, ``protocols.m`` contains instructions on how to reconstruct Notes on GECKO 1 and 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Due to significant refactoring of the code, GECKO version 3 is generally not backwards compatible with earlier versions. +Due to significant refactoring of the code, GECKO version 3 is generally not backwards compatible with earlier GECKO versions. -- Most notably, GECKO 3 ecModels have a `.ec` structure containing all enzyme and kcat information. -- In addition, enzymes are incorporated as MW/kcat in GECKO 3, while this was 1/kcat in GECKO 1 and 2. +- Most notably, GECKO 3 ecModels have an `.ec` structure containing all enzyme and kcat information. +- In addition, in GECKO 3 enzymes are incorporated in the S-matrix as MW/kcat, while in GECKO 1 and 2 this was 1/kcat (where the MW was instead considered in the protein exchange reactions). +- GECKO 3 ecModels can be stored in YAML file format that retains all model content. - Most functions in GECKO 3 do not work on ecModels generated with GECKO versions 1 or 2. - ecModels generated in GECKO 3 do not work with functions from GECKO versions 1 or 2. - At this moment, there are no Python functions to work with GECKO 3 formatted ecModels. @@ -89,5 +90,3 @@ Contributions are always welcome! Please read the `contributing guidelines