From c0da206fe4e909f14248a5f096e0ee1e52d4e142 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Mon, 27 May 2024 01:11:36 +0200 Subject: [PATCH] doc: update README.md with protocol change --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 77aab20e..42272682 100644 --- a/README.md +++ b/README.md @@ -10,6 +10,9 @@ The **GECKO** toolbox enhances a **G**enome-scale model to account for **E**nzym 💡 In the [`GECKO/tutorials`](https://github.com/SysBioChalmers/GECKO/tree/main/tutorials) folder there are examples of how GECKO can be applied to GEMs, in either of its _full_ or _light_ forms. Each `protocol.m` contains instructions on how to reconstruct and analyze an ecModel, demonstrating how different fuctions in GECKO can be used. These two scripts complement the [protocols paper](#citation). +### Significant changes since protocol publication +- GECKO 3.2.0: all protein usage reactions draw from the protein pool, even if they are constrained by proteomics data. This affects **Step 58** in the protocol, changing behaviour of `constrainEnzConcs` and making `updateProtPool` obsolete, `tutorials/full_ecModel/protocol.m` is updated to reflect this change. See [#357}(https://github.com/SysBioChalmers/GECKO/issues/375) for more details. + _**Note:** Regarding code and model compatibility with earlier GECKO versions, see [Previous versions: GECKO 1 and 2](https://github.com/SysBioChalmers/GECKO/wiki/Previous-versions:-GECKO-1-and-2)_. ## Cite us