From 975a27b23102526332f326a4fa7ce83d82d9d82c Mon Sep 17 00:00:00 2001 From: Benjamin Sanchez Date: Fri, 17 Jul 2020 12:13:16 +0200 Subject: [PATCH 1/2] doc: visualization instructions caffeine & metabolic atlas --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 09b59b15..afb2fdac 100644 --- a/README.md +++ b/README.md @@ -63,6 +63,11 @@ Make sure to load/save the model with the corresponding wrapper functions! io.write_yeast_model(model) # saving ``` +### Online Visualization/Simulation + +* You can visualize selected pathways of yeast-GEM and perform online constraint-based simulations using [Caffeine](https://caffeine.dd-decaf.eu/interactive-map), by creating a simulation with the latest yeast-GEM version available, and choosing any _S. cerevisiae_ map (currently only `iMM904` maps are available). Learn more about Caffeine [here](https://caffeine.dd-decaf.eu). +* Additionally, you can visualize 3D representations of all compartments and subsystems of yeast-GEM at [Metabolic Atlas](https://metabolicatlas.org/explore/map-viewer/yeast8). Learn more about Metabolic Atlas [here](https://www.metabolicatlas.org/documentation). + ## Model Files The model is available in `.xml`, `.txt`, `.yml`, `.mat` and `.xlsx` (the last 2 extensions only in `master`). Additionally, the following 2 files are available: From 9979fcd6b81bedb100f74b0e8fa9e0cf5c500a7a Mon Sep 17 00:00:00 2001 From: Benjamin Sanchez Date: Fri, 17 Jul 2020 15:11:51 +0200 Subject: [PATCH 2/2] doc: correct metabolic atlas links + some styling options --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index afb2fdac..c04910b0 100644 --- a/README.md +++ b/README.md @@ -65,8 +65,8 @@ Make sure to load/save the model with the corresponding wrapper functions! ### Online Visualization/Simulation -* You can visualize selected pathways of yeast-GEM and perform online constraint-based simulations using [Caffeine](https://caffeine.dd-decaf.eu/interactive-map), by creating a simulation with the latest yeast-GEM version available, and choosing any _S. cerevisiae_ map (currently only `iMM904` maps are available). Learn more about Caffeine [here](https://caffeine.dd-decaf.eu). -* Additionally, you can visualize 3D representations of all compartments and subsystems of yeast-GEM at [Metabolic Atlas](https://metabolicatlas.org/explore/map-viewer/yeast8). Learn more about Metabolic Atlas [here](https://www.metabolicatlas.org/documentation). +* You can visualize selected pathways of yeast-GEM and perform online constraint-based simulations using [Caffeine](https://caffeine.dd-decaf.eu/interactive-map), by creating a simulation with the latest yeast-GEM version available, and choosing any _S. cerevisiae_ map (currently only `iMM904` maps are available). Learn more [about Caffeine](https://caffeine.dd-decaf.eu). +* Additionally, you can interactively navigate model components and visualize 3D representations of all compartments and subsystems of yeast-GEM at [Metabolic Atlas](https://metabolicatlas.org/explore?selected=Yeast-GEM). Learn more [about Metabolic Atlas](https://www.metabolicatlas.org/about). ## Model Files