Merge pull request #218 from rasools/OMICSINT_H24

Update toplogy lab
NBISweden · Oct 9, 2024 · a2b336c · a2b336c
2 parents fa68dcf + 37ea333
commit a2b336c
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 0 deletions.
diff --git a/session_gems/lab/08-Predict-gene-knockout-strategies.ipynb b/session_gems/lab/08-Predict-gene-knockout-strategies.ipynb
@@ -99,6 +99,10 @@
     }
    ],
    "source": [
+    "ppp = phenotypic_phase_plane(model,\n",
+    "                             variables=[model.reactions.BIOMASS_Ecoli_core_w_GAM],\n",
+    "                             objective=model.reactions.EX_succ_e)\n",
+    "\n",
     "df = ppp.data_frame\n",
     "\n",
     "# Plot BIOMASS vs Objective (EX_succ_e)\n",

diff --git a/session_topology/Dockerfile b/session_topology/Dockerfile
@@ -44,6 +44,14 @@ RUN /opt/conda/envs/igraph/bin/pip install ipykernel && \
 RUN /opt/conda/envs/gseapy/bin/pip install ipykernel && \
     /opt/conda/envs/gseapy/bin/python -m ipykernel install --name gseapy --display-name "Python (gseapy)"
 
+# Create a data directory
+RUN mkdir -p /home/jovyan/lab/data
+# Install git to clone the repository
+RUN apt-get update && apt-get install -y git && \
+    git clone https://github.com/NBISweden/workshop_omics_integration.git /tmp/repo && \
+    cp -r /tmp/repo/session_topology/lab/data/* /home/jovyan/lab/data/ && \
+    rm -rf /tmp/repo
+
 # Fix permissions and make the script executable
 RUN chown -R jovyan:users /opt/conda /home/jovyan/.cache /home/jovyan/lab && \
     chmod -R a+rwx /home/jovyan/lab && \