From 37ea333feb9fcaadde3a46fb9ff1f51056bebb52 Mon Sep 17 00:00:00 2001 From: Rasool Saghaleyni Date: Wed, 9 Oct 2024 09:33:28 +0200 Subject: [PATCH] Update toplogy lab --- .../lab/08-Predict-gene-knockout-strategies.ipynb | 4 ++++ session_topology/Dockerfile | 8 ++++++++ 2 files changed, 12 insertions(+) diff --git a/session_gems/lab/08-Predict-gene-knockout-strategies.ipynb b/session_gems/lab/08-Predict-gene-knockout-strategies.ipynb index 481f467..e85fc50 100644 --- 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 index cdd6ec6..8d4613d 100644 --- 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 && \