Computational Systems Biology

anaconda environments installation

CSB1 used for L1

conda create --name CSB1 -c conda-forge python jupyterlab matplotlib pandas numpy biopython nglview

CSB2 used for all others but L7

conda create --name CSB2 -c conda-forge python jupyterlab matplotlib pandas numpy scipy

CSB3 used for L7

conda create --name CSB3 -c conda-forge python jupyterlab matplotlib pandas numpy=1.23.3 scipy cobra

CSB99 used for L99_with_mn (a wip/abandoned version of L99 final project)

conda create --name CSB99 -c conda-forge python jupyterlab matplotlib pandas numpy scipy manim

possibly need to conda install python=3.13 to install manim

how to run

# cd into respective lab nb directory
conda activate CSB2 # or CSB3 for L07
jupyter lab

conda deactivate # to exit the conda env