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Whole Cell Model of E. coli

These are the docs for a variety of topics on the Whole Cell Model.

setup

There are two alternative ways to set up to run the model.

Building a Docker Container Image takes one step -- one shell script. The Container will be isolated from your computer's operating system, versions of Python, binary libraries, and everything else installed on your development computer.

Building a pyenv virtual environment takes a lot of installation steps that depend on what's already installed. The result is isolated from other Python virtual environments but the binary libraries might impact the rest of your computer. On the other hand, this lets you edit, run, and debug without the complications of Docker mechanics.

  • Docker setup

    Install the Docker Desktop software.

    On Windows: To use Docker on Windows, do it within Windows Subsystem for Linux 2 (WSL2) which is a real Linux kernel that behaves the same as other Linux environments. Don't try to use VirtualBox.

    NOTE: Open Docker's Advanced Preferences and increase the memory allocation to 4GB. (The default allocation is 2GB which would make the model's Python code run out of memory, print "Killed", and stop with exit code 137.)

    Build and run the Docker Container Image locally like this:

    cloud/build-containers-locally.sh
docker run --name=wcm -it --rm wcm-code

    Or build a Docker Image using a Google Cloud Build server, pull the Image from the Google Cloud Package Registry, and run it locally (to do this you'll need to set up the Google Cloud project):

    cloud/build.sh
docker pull gcr.io/${PROJECT}/${USER}-wcm-code
docker run --name=wcm -it --rm gcr.io/${PROJECT}/${USER}-wcm-code

    NOTE: It's better to build the Docker Image on Linux (e.g. in Google Cloud Build or WSL2) than on macOS where build-containers-locally.sh has to work around a Docker bug by disabling AVX2 instructions in OpenBLAS. That change somehow makes the computation produce different results and run a little slower. An Image built on Linux won't have the AVX2 workaround and yet it runs fine on macOS. See xianyi/OpenBLAS#2244.

    Once you have a Docker Image, you can run the model's Python programs inside the Container. (PyCharm Pro should support debugging into a Docker Container but we haven't tested that.)

    After changing the model's source code in the wcEcoli/ directory, building an updated wcm-code Container Image via Google Cloud Build takes only a few minutes:

    cloud/build-wcm.sh

    TIP: To preserve the model's output files after the Container exits, bind its output directory /wcEcoli/out to a host directory like out/ by adding the option -v $PWD/out:/wcEcoli/out, where $PWD is the path to your cloned repo in the host computer.

    NOTE: -v needs absolute paths!

    You can share the entire /wcEcoli directory to also substitute the model's code inside the Container with the code in your host wcEcoli directory by changing that option to -v $PWD:/wcEcoli.

    TIP: When running in Docker on Linux or WSL2, the Container's output files will have the wrong host user and group ownership. You can change that by adding the --user "$(id -u):$(id -g)" option to the docker run command. That runs the process inside the Container as your host computer user and group so the files will be owned by you, but it adds other complications since it runs inside the Container without ownership of the existing files and directories.

  • pyenv setup

    1. Required development tools to install the development tools including pyenv, gcc, make, and git, then

    2. Creating the "pyenv" runtime environment to set up the Python runtime virtual environment for the model including binary libraries and Python packages. pyenv virtual environments take more steps to build and depend on your computer's OS, but are lighter weight to run and easier for debugging.

    You can then run the model with this version of Python.

    If you have Anaconda installed, you might have to take Anaconda off the $PATH temporarily to run the Whole Cell Model.

    This approach takes a bunch of steps that vary depending on your operating system. It will run ≈25% faster than inside a Container and works with any Python debugger.

    See:

  • Also

    After setting up the environment, copy the git hooks from the repo (see git hooks) to your .git directory to maintain an up to date environment while doing development:

    cp runscripts/git_hooks/*[^.md] .git/hooks/

running

development

relevant papers

dissertations

  • Computational Simulations of Whole Cells: Strategies for Framework Design and Model Parameterization, John Mason
  • Development and Application of Whole-Cell Computational Models for Science and Engineering, Jonathan Ross Karr
  • Toward a Whole-Cell Model of Escherichia coli, Derek Macklin
  • Towards a Whole-Cell Model of Growth Rate and Cell Size Control in Escherichia coli, Nicholas Ruggero
  • Transcriptional Regulation in Escherichia coli: A Systems Biology Approach, Markus Covert