BioSimulator Processes

Core implementations of process-bigraph.composite.Process() aligning with BioSimulators simulation tools. A complete environment with version-controlled dependencies already installed is available as a Docker container on GHCR.

Installation

There are two primary methods of interaction with biosimulator-processes:

A container available on ghcr:

1. Ensure that the Docker Daemon is running. Most users do this by opening the Docker Desktop application.

2. Pull the image from ghcr.io:

     docker pull ghcr.io/vivarium-collective/biosimulator-processes:latest
   

3. If there are any "dangling" or already-running jupyter servers running on your machine, the docker run command will not properly work. Run the following and close any servers already running, if necessary:

     jupyter server list && jupyter server stop
   

4. Run the image, ensuring that the running of the container is platform-agnostic:

     docker run --platform linux/amd64 -it -p 8888:8888 ghcr.io/vivarium-collective/biosimulator-processes:latest
   

MAC USERS: Please note that an update of XCode may be required for this to work on your machine.

As an alternative, there is a helper script that does this docker work and more. To use this script:

  1. Add the appropriate permissions to the file:
        
           chmod +x ./scripts/run-docker.sh

  2. Run the script:

           ./scripts/run-docker.sh

The Python Package Index. You may download BioSimulator Processes with:

     pip install biosimulator-processes

We recommend using an environment/package manager like Conda if downloading from PyPI to install the dependencies required for your use. Most of the direct UI content for this tooling will be in the form of a jupyter notebook. The installation for this notebook is provided below.

Using biosimulator_processes.smoldyn_process.SmoldynProcess():

Mac Users PLEASE NOTE:

Amici

You most likely have to install/update swig with brew, among other possible requirements. Please refer to the Amici Python Installation Documentation for more information.

Smoldyn

Due to the multi-lingual nature of Smoldyn, which is primarily developed in C++, the installation process for utilizing the SmoldynProcess process implementation requires separate handling. This is particularly relevant for macOS and Windows users, where setting up the Python bindings can be more complex.

For your convienience, we have created an installation shell script that will install the correct distribution of Smoldyn based on your Mac processor along with the codebase of this repo. To install Smoldyn and this repo on your Mac, please adhere to the following instructions:

1. Clone this repo from Github:

    git clone https://github.com/biosimulators/biosimulator-processes.git
   

2. Provide adminstrative access to the scripts directory within the cloned repo:

    cd biosimulator-processes
   

3. Look for the install-with-smoldyn-for-mac- shell script where corresponds to your machine's processor:

    ls scripts | grep <YOUR MAC PROCESSOR>
    chmod +x ./scripts/install-with-smoldyn-for-mac-<YOUR MAC PROCESSOR>
   

4. Run the appropriate shell script (for example, using mac silicon):

    scripts/install-with-smoldyn-for-mac-silicon.sh
   

Quick Start Example:

TODO: copy this from the prompter demo

A NOTE FOR DEVELOPERS:

This tooling implements version control for dynamically-created composite containers through poetry. The version control for content on the Python Package Index is performed by setup.py. Also, the PyTest configuration resides within ./pyproject.toml at the root of this repository.