wc_env_manager: Tools for managing computing environments for whole-cell modeling

wc_env_manager helps modelers and software developers setup customizable computing environments for developing, testing, and running whole-cell (WC) models and WC modeling software. This makes it easy for modelers and software developers to install and configure the numerous dependencies required for WC modeling. This helps modelers and software developers focus on developing WC models and software tools, rather than on installing, configuring, and maintaining complicated dependencies.

In addition, wc_env_manager facilitates collaboration by helping WC modelers and software developers share a common base computing environment with third party dependencies. Furthermore, wc_env_manager helps software developers anticipate and debug issues in deployment by enabling developers to replicate similar environments to those used to test and deploy WC models and tools in systems such as Amazon EC2, CircleCI, and Heroku.

wc_env_manager uses Docker to setup a customizable computing environment that contains all of the software packages needed to run WC models and WC modeling software. This includes

  • Required non-Python packages
  • Required Python packages from PyPI and other sources
  • WC models and WC modeling tools
  • Optionally, local packages on the user’s machine such as clones of these WC models and WC modeling tools

wc_env_manager supports both the development and deployment of WC models and WC modeling tools:

  • Development: wc_env_manager can run WC models and WC modeling software that is located on the user’s machine. This is useful for testing WC models and WC modeling software before committing it to GitHub.
  • Deployment: wc_env_manager can run WC models and WC modeling software from external sources such as GitHub.

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