Tools for managing computing environments for WC modeling
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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 eliminates the need for each modeler and software developer 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 and maintaining complicated dependencies.

In addition, wc_env_manager facilitates collaboration by helping WC modelers and software developers share a common computing environment. Furthermore, wc_env_manager helps software developers anticipate and debug issues in deployment by enabling developers to replicate the same environment 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 customizable computing environments 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 two modes:

  • 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.

Installation and usage

Please see the documentation.

Documentation

Please see the API documentation.

License

The package is released under the MIT license.

Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York, USA.

Questions and comments

Please contact the Karr Lab with any questions or comments.