karrlab/wc_env repository overview

wc_env is a Docker image which contains several whole-cell (WC) models and the complete wc_cli⁠ suite of WC modeling tools.

⁠Models in wc_env

wc_env contains the following models:

• h1_hesc⁠: model of H1 human embryonic stem cells
• mycoplasma_pneumoniae⁠: model of the small bacterium Mycoplasma pneumoniae
• rand_wc_model_gen⁠: tool for generated random models that represent typical bacteria

⁠WC modeling tools in wc_env

wc_env contains the following WC modeling tools:

• wc_cli⁠: integrated suite of WC models and WC modeling tools
  • kinetic-datanator⁠: tools for discovering, aggregating, and integrating the data needed for WC modeling
  • rand-wc-model-gen⁠: tool for generated random models that represent typical bacteria
  • wc-analysis⁠: tools for analyzing WC models, knowledge bases, and simulation results
  • wc-kb⁠: framework for representing the data needed for building and testing a WC model
  • wc-kb-gen⁠: framework for assembling the data needed for building and testing a WC model
  • wc-lang⁠: reaction network framework for representing WC models
  • wc-model-gen⁠: framework for generating WC models from data
  • wc-rules⁠: rule-based language for representing WC models
  • wc-sim⁠: tool for simulating WC models
  • wc-test⁠: framework for testing WC models
  • wc-utils⁠: utilities for WC modeling

⁠Tutorials in wc_env

wc_env also contains the examples in the An Introduction to Whole-Cell modeling⁠ WC modeling primer.

⁠Design of wc_env

wc_env is based on wc_env_dependencies⁠ which contains the comparatively stable third party dependencies needed for these WC models and WC modeling tools. This enables developers to quickly re-build wc_env with the latest versions of WC models and WC modeling tools without needing to re-build all of the comparatively stable third-party dependencies.

⁠Installing wc_env

1. Install Docker⁠
2. Install wc_env by running the following command

   docker pull karrlab/wc_env
   

   Copy

⁠Updating wc_env

wc_env can be updated by running the following command:

docker pull karrlab/wc_env

⁠Using wc_env

The following command illustrates how to use a container based on wc_env interactively with a bash shell:

docker run --interactive --tty --rm karrlab/wc_env:latest \
    bash

The following command illustrates how to execute a command inside a container based on wc_env:

docker run --tty --rm karrlab/wc_env:latest \
    bash -c "wc model h1-hesc sim"

⁠License

The MIT License (MIT)

Copyright (c) 2017-2018 Karr Lab

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the Software), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

⁠Development team

The images were developed by the Karr Lab⁠ at the Icahn School of Medicine at Mount Sinai in New York.

⁠Questions and comments

Please contact the Karr Lab⁠ with any questions or comments.