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Building containerized computational models

Organize the codebase

1. create / adopt a standardized filesystem layout
2. change code to use relative paths for all input / output file operations
3. ???

Formalize dependencies with Docker and platform-specific tools

For NetLogo, we focus on supporting a Linux / Ubuntu AMD64 build and X11 - also need to check for any external extensions dependencies that should be included inline

For R, first we need to determine what dependencies exist and set packrat to track them.

Using packrat to manage and install R dependencies:

@cpritcha was experiencing issues with packrat not storing a package in the packrat snapshot properly which turned out to be a bug in configuration (the glm package was being ignored).

general finding all dependencies packaging flow:

1. install packrat
2. install devtools
3. install glmmADMB
4. packrat snapshot (@cpritcha can fill in more details here)