sbrg/cobrame repository overview

⁠COBRAme, ECOLIme, and qMINOS using Docker

Builds of the latest versions of COBRAme and ECOLIme_ can be found on Docker Hub. This build also includes a compiled version of the qMINOS solver that can be used to solve ME-models using solvemepy_.

The Docker image initializes in the /home/meuser directory which contains a json and pickle of iJL1678b in the /home/meuser/me_models directory which were created from running build_me_model.py while building the Docker image.

Also contained in the /home/meuser directory is solve_demo.ipynb containing an example of how to load and solve ME-models in a jupyter notebook (instructions below).

The installed COBRAme and ECOLIme packages can be found in /source/.

Docker is cross-platform and allows Windows, Mac and Linux users to run ME-models without going through the process of installing each solver and dependency locally.

⁠Installation

To run a Docker container with everything required to build and solve the iJL1678b model of E. coli K-12 MG1655 using qMINOS:

1. Install Docker (https://docs.docker.com/install/⁠)
2. Pull the latest image from DockerHub with docker pull sbrg/cobrame:master
3. In the command line, run docker run -p 8888:8888 --rm -i -v $(pwd):/mount_point/ -t sbrg/cobrame:master bash.

This will initiate a Docker container (virtual machine) into the /home/meuser directory and mount the contents of the directory where the command was ran into the docker container at /mount_point/.

1. To start a jupyter notebook, run jupyter notebook --ip=0.0.0.0 --port=8888. Point the browser to localhost:8888 and input the provided token to access notebook.

⁠Building Docker image locally w/ SoPlex

To build a Docker image that can solve ME-models with SoPlex as well as qMINOS

1. Install Docker (https://docs.docker.com/install/⁠)
2. Download SoPlex version 3.1.1 (http://soplex.zib.de/#download⁠)
3. cp soplex-3.1.1.tgz [cobrame root]/docker
4. cd [cobrame root]/docker
5. docker build -t [repository:tag name] .

where the [repository:tag name] can be decided by the user

1. To run the Docker image, docker run -p 8888:8888 --rm -i -v $(pwd):/mount_point/ -t [repository:tag name] bash

This will initialize a Docker container with everything required to use ME-models and to solve them using qMINOS and SoPlex.

.. _ECOLIme: https://github.com/SBRG/ECOLIme⁠ .. _ZIB: http://soplex.zib.de/⁠ .. _soplex_cython: https://github.com/SBRG/soplex_cython⁠ .. _solvemepy: https://github.com/SBRG/solvemepy⁠ .. _COBRApy: https://github.com/opencobra/cobrapy⁠