Stoma Simulator

Biomechanical simulations of plant stomata.

The following instructions have been tested on macOS 10.12.5.

Python environment

To run the StomaSimulator software you will need Python 2.7. You will also need to install the project's dependencies.

The following instructions use Miniconda although a Python "virtual environment" could be used instead. Install Miniconda by downloading and running the installer. To setup the environment issue the following commands:

conda create -n stomaenv --yes python=2.7       # create Python 2.7 environment
source activate stomaenv                        # activate env.

Set up stomasimulator

Clone this repository (if you haven't already) and 'cd' into its directory Run the following to setup stomasimulator:

conda install --file requirements.txt --yes     # install dependencies
python setup.py install                         # to install stomasimulator

To uninstall stomasimulator remove the miniconda environment using

conda remove -n stomaenv --all --yes

Finite element software

This step is only required if you are going to rerun the simulations.

Download and install the FEBio finite element software (v2.3.0 was used).

Update the path to the executable in the stomasimulator.yml file at the top level of the stomasimulator package. You will have to run python setup.py install again.

See Maas et al. (2012) for details of FEBio.

Running stomasimulator

Activate the environment. Typing stomasimulator -h will show:

$ stomasimulator -h
************************************************************************************************************************
Reading configuration file '<path/to/repo>/stomasimulator/stomasimulator/stomasimulator.yml'...
Finished reading the configuration file

Configuration settings for stomasimulator...
FEBio executable     : <path/to/febio>/FEBio2
Model data directory : <path/to/repo>/stomasimulator/stomasimulator/.cfg
************************************************************************************************************************
usage: stomasimulator <command> [<args>]

The commands are:
  cfg          Output the configuration settings and model labels used by stomasimulator
  feb          Output a FEB file for the specified stoma model (the simulation can be run)
  opt          Optimise the material parameters for a given stoma model
  xplt         Process an XPLT file

Execute functions within the stomata biomechanics suite

positional arguments:
  command     Subcommand to run

optional arguments:
  -h, --help  show this help message and exit

where <path/to/repo> will show your path. These commands each have the -h option to show help.

Display the graphs

The graph plotting assumes you have gnuplot installed.

In a terminal, go to the figures/plotting directory.

Start gnuplot and run the scripts using, for example, call 'plot-fig1.gp'.

Rerun simulations

Rerunning the simulations will take several hours on one machine.

To rerun the simulations, go to the figures/simulations directory.

Run ./create-figures.sh to recreate all of the simulations.