Gareth Kennedy

data scientist and mathematical modeller

 

MECSim tools


Below are some general software tools that can be used with MECSim or to do post-simulation analysis. The software required to run these tools is compatible with windows, linux and mac.

Jupyter notebooks

Here jupyter (iPython) notebooks are used to perform various useful functions around MECSim. For example generating square waves (which MECSim can't simulate) using a Fourier transform composed of sinusoids (which MECSim can simulate). Another common use for these notebooks is for post-simulation visualisation both for single simulations and for parameter searches (using scripts).

For each tool three programs are given the py code (zipped for download) which can be used inside the scripts automatically, the jupyter notebooks (ipynb) which allow interactive running of the python code and the html for the web browser friendly output of the notebook.

Note that these programs (ipynb or py) will need numpy and matplotlib installed. To run the ipynb notebooks you'll need jupyter installed as well.

Name Download Description
MECSimPlotter html, ipynb,
zip (py)
MECSim output file plotter which outputs two image files; one of the current against voltage and one for current against time. Outputs to PNG, PS and PDF in a scientific paper friendly format.
MECSimTVCPlotter html, ipynb,
zip (py)
MECSim TVC output file plotter plots the time, voltage, concentration (at electrode surface) file MECSim uses when put into debug mode. Also plots the concentrations against distance from the electrode surface for the final timestep. Outputs each concentrations against time in PNG, PS and PDF image files.
SquareWaveGen html, ipynb,
zip (py)
Square wave generator which outputs ac sinusoids that can be used by MECSim after being copy/pasted into "Master.inp"
TwoParaPlotter html, ipynb,
zip (py)
Plot the results for a two parameter sweep using MECSim. Takes the "results.txt" file made by the two parameter bash script given below.
MECSim_EditEapp html, ipynb,
zip (py)
Set a custom applied potential. Takes an existing MECSim output file (for time range) and overwrites the applied potential with a user defined function, this is written to the text file "EInput.txt". To make MECSim use this input file the advanced ramp setting should be set to 2.

Converters

Conversion software for going from DigiSim to DigiPot format are available here. Note that the DigiPot format is the same format as option 1 in the "output file type" line in the MECSim input file.

Bayesian statistics package

For those at Monash the password protected zip files can be found here.

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