Controlling and measuring dynamic odorant stimuli

This repository contains code to go along with the paper

Controlling and measuring dynamic odorant stimuli in the laboratory

by Srinivas Gorur-Shandilya, Carlotta Martelli, Mahmut Demir and Thierry Emonet.

Contents

Code to reproduce papers in figure

Code to reproduce the primary figures in the paper is contained in the paper-figures/ folder. Once you have downloaded all the code and data (see below), you can run each script to make the figure as it appears in the paper.

For example,

fig_calibration

will generate Figure 3 in the paper.

Code to tune PID parameters of your Alicat MFC

A toolbox to talk to your Alicat MFC and automatically tune PID values is included in this repository. Click here for a quick overview on this.

A simple model of odorant puffs, with sliders to manipulate parameters

In our paper, we described a simple model that can reproduce the rich kinetics observed in identically delivered odorant stimuli. To get a feel for the model, you can interact with the model and manipulate sliders that are linked to every parameter in the model. The interactive demo looks something like this:

To start this, run the puff_explorer.m script in the puff-model folder.

natStimBuilder

natStimBuilder is a class that will help you iteratively tune control signals to match some desired stimulus statistics, as in Figure 3.

It's in the src folder.

Data

To make it possible to reproduce some of the figures in the paper, we have included data that went into these figures. You will have to manually download it.

Download data here

Installation

Prequisities

0. MATLAB
1. mtools (Helper functions)
2. data-manager (To link data)
3. puppeteer (For interactive manipulation of models)

Get the code

If you're using git, you can

git clone https://github.com/sg-s/srinivas.gs_mtools/
git clone https://github.com/sg-s/data-manager
git clone https://github.com/sg-s/puppeteer
git clone https://github.com/emonetlab/controlling-dynamic-stimuli

to get all code and dependencies.

Tell MATLAB where the data is

Navigate to the folder where you data is, and use dataManager to link the data. What dataManager does is search these files, hashes them, and builds a hash table that maps hashes to paths. That way, the scripts you want to run can request a certain piece of data, and dataManager can serve that up, and the primary script doesn't have to know where the data is.

cd /path/to/where/you/downloaded/data
dm = dataManager;
dm.rehash

Usage

Reproduce figures from the paper

Bugs? Issues?

Open an issue here

License

GPL v3