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The nicest neuron simulator out there. Very fast (written in C++). Flexible (fully object oriented). Immediate (live manipulation in MATLAB). Comes with a powerful parameter optimizer. Get started ➡️

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Aug 27, 2018

README.md

xolotl: a fast and flexible neuronal simulator

Documentation Status View xolotl on File Exchange

xolotl is a fast single-compartment and multi-compartment simulator written in C++ with a MATLAB interface that you'll actually enjoy using.

Why use xolotl? This is why:


xolotl is FAST

xolotl is written in C++, and it's fast. In our testing, it's more than 3 times faster than NEURON for single compartment neurons.


xolotl is easy to use

Want to set up a Hodgkin-Huxley model, inject current, integrate it and plot the voltage trace? This is all you need:

x = xolotl;
x.add('compartment', 'HH','A', 0.01);
x.HH.add('liu/NaV', 'gbar', 1000);
x.HH.add('liu/Kd', 'gbar', 300);
x.HH.add('Leak', 'gbar', 1);
x.I_ext = .2;
x.plot;

xolotl has documentation

Unlike certain widely used NEURON simulators that shall remain nameless, xolotl has documentation that actually... exists.

This is what it looks like:


xolotl is fully programmable

xolotl is designed to be used from within MATLAB. It gives you the best of both worlds: the high performance of C++ compiled code with the rich power of all the toolboxes MATLAB has to offer. You can:

  • write functions that pass models as arguments
  • optimize parameters of neuron models using the Global Optimization Toolbox
  • run simulations in parallel across multiple computers
  • have a single script to run the simulation and analyze results

Hooked? Get started here.

Where do I get this?

Click here to download, and click on the downloaded file to install.

How do I cite this?

We've published a technology report in Frontiers in Neuroinformatics.

@ARTICLE{10.3389/fninf.2018.00087,
AUTHOR={Gorur-Shandilya, Srinivas and Hoyland, Alec and Marder, Eve},   
TITLE={Xolotl: An Intuitive and Approachable Neuron and Network Simulator for Research and Teaching},      
JOURNAL={Frontiers in Neuroinformatics},      
VOLUME={12},      
PAGES={87},     
YEAR={2018},      
URL={https://www.frontiersin.org/article/10.3389/fninf.2018.00087},       
DOI={10.3389/fninf.2018.00087},      
ISSN={1662-5196},   
}

Papers that use xolotl

  1. Regulation of Eag by Ca2+/calmodulin controls presynaptic excitability in Drosophila
  2. Homeostatic plasticity rules that compensate for cell size are susceptible to channel deletion
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