xolotl: a fast and flexible neuronal simulator

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:

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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.

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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;

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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:

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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

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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 and projects 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
3. NBIO140 Lab 5 Lab for NBIO140 taught by Steven van Hooser
4. BlackBoxNeuron Neuron simulator designed for teaching and undergraduate research. Used for the Brandeis QBREC program
5. Core Course in Integrative Biosciences (BIMS 6000)