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:
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 and projects that use xolotl
- Regulation of Eag by Ca2+/calmodulin controls presynaptic excitability in Drosophila
- Homeostatic plasticity rules that compensate for cell size are susceptible to channel deletion
- NBIO140 Lab 5 Lab for NBIO140 taught by Steven van Hooser
- BlackBoxNeuron Neuron simulator designed for teaching and undergraduate research. Used for the Brandeis QBREC program
- Core Course in Integrative Biosciences (BIMS 6000)