xolotl
A MATLAB neuron simulator. Very fast (written in C++). Flexible (fully object oriented). Immediate (live manipulation in MATLAB). Comes with a powerful parameter optimizer. Get started ➡️
Science Score: 67.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 6 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org, frontiersin.org -
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○Scientific vocabulary similarity
Low similarity (13.5%) to scientific vocabulary
Keywords
Repository
A MATLAB neuron simulator. Very fast (written in C++). Flexible (fully object oriented). Immediate (live manipulation in MATLAB). Comes with a powerful parameter optimizer. Get started ➡️
Basic Info
- Host: GitHub
- Owner: sg-s
- License: gpl-3.0
- Language: C++
- Default Branch: master
- Homepage: https://go.brandeis.edu/xolotl
- Size: 20.6 MB
Statistics
- Stars: 46
- Watchers: 6
- Forks: 8
- Open Issues: 0
- Releases: 48
Topics
Metadata Files
README.md
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:
matlab
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)
Owner
- Name: Srinivas Gorur-Shandilya
- Login: sg-s
- Kind: user
- Location: Earth
- Company: @deeporiginbio
- Website: https://srinivas.gs
- Repositories: 173
- Profile: https://github.com/sg-s
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: "Gorur-Shandilya" given-names: "Srinivas" orcid: "https://orcid.org/0000-0002-7429-457X" - family-names: "Hoyland" given-names: "Alec" orcid: "https://orcid.org/0000-0002-4732-5932" title: "xolotl" version: 22.9.1 doi: 10.3389/fninf.2018.00087 date-released: 2018-11-26 url: "https://github.com/sg-s/xolotl"
GitHub Events
Total
- Issues event: 14
- Watch event: 2
Last Year
- Issues event: 14
- Watch event: 2
Dependencies
- mkdocs-material *
- python-markdown-math *
- simplejson *