/
mkdocs.yml
87 lines (84 loc) · 3.45 KB
/
mkdocs.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
site_name: xolotl
repo_url: https://github.com/sg-s/xolotl/
site_author: Srinivas Gorur-Shandilya
docs_dir: 'docs'
theme:
name: 'material'
logo: 'images/Xlogo.png'
palette:
primary: 'deep-purple'
accent: 'deep-purple'
pages:
- Home: index.md
- Tutorials:
- Getting Started: 'tutorials/start-here.md'
- Demos: 'tutorials/built-in-demos.md'
- Your first neuron: 'tutorials/first-neuron.md'
- Your first network: 'tutorials/first-network.md'
- How to:
- Install and configure: how-to/install-configure.md
- Construct models: how-to/construct-models.md
- Discover existing components: how-to/discover-components.md
- Specify initial conditions: how-to/specify-initial-conditions.md
- Modify existing models: how-to/change-existing-models.md
- Copy a model: how-to/copy-models.md
- Save and load models: how-to/save-load-models.md
- Run simulations: how-to/run-simulations.md
- Inspect conductances and mechanism: how-to/inspect-channels-and-mechanisms.md
- Voltage clamp a compartment: how-to/voltage-clamp.md
- Inject current: how-to/inject-current.md
- Make plots: how-to/make-plots.md
- Save configurations and use snapshots: how-to/snapshots.md
- Make your own components: how-to/make-own-models.md
- Manipulate a model: how-to/manipulate.md
- Create multi-compartment models: how-to/create-multi-compartment-models.md
- Fit a model to arbitrary constraints: how-to/fit-parameters.md
- Run simulations in parallel: how-to/run-simulations-in-parallel.md
- Use stochastic channels: how-to/stochastic-channels.md
- Construct complex self-assembling models: how-to/write-mechanisms-that-self-assemble.md
- Generate a database of models using random search: how-to/database-search.md
- Reference:
- Units: 'reference/units.md'
- C++ classes:
- conductance: 'reference/c++/conductance.md'
- compartment: 'reference/c++/compartment.md'
- synapse: 'reference/c++/synapse.md'
- network: 'reference/c++/network.md'
- mechanism: 'reference/c++/mechanism.md'
- MATLAB:
- conductance: reference/matlab/conductance.md
- xtools: reference/matlab/xtools.md
- xtest: reference/matlab/xtest.md
- xolotl: reference/matlab/xolotl.md
- cpplab: reference/matlab/cpplab.md
- xfit: reference/matlab/xfit.md
- xgrid: reference/matlab/xgrid.md
- How xolotl works:
- How cpplab binds code: explanation/cpplab.md
- How equations are integrated: explanation/integration.md
- How xolotl transpiles code: explanation/transpile.md
- How xolotl interfaces with its binary: explanation/mex-interface.md
- How hashing works in xolotl and cpplab: explanation/hashing.md
- Performance tips:
- Speed: 'performance/speed.md'
- Memory: 'performance/memory.md'
- Troubleshooting:
- Fixes to common problems: troubleshooting.md
- Meta:
- Development and future: 'meta/future.md'
- Documentation: 'meta/documentation.md'
- Testing: 'meta/testing.md'
- FAQ: 'faq.md'
- Contributing: 'contributing.md'
- Bibliography: 'bibliography.md'
- License: 'license.md'
use_directory_urls: true
markdown_extensions:
- admonition
- mdx_math:
enable_dollar_delimiter: True #for use of inline $..$
- toc:
permalink: true
- codehilite
# Required to load the MathJax javascript for the mdx_math.py
extra_javascript: ['https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS_HTML']