dendrotweaks 0.3.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- dendrotweaks/__init__.py +10 -0
- dendrotweaks/analysis/__init__.py +11 -0
- dendrotweaks/analysis/ephys_analysis.py +482 -0
- dendrotweaks/analysis/morphometric_analysis.py +106 -0
- dendrotweaks/membrane/__init__.py +6 -0
- dendrotweaks/membrane/default_mod/AMPA.mod +65 -0
- dendrotweaks/membrane/default_mod/AMPA_NMDA.mod +100 -0
- dendrotweaks/membrane/default_mod/CaDyn.mod +54 -0
- dendrotweaks/membrane/default_mod/GABAa.mod +65 -0
- dendrotweaks/membrane/default_mod/Leak.mod +27 -0
- dendrotweaks/membrane/default_mod/NMDA.mod +72 -0
- dendrotweaks/membrane/default_mod/vecstim.mod +76 -0
- dendrotweaks/membrane/default_templates/NEURON_template.py +354 -0
- dendrotweaks/membrane/default_templates/default.py +73 -0
- dendrotweaks/membrane/default_templates/standard_channel.mod +87 -0
- dendrotweaks/membrane/default_templates/template_jaxley.py +108 -0
- dendrotweaks/membrane/default_templates/template_jaxley_new.py +108 -0
- dendrotweaks/membrane/distributions.py +324 -0
- dendrotweaks/membrane/groups.py +103 -0
- dendrotweaks/membrane/io/__init__.py +11 -0
- dendrotweaks/membrane/io/ast.py +201 -0
- dendrotweaks/membrane/io/code_generators.py +312 -0
- dendrotweaks/membrane/io/converter.py +108 -0
- dendrotweaks/membrane/io/factories.py +144 -0
- dendrotweaks/membrane/io/grammar.py +417 -0
- dendrotweaks/membrane/io/loader.py +90 -0
- dendrotweaks/membrane/io/parser.py +499 -0
- dendrotweaks/membrane/io/reader.py +212 -0
- dendrotweaks/membrane/mechanisms.py +574 -0
- dendrotweaks/model.py +1916 -0
- dendrotweaks/model_io.py +75 -0
- dendrotweaks/morphology/__init__.py +5 -0
- dendrotweaks/morphology/domains.py +100 -0
- dendrotweaks/morphology/io/__init__.py +5 -0
- dendrotweaks/morphology/io/factories.py +212 -0
- dendrotweaks/morphology/io/reader.py +66 -0
- dendrotweaks/morphology/io/validation.py +212 -0
- dendrotweaks/morphology/point_trees.py +681 -0
- dendrotweaks/morphology/reduce/__init__.py +16 -0
- dendrotweaks/morphology/reduce/reduce.py +155 -0
- dendrotweaks/morphology/reduce/reduced_cylinder.py +129 -0
- dendrotweaks/morphology/sec_trees.py +1112 -0
- dendrotweaks/morphology/seg_trees.py +157 -0
- dendrotweaks/morphology/trees.py +567 -0
- dendrotweaks/path_manager.py +261 -0
- dendrotweaks/simulators.py +235 -0
- dendrotweaks/stimuli/__init__.py +3 -0
- dendrotweaks/stimuli/iclamps.py +73 -0
- dendrotweaks/stimuli/populations.py +265 -0
- dendrotweaks/stimuli/synapses.py +203 -0
- dendrotweaks/utils.py +239 -0
- dendrotweaks-0.3.1.dist-info/METADATA +70 -0
- dendrotweaks-0.3.1.dist-info/RECORD +56 -0
- dendrotweaks-0.3.1.dist-info/WHEEL +5 -0
- dendrotweaks-0.3.1.dist-info/licenses/LICENSE +674 -0
- dendrotweaks-0.3.1.dist-info/top_level.txt +1 -0
@@ -0,0 +1,70 @@
|
|
1
|
+
Metadata-Version: 2.4
|
2
|
+
Name: dendrotweaks
|
3
|
+
Version: 0.3.1
|
4
|
+
Summary: A toolbox for exploring dendritic dynamics
|
5
|
+
Home-page: https://dendrotweaks.dendrites.gr
|
6
|
+
Author: Roman Makarov
|
7
|
+
Author-email: dendrotweaks@dendrites.gr
|
8
|
+
License: GNU General Public License v3.0
|
9
|
+
Project-URL: Source, https://github.com/Poirazi-Lab/DendroTweaks
|
10
|
+
Project-URL: Documentation, https://dendrotweaks.readthedocs.io/
|
11
|
+
Keywords: dendrites,neuron,model,simulation,neuroscience
|
12
|
+
Classifier: Programming Language :: Python :: 3
|
13
|
+
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
|
14
|
+
Classifier: Operating System :: OS Independent
|
15
|
+
Requires-Python: >=3.9
|
16
|
+
Description-Content-Type: text/markdown
|
17
|
+
License-File: LICENSE
|
18
|
+
Requires-Dist: neuron>=8.2.6
|
19
|
+
Requires-Dist: neuron-reduce==0.0.7
|
20
|
+
Requires-Dist: numpy<2.0.0
|
21
|
+
Requires-Dist: pandas
|
22
|
+
Requires-Dist: pyparsing
|
23
|
+
Requires-Dist: symfit
|
24
|
+
Requires-Dist: matplotlib
|
25
|
+
Requires-Dist: scipy
|
26
|
+
Requires-Dist: jinja2
|
27
|
+
Requires-Dist: quantities
|
28
|
+
Provides-Extra: dev
|
29
|
+
Requires-Dist: sphinx; extra == "dev"
|
30
|
+
Requires-Dist: furo; extra == "dev"
|
31
|
+
Requires-Dist: sphinx-copybutton; extra == "dev"
|
32
|
+
Requires-Dist: build; extra == "dev"
|
33
|
+
Dynamic: license-file
|
34
|
+
|
35
|
+
# DendroTweaks
|
36
|
+
|
37
|
+
<img src="https://dendrotweaks.readthedocs.io/en/latest/_static/logo.png" width="25%">
|
38
|
+
<p>
|
39
|
+
|
40
|
+
**DendroTweaks** is a Python toolbox designed for creating and validating single-cell biophysical models with active dendrites.
|
41
|
+
|
42
|
+
It is available both as a standalone Python package and a web-based application.
|
43
|
+
|
44
|
+
## Learn More
|
45
|
+
|
46
|
+
- **Standalone Library**: Explore the [official documentation](https://dendrotweaks.readthedocs.io/en/latest/index.html) for detailed tutorials and API reference.
|
47
|
+
- **Web Application**: Access the GUI online via our platform at [dendrotweaks.dendrites.gr](https://dendrotweaks.dendrites.gr).
|
48
|
+
- **Quick Overview**: Check out our [e-poster](https://doi.org/10.57736/abba-7149), including a video demonstration, presented at the FENS Forum 2024 in Vienna.
|
49
|
+
|
50
|
+
## Publication
|
51
|
+
|
52
|
+
For an in-depth understanding of DendroTweaks, refer to our publication in *eLife*:
|
53
|
+
|
54
|
+
> Roman Makarov, Spyridon Chavlis, Panayiota Poirazi (2024).
|
55
|
+
> *DendroTweaks: An interactive approach for unraveling dendritic dynamics.*
|
56
|
+
> eLife 13:RP103324. [https://doi.org/10.7554/eLife.103324.1](https://doi.org/10.7554/eLife.103324.1)
|
57
|
+
|
58
|
+
If you find DendroTweaks helpful for your research, please consider citing our work:
|
59
|
+
|
60
|
+
```bibtex
|
61
|
+
@article{Makarov2024,
|
62
|
+
title={DendroTweaks: An interactive approach for unraveling dendritic dynamics},
|
63
|
+
author={Makarov, Roman and Chavlis, Spyridon and Poirazi, Panayiota},
|
64
|
+
journal={eLife},
|
65
|
+
volume={13},
|
66
|
+
pages={RP103324},
|
67
|
+
year={2024},
|
68
|
+
doi={10.7554/eLife.103324.1}
|
69
|
+
}
|
70
|
+
```
|
@@ -0,0 +1,56 @@
|
|
1
|
+
dendrotweaks/__init__.py,sha256=Oty4wVcVFs_9w7L9peCncnzQKFubqkRHyf4c3HKfwWY,385
|
2
|
+
dendrotweaks/model.py,sha256=wy17K85d95bD1ioibhDxs8rcNCzow3BP1OVam1b1bTM,67445
|
3
|
+
dendrotweaks/model_io.py,sha256=xwXKMcUle-Y0HoWFYVZu3G8v4pdQXmeaDfl2Xi65eHw,2137
|
4
|
+
dendrotweaks/path_manager.py,sha256=SfZ7Br-WmUhpvdRTgeOqMzaYVgLpXoSGbekxJvNkZT4,8794
|
5
|
+
dendrotweaks/simulators.py,sha256=cVbzbhE48D1ovn7Rg8bU0pI9ztbEqQF2da5gnEMu8Ec,6137
|
6
|
+
dendrotweaks/utils.py,sha256=jaUJNb39Bsevg3WJByP56bO7CLj1wzlh-uGZl-lxi1I,7131
|
7
|
+
dendrotweaks/analysis/__init__.py,sha256=SEYpoQ5iXiQXyHB20-IAdDHYI-7CR5GYFXIwr-O05Ug,858
|
8
|
+
dendrotweaks/analysis/ephys_analysis.py,sha256=oXRjad34tKMDiqEO11uZibHpe2auB2GCetcgd2rVP-o,14124
|
9
|
+
dendrotweaks/analysis/morphometric_analysis.py,sha256=5zohjGssyx-wezI-yY3Q-kYM_wzAQLLFBJ9Xk950_JY,3571
|
10
|
+
dendrotweaks/membrane/__init__.py,sha256=H3KsbVQonC1BKBnuchAIxGXj5Zl-xN3egOanVUkgs-o,322
|
11
|
+
dendrotweaks/membrane/distributions.py,sha256=ADPFPA-CN7AbRJj0Ry4TxFZJhdYXJm87iIGWZSDr5vI,10299
|
12
|
+
dendrotweaks/membrane/groups.py,sha256=qN4Q-YodXVLmpGRYvWlZ7Kd9gVnLSK1l4g2Qc0T8dYs,3483
|
13
|
+
dendrotweaks/membrane/mechanisms.py,sha256=F4b6VqI3IjyoOQ6GAFvcy7er5-BFCca8JFnQB_HmjmI,18352
|
14
|
+
dendrotweaks/membrane/default_mod/AMPA.mod,sha256=HY_pWzYvaSDV-w7qruenG2mnll8v79s40HFHjUCIi4U,980
|
15
|
+
dendrotweaks/membrane/default_mod/AMPA_NMDA.mod,sha256=ztv2ePUiEQZ93-23FTkGO2DC91rehQuqo0NUIbHZ368,2318
|
16
|
+
dendrotweaks/membrane/default_mod/CaDyn.mod,sha256=gwc69K_rxu2w_mV7CnOSOnVaCMc8Z-MfdBFf6lAj4kg,1298
|
17
|
+
dendrotweaks/membrane/default_mod/GABAa.mod,sha256=jdGRid-Wzw4y9kHvq74oSMogLhSiS-Ac2DDaLOrxVi8,983
|
18
|
+
dendrotweaks/membrane/default_mod/Leak.mod,sha256=u0lwMYGgl5kNZN5W4N6YHgRSeVxb-z2oM9fqou5rCV8,420
|
19
|
+
dendrotweaks/membrane/default_mod/NMDA.mod,sha256=tT4Q5UPoeztXcQ45uZc2PUO3-8OkDLCmrS7WDsn1yQQ,1185
|
20
|
+
dendrotweaks/membrane/default_mod/vecstim.mod,sha256=iSpJgR96O2Z3pLNUFIsZ7YJ529ncKUBaZqDJvA0_oV0,965
|
21
|
+
dendrotweaks/membrane/default_templates/NEURON_template.py,sha256=BlvA48B48f0AyiepXmrOmGJL5Xe5XDshG9w6h5gDEEs,14874
|
22
|
+
dendrotweaks/membrane/default_templates/default.py,sha256=vDxND86RJEw7XHajkg5P0vM2Oss5dyW5m_ugLMeCbT0,2145
|
23
|
+
dendrotweaks/membrane/default_templates/standard_channel.mod,sha256=Jpu2rxldAE6kxaylIlPc80F5wpKETodpOvoMbFXhWTA,2861
|
24
|
+
dendrotweaks/membrane/default_templates/template_jaxley.py,sha256=t-GsCSUyQ7rDoaLmyuWd9bIxB8W3bCqJdnikD59EVvI,3676
|
25
|
+
dendrotweaks/membrane/default_templates/template_jaxley_new.py,sha256=I62KhnOYNV1bT-nPsDTxjIISYmDcso2X8rnsos28nYs,3631
|
26
|
+
dendrotweaks/membrane/io/__init__.py,sha256=r84iLBrdmCgGP-dG9iaamBHUGldtAgPyqSujU-3U8ik,584
|
27
|
+
dendrotweaks/membrane/io/ast.py,sha256=wnJNy2ga1DsZWQ1lpp1QhK2jvM4aDph7u_27VmyJcXw,5894
|
28
|
+
dendrotweaks/membrane/io/code_generators.py,sha256=jhyjvTisV-tavz_yuQ-tOa3JJ56UNUk_pkN9xS6GEqQ,11407
|
29
|
+
dendrotweaks/membrane/io/converter.py,sha256=vNCKDk0JqdoqxMWGi2AxT-TZ2YS2itUc7bpm9pRX-6o,3374
|
30
|
+
dendrotweaks/membrane/io/factories.py,sha256=rCfZiubZPmikB8nxfjh3Dzg4ZHUXgZX79kmJZDLovwI,4979
|
31
|
+
dendrotweaks/membrane/io/grammar.py,sha256=TJLTDlr8Ajp3J9DJ4IvulOCcpUkYr7HnoI0TGnNuEPc,11677
|
32
|
+
dendrotweaks/membrane/io/loader.py,sha256=vUh6YMozKD-MvrP2mNyW4-vRoYxXJwK1W4QFUSgcLGU,3042
|
33
|
+
dendrotweaks/membrane/io/parser.py,sha256=-SuY9PxlIS5l0bAGuEgLAn89n3F2Ss-X24ehGGZY81o,17921
|
34
|
+
dendrotweaks/membrane/io/reader.py,sha256=JWm5WM9illvSfDkhWEmWBcj8Y7PSi8zeZX9j1ARUHVU,6576
|
35
|
+
dendrotweaks/morphology/__init__.py,sha256=aqJTQOpRVOYcbWqZ2q4e-Oy735r9_ubW-uE_5cFZVtI,323
|
36
|
+
dendrotweaks/morphology/domains.py,sha256=Y4txcGdBdl2aK1DfbTRziNtDyd6bChczwpCWE7lTFzg,2391
|
37
|
+
dendrotweaks/morphology/point_trees.py,sha256=5dUPaQXYPdJbWoD3pFI2DV2XnuFRhB5d0wTBlfmmIeI,21600
|
38
|
+
dendrotweaks/morphology/sec_trees.py,sha256=FMreuh5mN3oXtvy13oqEc8t-r8a36CPfdkaOqeNo2ts,36894
|
39
|
+
dendrotweaks/morphology/seg_trees.py,sha256=uwL1X9qeFNyJVHua1I3rhp0fLSRrS2TAVyb1Fnw4RwQ,3595
|
40
|
+
dendrotweaks/morphology/trees.py,sha256=NrNvPMR-U0clt63eqwVJqU0H8NJgY53QGA_BkdcwkQI,16033
|
41
|
+
dendrotweaks/morphology/io/__init__.py,sha256=gAZqZdf5VKPb6ksK8Lwt7MbTAq8TDP8uq3Vs_ebNFEY,324
|
42
|
+
dendrotweaks/morphology/io/factories.py,sha256=NngNINw73diGK7fud314JzWVhxv2aYLuA9wUuQA0Diw,6344
|
43
|
+
dendrotweaks/morphology/io/reader.py,sha256=hW3c541WtG1rNag_YreEhvrLzm8-OTtw0fQREeHDthM,1913
|
44
|
+
dendrotweaks/morphology/io/validation.py,sha256=lVkYw9y9yG5QpRh_N0YQ3FbZwuSUsQfSqJTMumMcDdc,7872
|
45
|
+
dendrotweaks/morphology/reduce/__init__.py,sha256=p6Mg3KDHxTt8S4DtI0m7L7MqV6dS2pdIYAwB7B-toVw,921
|
46
|
+
dendrotweaks/morphology/reduce/reduce.py,sha256=5czZDrG3xsvHn3c_tbYhUOlXgST989-RS-ntbhlvvA0,6361
|
47
|
+
dendrotweaks/morphology/reduce/reduced_cylinder.py,sha256=jGJ4J-amukRr-3DPirVR5pzNO-6H7_sZF1N_X57ZGdw,5132
|
48
|
+
dendrotweaks/stimuli/__init__.py,sha256=bFfSEZhCVpwOVEBgLe65iiY3SdpjKPhyLemC1z5OX9I,153
|
49
|
+
dendrotweaks/stimuli/iclamps.py,sha256=NjkhhwZKJR1f_g3N9BVxMVoO9ubBk5WkQ6h9Bnf9xgA,1681
|
50
|
+
dendrotweaks/stimuli/populations.py,sha256=wZwy3PC1uRmQa-WnTLZLy7PGKCQrRJgmmhRIaGdJlLU,7991
|
51
|
+
dendrotweaks/stimuli/synapses.py,sha256=g4MgWTske2TZ2i9FIIOE8-KXNx_3dWa3zEhB2rcqYig,5470
|
52
|
+
dendrotweaks-0.3.1.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
|
53
|
+
dendrotweaks-0.3.1.dist-info/METADATA,sha256=jcnz3Eq3NdoALKHhwoE8lnrA5iSNAcO6oPBU3yZ0GJs,2687
|
54
|
+
dendrotweaks-0.3.1.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
|
55
|
+
dendrotweaks-0.3.1.dist-info/top_level.txt,sha256=OzT_2BSI5j5zxC447K6Y-0W-GHbued7iX-_hFGAKMxY,13
|
56
|
+
dendrotweaks-0.3.1.dist-info/RECORD,,
|