dendrotweaks 0.3.1__py3-none-any.whl

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Files changed (56) hide show
  1. dendrotweaks/__init__.py +10 -0
  2. dendrotweaks/analysis/__init__.py +11 -0
  3. dendrotweaks/analysis/ephys_analysis.py +482 -0
  4. dendrotweaks/analysis/morphometric_analysis.py +106 -0
  5. dendrotweaks/membrane/__init__.py +6 -0
  6. dendrotweaks/membrane/default_mod/AMPA.mod +65 -0
  7. dendrotweaks/membrane/default_mod/AMPA_NMDA.mod +100 -0
  8. dendrotweaks/membrane/default_mod/CaDyn.mod +54 -0
  9. dendrotweaks/membrane/default_mod/GABAa.mod +65 -0
  10. dendrotweaks/membrane/default_mod/Leak.mod +27 -0
  11. dendrotweaks/membrane/default_mod/NMDA.mod +72 -0
  12. dendrotweaks/membrane/default_mod/vecstim.mod +76 -0
  13. dendrotweaks/membrane/default_templates/NEURON_template.py +354 -0
  14. dendrotweaks/membrane/default_templates/default.py +73 -0
  15. dendrotweaks/membrane/default_templates/standard_channel.mod +87 -0
  16. dendrotweaks/membrane/default_templates/template_jaxley.py +108 -0
  17. dendrotweaks/membrane/default_templates/template_jaxley_new.py +108 -0
  18. dendrotweaks/membrane/distributions.py +324 -0
  19. dendrotweaks/membrane/groups.py +103 -0
  20. dendrotweaks/membrane/io/__init__.py +11 -0
  21. dendrotweaks/membrane/io/ast.py +201 -0
  22. dendrotweaks/membrane/io/code_generators.py +312 -0
  23. dendrotweaks/membrane/io/converter.py +108 -0
  24. dendrotweaks/membrane/io/factories.py +144 -0
  25. dendrotweaks/membrane/io/grammar.py +417 -0
  26. dendrotweaks/membrane/io/loader.py +90 -0
  27. dendrotweaks/membrane/io/parser.py +499 -0
  28. dendrotweaks/membrane/io/reader.py +212 -0
  29. dendrotweaks/membrane/mechanisms.py +574 -0
  30. dendrotweaks/model.py +1916 -0
  31. dendrotweaks/model_io.py +75 -0
  32. dendrotweaks/morphology/__init__.py +5 -0
  33. dendrotweaks/morphology/domains.py +100 -0
  34. dendrotweaks/morphology/io/__init__.py +5 -0
  35. dendrotweaks/morphology/io/factories.py +212 -0
  36. dendrotweaks/morphology/io/reader.py +66 -0
  37. dendrotweaks/morphology/io/validation.py +212 -0
  38. dendrotweaks/morphology/point_trees.py +681 -0
  39. dendrotweaks/morphology/reduce/__init__.py +16 -0
  40. dendrotweaks/morphology/reduce/reduce.py +155 -0
  41. dendrotweaks/morphology/reduce/reduced_cylinder.py +129 -0
  42. dendrotweaks/morphology/sec_trees.py +1112 -0
  43. dendrotweaks/morphology/seg_trees.py +157 -0
  44. dendrotweaks/morphology/trees.py +567 -0
  45. dendrotweaks/path_manager.py +261 -0
  46. dendrotweaks/simulators.py +235 -0
  47. dendrotweaks/stimuli/__init__.py +3 -0
  48. dendrotweaks/stimuli/iclamps.py +73 -0
  49. dendrotweaks/stimuli/populations.py +265 -0
  50. dendrotweaks/stimuli/synapses.py +203 -0
  51. dendrotweaks/utils.py +239 -0
  52. dendrotweaks-0.3.1.dist-info/METADATA +70 -0
  53. dendrotweaks-0.3.1.dist-info/RECORD +56 -0
  54. dendrotweaks-0.3.1.dist-info/WHEEL +5 -0
  55. dendrotweaks-0.3.1.dist-info/licenses/LICENSE +674 -0
  56. dendrotweaks-0.3.1.dist-info/top_level.txt +1 -0
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+ Metadata-Version: 2.4
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+ Name: dendrotweaks
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+ Version: 0.3.1
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+ Summary: A toolbox for exploring dendritic dynamics
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+ Home-page: https://dendrotweaks.dendrites.gr
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+ Author: Roman Makarov
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+ Author-email: dendrotweaks@dendrites.gr
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+ License: GNU General Public License v3.0
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+ Project-URL: Source, https://github.com/Poirazi-Lab/DendroTweaks
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+ Project-URL: Documentation, https://dendrotweaks.readthedocs.io/
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+ Keywords: dendrites,neuron,model,simulation,neuroscience
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
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+ Classifier: Operating System :: OS Independent
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+ Requires-Python: >=3.9
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ Requires-Dist: neuron>=8.2.6
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+ Requires-Dist: neuron-reduce==0.0.7
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+ Requires-Dist: numpy<2.0.0
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+ Requires-Dist: pandas
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+ Requires-Dist: pyparsing
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+ Requires-Dist: symfit
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+ Requires-Dist: matplotlib
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+ Requires-Dist: scipy
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+ Requires-Dist: jinja2
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+ Requires-Dist: quantities
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+ Provides-Extra: dev
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+ Requires-Dist: sphinx; extra == "dev"
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+ Requires-Dist: furo; extra == "dev"
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+ Requires-Dist: sphinx-copybutton; extra == "dev"
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+ Requires-Dist: build; extra == "dev"
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+ Dynamic: license-file
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+
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+ # DendroTweaks
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+
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+ <img src="https://dendrotweaks.readthedocs.io/en/latest/_static/logo.png" width="25%">
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+ <p>
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+
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+ **DendroTweaks** is a Python toolbox designed for creating and validating single-cell biophysical models with active dendrites.
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+
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+ It is available both as a standalone Python package and a web-based application.
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+
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+ ## Learn More
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+
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+ - **Standalone Library**: Explore the [official documentation](https://dendrotweaks.readthedocs.io/en/latest/index.html) for detailed tutorials and API reference.
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+ - **Web Application**: Access the GUI online via our platform at [dendrotweaks.dendrites.gr](https://dendrotweaks.dendrites.gr).
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+ - **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.
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+
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+ ## Publication
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+
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+ For an in-depth understanding of DendroTweaks, refer to our publication in *eLife*:
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+
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+ > Roman Makarov, Spyridon Chavlis, Panayiota Poirazi (2024).
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+ > *DendroTweaks: An interactive approach for unraveling dendritic dynamics.*
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+ > eLife 13:RP103324. [https://doi.org/10.7554/eLife.103324.1](https://doi.org/10.7554/eLife.103324.1)
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+
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+ If you find DendroTweaks helpful for your research, please consider citing our work:
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+
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+ ```bibtex
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+ @article{Makarov2024,
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+ title={DendroTweaks: An interactive approach for unraveling dendritic dynamics},
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+ author={Makarov, Roman and Chavlis, Spyridon and Poirazi, Panayiota},
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+ journal={eLife},
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+ volume={13},
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+ pages={RP103324},
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+ year={2024},
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+ doi={10.7554/eLife.103324.1}
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+ }
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+ ```
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+ dendrotweaks/model.py,sha256=wy17K85d95bD1ioibhDxs8rcNCzow3BP1OVam1b1bTM,67445
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+ dendrotweaks/model_io.py,sha256=xwXKMcUle-Y0HoWFYVZu3G8v4pdQXmeaDfl2Xi65eHw,2137
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+ dendrotweaks/path_manager.py,sha256=SfZ7Br-WmUhpvdRTgeOqMzaYVgLpXoSGbekxJvNkZT4,8794
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+ dendrotweaks/simulators.py,sha256=cVbzbhE48D1ovn7Rg8bU0pI9ztbEqQF2da5gnEMu8Ec,6137
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+ dendrotweaks/utils.py,sha256=jaUJNb39Bsevg3WJByP56bO7CLj1wzlh-uGZl-lxi1I,7131
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+ dendrotweaks/analysis/__init__.py,sha256=SEYpoQ5iXiQXyHB20-IAdDHYI-7CR5GYFXIwr-O05Ug,858
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+ dendrotweaks/analysis/ephys_analysis.py,sha256=oXRjad34tKMDiqEO11uZibHpe2auB2GCetcgd2rVP-o,14124
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+ dendrotweaks/analysis/morphometric_analysis.py,sha256=5zohjGssyx-wezI-yY3Q-kYM_wzAQLLFBJ9Xk950_JY,3571
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+ dendrotweaks/membrane/__init__.py,sha256=H3KsbVQonC1BKBnuchAIxGXj5Zl-xN3egOanVUkgs-o,322
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+ dendrotweaks/membrane/distributions.py,sha256=ADPFPA-CN7AbRJj0Ry4TxFZJhdYXJm87iIGWZSDr5vI,10299
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+ dendrotweaks/membrane/default_mod/AMPA.mod,sha256=HY_pWzYvaSDV-w7qruenG2mnll8v79s40HFHjUCIi4U,980
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+ dendrotweaks/membrane/default_mod/AMPA_NMDA.mod,sha256=ztv2ePUiEQZ93-23FTkGO2DC91rehQuqo0NUIbHZ368,2318
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+ dendrotweaks/membrane/default_mod/CaDyn.mod,sha256=gwc69K_rxu2w_mV7CnOSOnVaCMc8Z-MfdBFf6lAj4kg,1298
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+ dendrotweaks/membrane/default_mod/GABAa.mod,sha256=jdGRid-Wzw4y9kHvq74oSMogLhSiS-Ac2DDaLOrxVi8,983
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+ dendrotweaks/membrane/default_mod/Leak.mod,sha256=u0lwMYGgl5kNZN5W4N6YHgRSeVxb-z2oM9fqou5rCV8,420
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+ dendrotweaks/membrane/default_mod/NMDA.mod,sha256=tT4Q5UPoeztXcQ45uZc2PUO3-8OkDLCmrS7WDsn1yQQ,1185
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+ dendrotweaks/membrane/default_mod/vecstim.mod,sha256=iSpJgR96O2Z3pLNUFIsZ7YJ529ncKUBaZqDJvA0_oV0,965
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+ dendrotweaks/membrane/default_templates/NEURON_template.py,sha256=BlvA48B48f0AyiepXmrOmGJL5Xe5XDshG9w6h5gDEEs,14874
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+ dendrotweaks/membrane/default_templates/default.py,sha256=vDxND86RJEw7XHajkg5P0vM2Oss5dyW5m_ugLMeCbT0,2145
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+ dendrotweaks/membrane/default_templates/standard_channel.mod,sha256=Jpu2rxldAE6kxaylIlPc80F5wpKETodpOvoMbFXhWTA,2861
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+ dendrotweaks/membrane/default_templates/template_jaxley.py,sha256=t-GsCSUyQ7rDoaLmyuWd9bIxB8W3bCqJdnikD59EVvI,3676
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+ dendrotweaks/membrane/default_templates/template_jaxley_new.py,sha256=I62KhnOYNV1bT-nPsDTxjIISYmDcso2X8rnsos28nYs,3631
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+ dendrotweaks/membrane/io/__init__.py,sha256=r84iLBrdmCgGP-dG9iaamBHUGldtAgPyqSujU-3U8ik,584
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+ dendrotweaks/membrane/io/ast.py,sha256=wnJNy2ga1DsZWQ1lpp1QhK2jvM4aDph7u_27VmyJcXw,5894
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+ dendrotweaks/membrane/io/code_generators.py,sha256=jhyjvTisV-tavz_yuQ-tOa3JJ56UNUk_pkN9xS6GEqQ,11407
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+ dendrotweaks/membrane/io/converter.py,sha256=vNCKDk0JqdoqxMWGi2AxT-TZ2YS2itUc7bpm9pRX-6o,3374
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+ dendrotweaks/membrane/io/factories.py,sha256=rCfZiubZPmikB8nxfjh3Dzg4ZHUXgZX79kmJZDLovwI,4979
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+ dendrotweaks/membrane/io/grammar.py,sha256=TJLTDlr8Ajp3J9DJ4IvulOCcpUkYr7HnoI0TGnNuEPc,11677
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+ dendrotweaks/membrane/io/loader.py,sha256=vUh6YMozKD-MvrP2mNyW4-vRoYxXJwK1W4QFUSgcLGU,3042
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+ dendrotweaks/membrane/io/parser.py,sha256=-SuY9PxlIS5l0bAGuEgLAn89n3F2Ss-X24ehGGZY81o,17921
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+ dendrotweaks/membrane/io/reader.py,sha256=JWm5WM9illvSfDkhWEmWBcj8Y7PSi8zeZX9j1ARUHVU,6576
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+ dendrotweaks/morphology/__init__.py,sha256=aqJTQOpRVOYcbWqZ2q4e-Oy735r9_ubW-uE_5cFZVtI,323
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+ dendrotweaks/morphology/domains.py,sha256=Y4txcGdBdl2aK1DfbTRziNtDyd6bChczwpCWE7lTFzg,2391
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+ dendrotweaks/morphology/point_trees.py,sha256=5dUPaQXYPdJbWoD3pFI2DV2XnuFRhB5d0wTBlfmmIeI,21600
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+ dendrotweaks/morphology/sec_trees.py,sha256=FMreuh5mN3oXtvy13oqEc8t-r8a36CPfdkaOqeNo2ts,36894
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+ dendrotweaks/stimuli/__init__.py,sha256=bFfSEZhCVpwOVEBgLe65iiY3SdpjKPhyLemC1z5OX9I,153
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+ dendrotweaks/stimuli/iclamps.py,sha256=NjkhhwZKJR1f_g3N9BVxMVoO9ubBk5WkQ6h9Bnf9xgA,1681
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+ dendrotweaks/stimuli/populations.py,sha256=wZwy3PC1uRmQa-WnTLZLy7PGKCQrRJgmmhRIaGdJlLU,7991
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+ dendrotweaks/stimuli/synapses.py,sha256=g4MgWTske2TZ2i9FIIOE8-KXNx_3dWa3zEhB2rcqYig,5470
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+ dendrotweaks-0.3.1.dist-info/RECORD,,
@@ -0,0 +1,5 @@
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+ Wheel-Version: 1.0
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+ Generator: setuptools (77.0.3)
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+ Root-Is-Purelib: true
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+ Tag: py3-none-any
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+