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Tools and curated datasets to build quantitative models of C. elegans ion channels
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channelworm
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README.md

ChannelWorm

Build Status

The aim of ChannelWorm is to build quantitative models of ion channel behavior in C. elegans neurons. The resulting models are exported to PyOpenWorm, OpenWorm's data access layer for storing both static physiological information as well as dynamic models about the nematode. Ultimately, these models are used by c302 for simulating nervous system dynamics.

Installation

To install this project, clone it locally with git and run pip install -r requirements.txt at a console. Please be sure to look at the contents of requirements.txt for certain dependencies cannot be installed automatically via pip.

Objectives

  • Information Management of Primary Data Sources
    • Integrate and structure data related to ion channels in C. elegans, from genotype to phenotype.
    • Develop APIs for accessing data.
    • Regularly curate data to ensure data quality.
    • Develop collaborations with academic labs to collect new data.
  • Ion channel modeling
    • Build Hodgkin-Huxley models for ion channels based on experimental patch clamp studies.
    • Estimate kinetics for ion channels with no patch clamp data available based on homologous channel types.
    • Create verification & validation tests to prove matching of the models with experimental data using SciUnit.
  • Integration with Simulation Platform
    • Export models in NeuroML2 for storage in PyOpenWorm.
    • Built data access pipeline for c302 to access ion channel models from PyOpenWorm.

Repository Contents

  • channelworm/- a variety of tools for digitizing plots, fitting parameters, and exporting models.
  • data/- spreadsheet with curated information about ion channels.
  • docs/- documentation for plot digitization, parameter extraction, and validation tools.
  • models/- NeuroML2 files generated from the parameter fitting process. These are temporarily housed here, but will ultimately be accessed by the simulation platform through PyOpenWorm.
  • scripts/- miscellaneous scripts for channel modeling.
  • tests/- standard software tests as well as model validation tests. Some of the tests in this folder are unit / integration tests. The model validation tests in the Python framework SciUnit have now been moved to a separate, project-wide repository for housing and running model validation tests, simply called openworm/tests.