ChannelWorm2

The aim of ChannelWorm2 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

There are currently no installation scripts. Simply clone the repository to begin working with the data and associated code.

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.
  • Use SciUnit to create verification & validation tests to confirm that models correspond to experimental data.
• Integration with Simulation Platform
  • Export models in NeuroML2 for storage in PyOpenWorm.
  • Build data access pipeline for c302 to access ion channel models from PyOpenWorm.

Repository Contents

• docs/- documentation for plot digitization, parameter extraction, and validation tools. Will be deployed to channelworm2.readthedocs.io (see associated issue).
• parameter_fitting/- genetic algorithms for extracting parameters for Hodgkin-Huxley type ion channel models.
• raw_data/- spreadsheets with curated data about ion channels, relevant plots from publications, and digitized time series to be used for parameter extraction.
• NML2_models/- NeuroML2 files generated from the parameter fitting process.

News & Release Notes

• 8/28/2018: All plots and JSON files from Chopen are now in raw_data.

• 8/27/2018: Major restructuring of repository. Previous version of ChannelWorm been archived. See associated issues and milestones for tasks related to incorporating this work into the current setup. New structure is organized around the raw data exported from Chopen.