ChannelWorm

The aim of the ChannelWorm is to integrate information and tools related to modeling ion channels in C. elegans for the OpenWorm Project.

Objectives

• Information Management
  • Integrate and structure data related to ion channels in C. elegans, from genotype to phenotype
  • Develop APIs for accessing data
  • Keep data up-to-date
• Ion channel modeling
  • Build Hodgkin-Huxley models for ion channels based on experimental patch clamp studies
  • Estimate kinetics and build models 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
• Setting up a simulation environment
  • Simulate the computational analysis phase of a patch clamp experiment
  • Simulate and run customized versions of ion channel(s) in cell(s)
  • Check if the simulation fits the biological boundaries

Some use cases

• I want to know which type of ion channels we have in C. elegans!
• I want to know in which cell which gene encodes which protein/subtype of which ion channel!
• I want to view, build, or validate a model of an ion channel
• I want to check references that data or models are based on
• I have some graphs/data from a patch clamp experiment and want to build a HH model
• I want to have a customized version of an ion channel model (e.g. of a mutant)
• I want to run my customized model of ion channel(s) (along with other ion channels) in a simulation environment
• I want to simulate a patch clamp experiment with known mutations in genes encoding ion channels in C. elegans
• I want to simulate ion channel diseases (channelopathies), and investigate defects in neuromuscular transmission, C. elegans movement, etc.

Note: All the models are generated in NeuroML2 format and all the simulations in LEMS, and the verified models can be run in the Geppetto simulation platform.