The aim of the ChannelWorm is to integrate information and tools related to modeling ion channels in C. elegans for the OpenWorm Project.
To install this project, just clone it locally and do pip install -r requirements.txt.
Also, take a look at the comments in requirements.txt for some requirements that can not be installed automatically via pip.
- 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
- 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.
As part of the OpenWorm's Muscle-Neuron-Channel integration plan, ChannelWorm is developing based on the following components:
- The PyOpenWorm is the main data layer API for the knowledge base.
- The Django app is being used as an interface for digitization, data representation and user interaction.
- Collected data fits to dynamic models using cwFitter optimization engine.
- Using the Test suite, verification tests are applied, and models validating by SciUnit testing framework.
- Final models are generated in NeuroML2 format, in addition to LEMS files for simulation environments.
- Verified models and simulations can be run in the Geppetto simulation platform.