Ion Channel model standardization and mutation analysis

[VahidGh]

Is your feature request related to a problem? Please describe.

• Currently there are different ion channel modeling approaches available
  • Including HH-style and Markov models
• Each approach has it's own formulation and parameter set
• So, we have different formulations and parameter sets describing characteristics of even a single ion channel
• Using mutation analysis techniques we can look into these characteristics from both the evolutionary and pharmaceutical points of view
  • E.g. Using Machine Learning for analyzing ion channel kinetics for different mutants
  • Using Probabilistic techniques for drug design
• Techniques like Machine Learning need a standard set of parameters for comparability reasons

Describe the solution you'd like A database of ion channel models with a standard NeuroML-based definition including a fixed formulation and number of parameters can help solving this problem.

Describe alternatives you've considered As part of the OpenWorm project, we have started some initial works in the following repos:

• https://github.com/openworm/ChannelWorm
• https://github.com/openworm/ChannelWorm2
• https://github.com/VahidGh/chopen
• https://github.com/VahidGh/chModeler/tree/dev
  • This repo represents an under-development modeling approach with some initial proofs describing feasibility of the approach
    • https://github.com/VahidGh/chModeler/tree/dev/data/2ndFit

[pgleeson]

@scrook @rgerkin @JustasB This is relevant for NeuroML-DB also

[scrook]

Yes, this is an interesting idea. Adding in @vrhaynes

[pgleeson]

Related to this, an earlier version of an ion channel "super model" in LEMS: https://github.com/OpenSourceBrain/IonChannelGenealogyShowcase/blob/master/NeuroML2/ICGSupermodel.nml

[pgleeson]

... and some initial code for the unifying model of @VahidGh in LEMS: https://github.com/VahidGh/chModeler/blob/neuroml/NeuroML2/UnifiedChannel.xml

[VahidGh]

Actually, I've been working on the method from different points of view for a while now (especially from a biophysically reductionist perspective). The new updates are not published yet. Would be glad to contribute, especially if there could be any chance for a long-term plan.