OpenWorm muscle cells: the story so far

[Stephen Larson]

Hi all,

  We got an inquiry from a scientist about where we are with muscle cell modeling so I wanted to write a brief history here.  Where more is needed, please fill in (looks in Mike's direction).

  Muscle cells are the key starting point for us so here's the story so far.

  We've looked to the work of Netta Cohen to get started with muscle cells.  They've let us know that their current model isn't fully correct, as they predicted no spikes in the muscle, and in fact there are spikes.

   HOWEVER -- their formulation of the muscle model is still useful, even if the details of the parameters they have used didn't quite fit.  Key points of their formulation:

• Used a conductance based approach to the model
• Included fast and slow potassium currents in addition to a calcium and leak current
• Used a model optimization approach to tune their model to available data

    Volunteers on the project have worked with the model as it was described in their paper and have loaded it up in NeuroML2.  You can read more about NeuroML here: https://github.com/openworm/OpenWorm/wiki/FAQ#what-is-neuroml-and-what-does-it-represent

     Here's the specific link to the model via OpenSourceBrain:

http://opensourcebrain.org/projects/muscle_model/wiki

     NOW: there is additional work going on right now to better tune up this muscle model so it fits the spiking characteristics of the real muscle cell.  If you look at the bottom of the previous link, you see a graph where the muscle cells are spiking.  This is still work under development but I'm sure Mike would appreciate some help with this part as he is getting pretty close.  There are some arcane infrastructural hurdles that are being addressed in parallel with this (fair warning), but nothing that can't be addressed with a little explanation via Google hangout, I'm sure.

     OK, so far we've only touched on the conductance based side.  To address the physics of the muscles we have a longer road we are traveling on, but thankfully we've made good progress recently.  

     Here you'll see video of the physics side working. 

https://www.youtube.com/watch?feature=player_detailpage&v=DDNR1IoZKCs&t=143

      These are five abstract muscle compartments working together to bend in isolation on a virtual dish with virtual liquid.  I say "abstract" because we have not yet made sure the compartments are correctly sized, have the right mass, have the right elasticity, or have the right shape.  We've been single-mindedly focused on getting this infrastructure up and we are getting really close to start plugging those details in.  This is on the roadmap and we could use help to collect these actually.  The team working on this part includes Andrey Palyanov, Sergey Khayrulin and Giovanni Idili.

     To the list: if I left anything out or messed anything up, please amend as necessary.

     To the scientist -- please let us know how we can help.  You can get your hands on any of this code and we can help you set it up and play with it today.  There is still quite a bit of work to achieve the goal of making the worm wiggle as we want it but I suspect we can help each other out greatly getting there.  I've put in bold some potential intersection points that we could work on together.

Thanks,

  Stephen

[Mike Vella]

Stephen sums the progress on this up quite well. If anyone is interested in getting the optimized HH model of the muscle cell running on their machine contact me. In future this will be better documented.

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