Modelling other mechanisms that affect Current/Voltage
Posted: Fri Jun 05, 2015 7:51 am
Hello,
I am new to NEURON, I have recently started a PhD and we are trying to model certain things besides the typical ion concentrations that affect the firing rate of neurons and other properties of a neural network. My background is in computer science and I've learnt a few things in neuroscience but very basic.
Some of the things I would like to model are pathogenic proteins(i.e. dementia diseases), nutrients that may affect the neuron, etc. I have looked up to half way into these tutorials: http://www.anc.ed.ac.uk/school/neuron/t ... /tutD.html
It seems like I may be able to "hack" model these things as "ion" concentrations in the intra and extracellular parts of the membrane. Since NEURON is so old and vast and the code is too much to read all of it and understand everything, I was wondering if you could help guide me a bit as to what I should read to do something like this. Basically I think I primarily want 3 things:
Somehow model that outside of neuron #1 there is say x amount of pathogenic protein(e.g. beta-amyloid) and inside of it y amount. This y amount can affect the current/ion/voltage buildup and affect the firing rate through some equation that I will define(how?). The pathogenic proteins can also propagate through synapses from neuron #1 to another neuron(can this be modelled during the simulation somehow easily?). Lastly, is it possible to change things during the simulation? For example, if there is a high amount of the pathogenic protein inside the neuron, to somehow model that this neuron "dies" and its synapses do not work anymore?(i.e., the simulation will check at every timestep whether the concentration of this protein inside each and every neuron is above a threshold and then do something)
Finally and perhaps most importantly, can I do all of these as a "hack" through NMODL and hoc code or will I need to change the source code of NEURON for some of these?
Any help is greatly appreciated! Thank you very much,
Konstantinos
I am new to NEURON, I have recently started a PhD and we are trying to model certain things besides the typical ion concentrations that affect the firing rate of neurons and other properties of a neural network. My background is in computer science and I've learnt a few things in neuroscience but very basic.
Some of the things I would like to model are pathogenic proteins(i.e. dementia diseases), nutrients that may affect the neuron, etc. I have looked up to half way into these tutorials: http://www.anc.ed.ac.uk/school/neuron/t ... /tutD.html
It seems like I may be able to "hack" model these things as "ion" concentrations in the intra and extracellular parts of the membrane. Since NEURON is so old and vast and the code is too much to read all of it and understand everything, I was wondering if you could help guide me a bit as to what I should read to do something like this. Basically I think I primarily want 3 things:
Somehow model that outside of neuron #1 there is say x amount of pathogenic protein(e.g. beta-amyloid) and inside of it y amount. This y amount can affect the current/ion/voltage buildup and affect the firing rate through some equation that I will define(how?). The pathogenic proteins can also propagate through synapses from neuron #1 to another neuron(can this be modelled during the simulation somehow easily?). Lastly, is it possible to change things during the simulation? For example, if there is a high amount of the pathogenic protein inside the neuron, to somehow model that this neuron "dies" and its synapses do not work anymore?(i.e., the simulation will check at every timestep whether the concentration of this protein inside each and every neuron is above a threshold and then do something)
Finally and perhaps most importantly, can I do all of these as a "hack" through NMODL and hoc code or will I need to change the source code of NEURON for some of these?
Any help is greatly appreciated! Thank you very much,
Konstantinos