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@ Michael
Could you clarify, what do you mean by

large memory bandwidth limited models

?

When I instantiating a morphology in NEURON, is there a way of getting section types (or segment types) in the same format as in the swc file? Basically, I would like to be able to have one of the following integer values for a give section/segment: type of neuronal compartment: 0 - undefined 1 - so...

Thanks for pointing out the get_loc() method. I followed your recommendation and it works.

Is there a way of getting a list of synapses existing on a section? It is assumed that synapse were created, of course. I wanted to calculate x,y,z coordinates of synapses for visulaization purposes. So, I would like to be able to loop through sections in a particular cell and for each section get l...

I was trying to install NEURON and run it with python as an interpreter on my laptop just before the parallel course. However, my windos 32 installation is having issues as it refuses to recognize numpy and gives error message "ImportError: No module named testing". Please see below the ou...

Thanks for clarification. I realize that this is what is happening. My confusion is with why this happens given that objects in python are passed by assignment not by value. So if the element of an array (or a list) were assigned to objects once, then the updates to the values stored in those object...

Great, it works now. I would have never figured that out on my own. Could you please tell whether h.cvode.cache_efficient(1) works when using a constant time step? I am still puzzled with the conceptual issue of why simply populating a numpy array or (a python list) with segment currents as shown be...

I do have self.pVec initialized in the costructor and I ruturn numpy array as you recommended.

Thanks Michael, however I am still not able to make it work. Below is the code for my Cell class which basically only has functions for setting and getting i_membrane: getMemCurArrSlow() is a slow implementation where I loop through the tree at each time step. Following your suggestion I used the Pt...

I would like to efficiently access membrane currents for each segment in the cell at each time step to multiply them by some matrix. Currently I populate a numpy array on each time step before performing matrix multiplication: jseg = 0 # iseg for the entire cell for sec in cell.hoc.all: # for seg in...

I prefer to modify the proc advance() rather than using pybs.mod. Now I get the idea for accesing Python object from inside the hoc. However the code: h(''' objref po po = new PythonObject() proc advance() { fadvance() po.mypopulation.calc_csd() } does not seem to work because during the execution I...

Thanks for the detailed response. Certainly I got confused in distinction between Python and the Hoc. I do programming in Python and access the Hoc with neuron import h as you mentioned. It still remains a mistery to me how to modify proc advance() from Python in order to insert in it the call to Py...

Of course, I still need to call calc_csd, thanks for pointing that out. I did this in my serial implementation in the past, but got confused that with Vector.record it is not necessary because calling the member function csd_calc() once in the constuctor would reference self.csd to self.W*self.i_mem...

Mike, thanks for pointing out the bug. I am glad I am on the right track, however, I got confused with your statement: Forget that suggestion and keep on with your calc_csd and modified proc advance(). I thougth that I do not need to modify the proc_advance() to store the csd vector since I can use ...

Thanks for the detailed response. However, it is still unclear to me whether I must use the mod file to save my csd without modifying the proc advance() or I can get away withot inroducing a mod file.( I am reluctant to use mod file because it will be cell mechanism, whereas CSD is not a cell mechan...