## Search found 11 matches

Thu Nov 12, 2020 5:58 pm
Forum: OS X
Topic: Program editors for OS X
Replies: 8
Views: 8267

### Re: Program editors for OS X

Hello, I have tried using XCode to edit *.mod files but the software recognises the files as audio mod. Can someone suggest a fix? Any pointers will be appreciated. Also, is there a plugin for XCode to recognise NEURON commands? Thank you.
Wed Aug 14, 2019 1:34 pm
Forum: Reaction-diffusion in NEURON
Topic: Modelling a channel with multiple markov states
Replies: 7
Views: 1911

### Re: Modelling a channel with multiple markov states

Thank you sir. I will try this out
Wed Aug 07, 2019 3:43 am
Forum: Reaction-diffusion in NEURON
Topic: Modelling a channel with multiple markov states
Replies: 7
Views: 1911

### Re: Modelling a channel with multiple markov states

Hello, I have been working on this for a while and I'm quite lost. As explained in the first post, I am trying to create a multiple state Markov model. It is of the form: r1 = rxd.Rate(C1, ((kim*C2)-(ki*ca[cyt]*C1))-((ko*ca[cyt]**2*C1)-(kom*O))) r2 = rxd.Rate(C2, (((ki*ca[cyt]*O)-(kim*C2))-((kom*C2)...
Sun Jul 07, 2019 7:10 am
Forum: Reaction-diffusion in NEURON
Topic: Modelling a channel with multiple markov states
Replies: 7
Views: 1911

### Re: Modelling a channel with multiple markov states

This channel has a parameter that is gated by ca[er]. I have an NMODL equivalent of this channel but I don't know how to make that .mod file read the changes in ca[er]. That's why I thought of modelling it in RxD, where I can declare its 'Region' and 'Direction of action'. How did you overcome this ...
Sun Jul 07, 2019 1:58 am
Forum: Reaction-diffusion in NEURON
Topic: Modelling a channel with multiple markov states
Replies: 7
Views: 1911

### Modelling a channel with multiple markov states

Hello, I'm trying to model a channel that is governed by 4 states, C1,C2,C3,O. The transitions from 1 state to another are bidirectional. I have initialised these states using the rxd.State and tried to model them using rxd.Rate, but am getting a compilation error "TypeError: unsupported operand typ...
Sat Jul 06, 2019 3:12 pm
Forum: Reaction-diffusion in NEURON
Topic: basic questions on RxD
Replies: 7
Views: 4313

### Re: basic questions on RxD

This worked. Thank you so much! I have another query. According to the RxD Tutorial 1.0.0 documentation, the unit of concentration is mM. However, in the same tutorial, "Calcium Waves in RxD", even though cac_init is initialised to 0.0001 mM (~100 nM) and kserca is initialised to 0.1 mM, ca[cyt] is ...
Sat Jul 06, 2019 10:54 am
Forum: Reaction-diffusion in NEURON
Topic: basic questions on RxD
Replies: 7
Views: 4313

### Re: basic questions on RxD

This one still gives the same error "no such region"
I'm using Python 3.7 on a Windows 64bit system
Sat Jul 06, 2019 9:54 am
Forum: Reaction-diffusion in NEURON
Topic: basic questions on RxD
Replies: 7
Views: 4313

### Re: basic questions on RxD

Hi, Is it possible to initialise the calcium concentrations of both cytosol and er to separate values? From what I understand, the following statement initializes the concentrations of ca[cyt] and ca[er] to the same value, cac_init ca = rxd.Species([cyt, er], d=caDiff, name='ca' ,charge=2,initial=ca...
Thu Sep 08, 2016 5:49 am
Forum: Reaction-diffusion in NEURON
Topic: Basic modelling question
Replies: 7
Views: 15338

### Re: Basic modelling question

Hi, We are also trying to implement a similar setup. We have two compartments, the ER and the cytosol and have a mod file, whose parameters we need to access via the RxD module. We have a couple of queries regarding this: 1. Is it possible to ensure bidirectional communication between mod file and t...
Mon Mar 14, 2016 10:42 pm
Forum: MSWin
Topic: Neuron as a Python Module Redux
Replies: 8
Views: 13183

### Re: Neuron as a Python Module Redux

Thank you very much sir. This worked!
Wed Mar 09, 2016 5:36 am
Forum: MSWin
Topic: Neuron as a Python Module Redux
Replies: 8
Views: 13183

### Re: Neuron as a Python Module Redux

We are running Neuron 7.4 and Python 2.7.11 in Windows 7 ( 64 bit). We were also facing the exact same problem and we implemented the solutions suggested. However, we are still unable to import Neuron on the Python terminal. Please advice as to what we can do next. Deactivating environment "C:\Users...