Search found 10 matches

by SurG
Wed Aug 14, 2019 1:34 pm
Forum: Reaction-diffusion in NEURON
Topic: Modelling a channel with multiple markov states
Replies: 7
Views: 1190

Re: Modelling a channel with multiple markov states

Thank you sir. I will try this out
by SurG
Wed Aug 07, 2019 3:43 am
Forum: Reaction-diffusion in NEURON
Topic: Modelling a channel with multiple markov states
Replies: 7
Views: 1190

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)...
by SurG
Sun Jul 07, 2019 7:10 am
Forum: Reaction-diffusion in NEURON
Topic: Modelling a channel with multiple markov states
Replies: 7
Views: 1190

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 ...
by SurG
Sun Jul 07, 2019 1:58 am
Forum: Reaction-diffusion in NEURON
Topic: Modelling a channel with multiple markov states
Replies: 7
Views: 1190

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...
by SurG
Sat Jul 06, 2019 3:12 pm
Forum: Reaction-diffusion in NEURON
Topic: basic questions on RxD
Replies: 7
Views: 2921

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 ...
by SurG
Sat Jul 06, 2019 10:54 am
Forum: Reaction-diffusion in NEURON
Topic: basic questions on RxD
Replies: 7
Views: 2921

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
by SurG
Sat Jul 06, 2019 9:54 am
Forum: Reaction-diffusion in NEURON
Topic: basic questions on RxD
Replies: 7
Views: 2921

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...
by SurG
Thu Sep 08, 2016 5:49 am
Forum: Reaction-diffusion in NEURON
Topic: Basic modelling question
Replies: 7
Views: 14436

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...
by SurG
Mon Mar 14, 2016 10:42 pm
Forum: MSWin
Topic: Neuron as a Python Module Redux
Replies: 8
Views: 12080

Re: Neuron as a Python Module Redux

Thank you very much sir. This worked!
by SurG
Wed Mar 09, 2016 5:36 am
Forum: MSWin
Topic: Neuron as a Python Module Redux
Replies: 8
Views: 12080

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...