Search found 220 matches

by Raj
Fri Feb 09, 2007 1:44 pm
Forum: Modeling networks
Topic: Cvode::interpolate assert error
Replies: 5
Views: 5794

It was a 5.9 version but pre 5.9.10 (The one current at July 18 2006), but because I got caught in some other problem I cannot give the built number. As a result I am in the middle of updating. As a dutch saying formulates it: 'An accident never comes alone.' When all updating is done I'll rerun the...
by Raj
Fri Feb 09, 2007 5:09 am
Forum: Modeling networks
Topic: Cvode::interpolate assert error
Replies: 5
Views: 5794

Cvode::interpolate assert error

Dear forum, I'm running network simulations with 160 cells and am using Cvode with use_local_dt switched on. During parameter searches on the network parameters I occasionally get the following errors: ... Cvode::interpolate assert error t0=197.657 tout-t0=-2.84217e-14 eps*t_=4.38888e-12 ... Cvode::...
by Raj
Fri Jan 19, 2007 5:04 am
Forum: Getting started
Topic: Question about saving current data
Replies: 3
Views: 3987

Where is your run() command?

General structure should be something like this (in pseudo code):

Code: Select all

myVector.record

run()

myVector.save
by Raj
Tue Jan 16, 2007 5:41 am
Forum: Employment and educational opportunities
Topic: PhD position available at Vrije Universiteit Amsterdam
Replies: 0
Views: 8685

PhD position available at Vrije Universiteit Amsterdam

In our modeling group which is part of an experimental neurophysiology group we have a PhD position in modeling available for a non-Dutch researcher, see the job announcement attached. For an impression of our group you can go to our websites. Experimental Neurophysiology Website: http://www.cncr.vu...
by Raj
Tue Jan 09, 2007 11:25 am
Forum: Adding new mechanisms and functions to NEURON
Topic: pump kinetic scheme
Replies: 20
Views: 33340

The modification made is that a phenomenological lag term, tau_pump, has been added. Unfortunately this modification makes the mechanism unstable, I think because it promotes/allows negative values of nai. Which phenomenom are you trying to model with tau_pump? Normally in reaction or reaction diff...
by Raj
Sun Jan 07, 2007 4:24 am
Forum: Adding new mechanisms and functions to NEURON
Topic: pump kinetic scheme
Replies: 20
Views: 33340

What is your initial value nai? If it is very small or (less likely) large compared to km it might explain your error. The assignments to the currents do belong in the breakpoint block. You might try to avoid evaluating pow for small and large km/nai values: Define what you find large and what small...
by Raj
Fri Jan 05, 2007 3:35 am
Forum: Adding new mechanisms and functions to NEURON
Topic: pump kinetic scheme
Replies: 20
Views: 33340

My comment regards your non-kinetic solution to the problem and indicates the probable cause of its failing. The thread I directed you to can help you with correctly implementing the change you had in mind without reimplementing the whole mechansim as a kinetic scheme. It is up to you to decide whet...
by Raj
Thu Jan 04, 2007 2:56 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: pump kinetic scheme
Replies: 20
Views: 33340

I remember a discussion in this forum with David Sterratt about how to add non-linearities to your differential equations. Michael Hines in response to our attempts to do an analysis discussed in some detail what is the problem and what is the way out. You might want to have a look at his post in th...
by Raj
Sun Dec 31, 2006 8:31 am
Forum: Other questions
Topic: bug in strcmp ?
Replies: 2
Views: 4168

I checked neuron 5.8 on windows and found the same behavior as Darwin shows. A non-exhaustive examination of the source code suggests that Neuron is using strcmp implementation that comes with the compiler, and as a result the outcome of strcmp can depend on the compiler/c-library implementation use...
by Raj
Thu Dec 07, 2006 5:34 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: neuron as exe file
Replies: 3
Views: 4302

Although it is not exactly an executable it is possible to start a simulation from a batch file:
https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=444
by Raj
Fri Dec 01, 2006 1:45 am
Forum: Optimization
Topic: Segmentation violation when load_file a .ses file
Replies: 4
Views: 10633

You might want to have a look at this discussion on how to use the standard run system:
https://www.neuron.yale.edu/phpBB2/view ... initialize
by Raj
Thu Nov 30, 2006 4:10 am
Forum: Adding new mechanisms and functions to NEURON
Topic: membrane compartmentalisation
Replies: 13
Views: 7000

A possible (sketchy) solution can be in the use of sectionlist. Create three section list: - Channel1Sections - Channel2Sections - SeparotorSections Now you can use 'forsec' to loop over the different sections types and set properties like the lengths of the sections and the channel density. Put the...
by Raj
Tue Nov 07, 2006 4:25 am
Forum: Getting started
Topic: trac a branch!
Replies: 3
Views: 3675

With sectionref's parent method you can find the parent of a section. So writing a while loop in which you get a new parent untill you are at the root should not be a problem. With sectionref's nchild method you can establish the number of children, if this is zero you are at an endsegment. With for...
by Raj
Mon Oct 30, 2006 4:43 am
Forum: Getting started
Topic: CVODE and *.mod file
Replies: 4
Views: 5473

By coincidence I was just working on the cells given by Destexhe: http://senselab.med.yale.edu/senselab/modeldb/ShowModel.asp?model=3817 The code already contains commented out code which does not use the exact solution which relies on a fixed time step. Removing these comments and commenting out th...
by Raj
Sat Oct 28, 2006 12:22 pm
Forum: Modeling networks
Topic: modeling networks
Replies: 2
Views: 4059

From the documentation page:
http://www.neuron.yale.edu/neuron/docs

You can goto the netbuilder tutorial:
http://www.neuron.yale.edu/neuron/stati ... /main.html