Search found 5785 matches

by ted
Mon Sep 26, 2005 4:29 pm
Forum: Modeling networks
Topic: how to use SaveState()?
Replies: 18
Views: 21016

This is the first time I ever heard of SaveState needing a currently accessed section. Probably the best way to deal with this is to pick one section that is "conceptually privileged" (e.g, if you were to plot v(0.5) vs. t for a single section, which section would you prefer to see?) and then make t...
by ted
Sun Sep 25, 2005 1:58 pm
Forum: Other questions
Topic: Survey: need for large-scale computational support
Replies: 6
Views: 7255

Interim survey results

So far a total of 25 users have responded to this survey (including those who replied to the msg I posted to the NEURON Users' Group mailing list). The survey is still "active" so any stragglers who want to add their two bits are encouraged to do so. Most are doing optimization/parameter search simu...
by ted
Sun Sep 25, 2005 1:18 pm
Forum: Modeling networks
Topic: how to use SaveState()?
Replies: 18
Views: 21016

I do admit the code above is not very elegant It's not a question of elegance that puzzles me, it's why you need to save states in the context of a particular section of a particular cell. I thought that SaveState.save() saved all states throughout an entire model, regardless of how many cells exis...
by ted
Fri Sep 23, 2005 12:55 pm
Forum: Modeling networks
Topic: how to use SaveState()?
Replies: 18
Views: 21016

Sorry, but the binary file was saved by the same version of nrn that opens it! Ah, (1) the ambiguities of language and intent, and (2) the imperfections of human knowledge (or at least my knowledge). (1) My message was almost purely generic, especially the statement that SaveState data are likely t...
by ted
Fri Sep 23, 2005 11:54 am
Forum: Modeling networks
Topic: how to use SaveState()?
Replies: 18
Views: 21016

Re: how to use SaveState()?

Excellent questions, and they pertain to all kinds of models, not just network models. This objref svstate svstate = new SaveState() svstate.save() creates a SaveState object that contains the present values of "all" states, regardless of the size and complexity of (and number of cells in) your mode...
by ted
Thu Sep 22, 2005 2:54 pm
Forum: Hot tips
Topic: A course on how to develop software
Replies: 0
Views: 4179

A course on how to develop software

Software Carpentry http://software-carpentry.org/ This site has tutorial materials (lecture notes and exercises) from a course on basic software development practices, designed for scientists and engineers. Well worth a look, even if you don't do any of the exercises, let alone follow all of the rec...
by ted
Tue Sep 20, 2005 12:47 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: dllbuild error: Method cnexp can't be used...
Replies: 3
Views: 5418

thanks for pointing out the obvious mistake - how on earth could i have missed that. Everybody does that kind of thing. In fact I just did it yesterday on two separate occasions myself. I'm interested in watching how the the ionic concentration of the different ions changes during the simulation - ...
by ted
Tue Sep 20, 2005 12:33 pm
Forum: Getting started
Topic: plotting data as the simulation runs
Replies: 5
Views: 5996

When it comes to CVode I'm not sure whether this code will do the job in combination with a variable timestep. In my experience some variables just jump around like mad and even error messages result from having a graph open. That's very strange; I haven't ever seen such behavior. Graphs spawned fr...
by ted
Mon Sep 19, 2005 8:26 pm
Forum: Other questions
Topic: Survey: need for large-scale computational support
Replies: 6
Views: 7255

Survey: need for large-scale computational support

Note: the easiest way to reply to this poll will be to click on the quote button (just to the right of the Post subject line above), and just type your answers right into my questions. To help us meet the ever-changing needs of NEURON users, please let us know if your modeling work is presenting eit...
by ted
Mon Sep 19, 2005 7:59 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: dllbuild error: Method cnexp can't be used...
Replies: 3
Views: 5418

Re: dllbuild error: Method cnexp can't be used...

If this is true the relevent parts of the model BREAKPOINT { SOLVE scheme METHOD cnexp } DERIVATIVE states { cai' = (minf-cai/cb)/mtau + ica/(FARADAY*svRatio) } the fix is pretty clear: change scheme to states and the error msg should go away. does anyone know of any NEURON models that simulate ioni...
by ted
Fri Sep 16, 2005 10:04 am
Forum: Getting started
Topic: HH model and high temperature
Replies: 1
Views: 3449

Adjust stimulus intensity. Hint: stimulus duration should be short (0.1 ms or so). A few facts about the Hodgkin-Huxley model: 1. It only spikes for stimuli that lie within a relatively narrow range of intensities. 2. As temperature increases, this range becomes even narrower, the spikes are shorter...
by ted
Fri Sep 16, 2005 9:51 am
Forum: Getting started
Topic: add *.mod from Build->single compartment
Replies: 3
Views: 4057

I think the easiest (and more direct) way to plainly see what mechanisms are present is Tools --> Distributed Mechanisms --> Managers --> Inserter. Isn't it? Thanks for pointing that out. It does the job quite nicely. I must admit that the last time I looked at that particular tool was at least 5 o...
by ted
Thu Sep 15, 2005 5:35 pm
Forum: Getting started
Topic: add *.mod from Build->single compartment
Replies: 3
Views: 4057

use psection() to discover the properties of a secton

Build / single compartment is not the right tool to use to check what mechanisms have been inserted into a section. Instead, type psection() at the oc> prompt, or type secname psection() where secname is the name of a section other than the default section. Another way to discover the properties of ...
by ted
Thu Sep 15, 2005 11:49 am
Forum: Getting started
Topic: plotting data as the simulation runs
Replies: 5
Views: 5996

combining the GUI and hoc, or stealing code from yourself

In a separate posting, I discussed NEURON's use of staggered time steps and touched on what this implies for plotting variables. All of this raises a big question for people who write hoc code to bring up graphs: how make sure that their code plots things at the proper times? There's a very quick an...
by ted
Thu Sep 15, 2005 10:56 am
Forum: Getting started
Topic: plotting data as the simulation runs
Replies: 5
Views: 5996

accuracy and staggered time steps

The difference between newPlotS, newPlotV, newPlotI is due to the numerical algorythm which uses a staggered time step, using these functions makes your program plot them at the time when they are known at the highest accuracy. The story is a bit more complicated. Staggered time steps are used only...