Search found 6290 matches

by ted
Tue Oct 17, 2006 10:51 pm
Forum: Modeling networks
Topic: net_send and net_receive
Replies: 1
Views: 4742

The contents of the NET_RECEIVE block specify what happens when an event is delivered to a point process or artificial spiking neuron. There is no net_send block. net_send is used to send a self event (an event that is delivered, after some delay, to the same point process or artificial spiking cell...
by ted
Tue Oct 17, 2006 9:05 am
Forum: Anatomically detailed models
Topic: topology and geometry
Replies: 3
Views: 5767

No need to apologize. You asked a very good question, which raised several important points. The fact that {the size of the branches displayed in the CellBuilder's shape plot} is independent of {the actual physical dimensions of the specified model} has not been explained elsewhere. And even though ...
by ted
Mon Oct 16, 2006 7:50 pm
Forum: Anatomically detailed models
Topic: topology and geometry
Replies: 3
Views: 5767

The flow of execution is 1. sections are created 2. the objrefs, that will eventually become subsets, are created 3. access soma 4. proc celldef() is called. celldef() calls topol() subsets() geom() biophys() geom_nseg() in that sequence. 5. topol() assembles the sections into the correct branched a...
by ted
Mon Oct 16, 2006 10:10 am
Forum: Other questions
Topic: prntout of plots
Replies: 2
Views: 4802

is there any other way of changing parameters(conductance) for neurons while network modelling using network builder? Changes made with the NetReadyCellGUI tool are effective only if they are made before the NetGUI is created. After the NetGUI tool has been created, the only way to change cell prop...
by ted
Mon Oct 16, 2006 9:53 am
Forum: Getting started
Topic: what is drive_channel in ATPase Ca-pump
Replies: 2
Views: 4106

The mechanism is actually a calcium accumulation mechanism. In other words, it embodies the law of conservation of mass, expressed in the form cai' = influx_of_ca - efflux_of_ca You really should read the original paper to understand the authors' intent, i.e. what they had in mind when they created ...
by ted
Mon Oct 16, 2006 9:30 am
Forum: Modeling networks
Topic: my channel in synapse
Replies: 8
Views: 7923

NMODL of CaGluSK channel (ch) calls Transmitter release mod, concentration mod, and pump mod. When I implement it between two simple somata, I could see channels opened, current flowed. But when I replace the postsynaptic soma with an easy cell with a soma and a dendrite and do the same try as abov...
by ted
Sun Oct 15, 2006 5:41 pm
Forum: Anatomically detailed models
Topic: coupling compartment
Replies: 2
Views: 5010

There are at least two ways to insert a resitance between two sections. One is to put a third section in between the other two, being careful to make the dimensions and Ra of the intermediate section such that the desired resistance is obtained; be sure to set that section's cm to 1e-9. The other wa...
by ted
Fri Oct 13, 2006 10:59 pm
Forum: Modeling networks
Topic: my channel in synapse
Replies: 8
Views: 7923

Without seeing the actual code that you're using, I haven't the foggiest idea of what to tell you. You don't have to post it in the Forum--in fact, it's probably best that you don't; the Forum is really only suited for short code extracts. So if I am have a rational basis for further specific commen...
by ted
Fri Oct 13, 2006 10:50 pm
Forum: Other questions
Topic: basal and apical dendrites
Replies: 1
Views: 3447

Bring up a shape plot of the model cell and look at it (or ask an anatomist to look at it). NEURON Main Menu / Graph / Shape plot If you need to discover the name of a section, use NEURON Main Menu / Tools / Distributed Mechanisms / Viewers / Shape name If you click on a section in this tool's shape...
by ted
Fri Oct 13, 2006 10:40 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Concerning LONGITUDINAL_DIFFUSION
Replies: 6
Views: 5508

That "hines" guy is Michael Hines, not me. Thanks, Mike!
by ted
Wed Oct 11, 2006 9:06 am
Forum: Modeling networks
Topic: my channel in synapse
Replies: 8
Views: 7923

Re: Things I don't well understand

Does it really need NET_RECEIVE block? CaGluSK channel refers to an AMPA receptor channel. It has following mechanisms: Transmitter release Glutamate concentration calculation Ca++ pump Sounds like a good example of how not to write NMODL code. The calcium accumulation mechanism should really be sp...
by ted
Tue Oct 10, 2006 10:52 am
Forum: Getting started
Topic: Initialization for steady states - custom
Replies: 3
Views: 4535

Re: Initialization

Will this "SaveState" method save all the states, ie 3 states per section, and 15 unique states for all the sections at the end of the run? Yes. But why don't you test to verify this for yourself? Will I need give the m and h states in the dendrites different names? Will there be a confli...
by ted
Mon Oct 09, 2006 5:53 pm
Forum: Getting started
Topic: Initialization for steady states - custom
Replies: 3
Views: 4535

While I see how this works for just one section like the soma, how do I make use of this when I have multiple dendrites with multiple ion channels and multiple states ? The same way you'd use it for a model with a single section. Please read the first paragraph of the documentation on SaveState in ...
by ted
Sat Oct 07, 2006 12:37 pm
Forum: Modeling networks
Topic: my channel in synapse
Replies: 8
Views: 7923

The central question is whether your conceptual model of synaptic transmission demands that the synaptic conductance is closely coupled to some variable (v, cai) in the presynaptic terminal, or whether it is enough to watch the presynaptic cell for a spike, and then after some delay produce a conduc...
by ted
Fri Oct 06, 2006 10:15 pm
Forum: The GUI
Topic: Closing windows programmatically
Replies: 1
Views: 4673

destroying, unmapping, and mapping graphical objects

If you want to destroy an object, re-initialize all objrefs that point to it. Works for objects spawned from any of NEURON's object classes, not just Graphs. Example: objref gr gr // hoc will print NULLobject gr = new Graph() // creates a new Graph object and maps it to the screen gr // this will pr...