Search found 5786 matches

by ted
Fri May 27, 2005 10:55 am
Forum: Modeling networks
Topic: parallel simulations of networks
Replies: 6
Views: 9439

parallel simulations of networks

On 12/1/2004 Ulf Knoblich <knoblich@csail.mit.edu> asked: we're thinking about simulating a large network of "biological" neurons (as opposed to "artificial" ones), i.e. neurons with membrane currents etc. Has anyone ever tried to distribute computations over a cluster using NEURON, e.g. running a f...
by ted
Fri May 27, 2005 12:39 am
Forum: Other questions
Topic: Defining objects within a procedure
Replies: 2
Views: 3610

A variable must be declared to be an objref before it can be used as an objref. Objrefs must be declared at the top level of the interpreter. Statements that appear within a proc or func are not at the top level of the interpreter. So this works objref fap proc foo() { fap = new Classname() } but th...
by ted
Thu May 26, 2005 11:48 pm
Forum: Other questions
Topic: Command line arguments?
Replies: 8
Views: 11363

Here Documents

On 11/30/2005 Michael Hines <michael.hines@yale.edu> replied: I generally use the shell feature called a "here" script. i.e nrniv funcdef.hoc - << here foo(p1, p2) here The sh man page states: Here Documents This type of redirection instructs the shell to read input from the current source until a l...
by ted
Thu May 26, 2005 11:45 pm
Forum: Other questions
Topic: Command line arguments?
Replies: 8
Views: 11363

Command line arguments?

On 11/30/2004 Jose Ambros-Ingerson <jose@kiubo.net> wrote: It would be very convenient to be able to run nrniv from a shell script and be able to execute a function call. A line in this script would look something like: $ nrniv funcdef.hoc -e "foo(p1,p2)" which would mean "load file funcdef.hoc and ...
by ted
Thu May 26, 2005 5:04 pm
Forum: Other questions
Topic: How to use random numbers from within a mod file?
Replies: 3
Views: 4926

There are several ways to make pseudorandom sequences available to mechanisms. The "best" way depends on the details of what you want to do. For example, if all you need is a point source of noisy current, there's no need to write any NMODL code at all. Just use the Random class's play() method to d...
by ted
Thu May 26, 2005 4:56 pm
Forum: Other questions
Topic: How to use random numbers from within a mod file?
Replies: 3
Views: 4926

How to use random numbers from within a mod file?

On 4/21/2005 Luca Finelli <lfinelli@salk.edu> asked:
What's the best way to have a random number generator available
inside a mod file (can one use the syntax for Random in hoc files?).
by ted
Thu May 26, 2005 4:51 pm
Forum: Other questions
Topic: How to save a vector to a file?
Replies: 1
Views: 3748

This stuff libpvm [pid3009] /tmp/pvmd.501: No such file or directory libpvm [pid3009] /tmp/pvmd.501: No such file or directory libpvm [pid3009] /tmp/pvmd.501: No such file or directory libpvm [pid3009]: pvm_parent(): Can't contact local daemon is irrelevant unless you are using PVM to implement a wo...
by ted
Thu May 26, 2005 4:48 pm
Forum: Other questions
Topic: How to save a vector to a file?
Replies: 1
Views: 3748

How to save a vector to a file?

I get the following error when trying to save a vector to a file. first instance of A first instance of k1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 libpvm [pid3009] /tmp/pvmd.501: No such file or directory libpvm [pid3009] /tmp/pvmd.501: No such file or directory libpvm [pid3009] /tmp/pvmd.501: No such file ...
by ted
Thu May 26, 2005 4:44 pm
Forum: Other questions
Topic: How can I control the extracellular environment?
Replies: 1
Views: 3161

If your model has no ion accumulation mechanisms (diffusion, buffers, transport mechanisms), ionic equilibrium potentials are treated as constants and are specified with simple assignment statements. When there is an ion accumulation mechanism, the affected ionic species becomes a state variable in ...
by ted
Thu May 26, 2005 4:43 pm
Forum: Other questions
Topic: How can I control the extracellular environment?
Replies: 1
Views: 3161

How can I control the extracellular environment?

On 3/31/2005 a NEURON user asked:
How can I control the extracellular environment?
by ted
Thu May 26, 2005 4:41 pm
Forum: Modeling networks
Topic: Can a network model contain two different kinds of cells?
Replies: 3
Views: 5884

It can contain as many different kinds as you like. If your net has only a few cells, you can do the whole thing with the Network Builder (see tutorial at http://www.neuron.yale.edu/neuron/docs ). If your net has > 5 or 6 cells and many synaptic connections, use the approach described in chapter 11 ...
by ted
Thu May 26, 2005 4:40 pm
Forum: Modeling networks
Topic: Can a network model contain two different kinds of cells?
Replies: 3
Views: 5884

Can a network model contain two different kinds of cells?

On 3/31/2005 a NEURON user aked:
Can a network model contain two different kinds of cells?
by ted
Thu May 26, 2005 4:36 pm
Forum: Modeling networks
Topic: How to use an anatomically detailed model cell in a network?
Replies: 1
Views: 4151

Import the morphology into the CellBuilder, then use the CellBuilder to specify biophysical properties and spatial discretization (use the d_lambda strategy). Then use the CellBuilder to create a template 1. Management page / Cell Type button 2. Use the Classname button to assign a name to the cell ...
by ted
Thu May 26, 2005 4:05 pm
Forum: Modeling networks
Topic: How to use an anatomically detailed model cell in a network?
Replies: 1
Views: 4151

How to use an anatomically detailed model cell in a network?

On 3/31/2005 a NEURON user wrote:
I have a model neuron based on a detailed morphometric reconstruction
that I want to use it in a network model. How do I turn this model cell into
a template for a new cell class?
by ted
Tue May 24, 2005 9:06 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: How to use a new channel?
Replies: 0
Views: 3456

How to use a new channel?

On 2/24/2005 a NEURON user asked: > I have just created a channel with NMODL (successfully! exciting.) > > Yet, I cannot figure out how I can insert this newly created channel (a mod > file) into a cell using the GUI!? As a temporary solution I have written a > hoc file of a cell that inserts the ne...