Search found 41 matches

Wed Jan 30, 2019 11:56 am
Forum: Reaction-diffusion in NEURON
Topic: 3D Dimensional RXD/CRXD
Replies: 4
Views: 1782

Re: 3D Dimensional RXD/CRXD

The discretization used to build the mesh (dx), is an optional argument for rxd.Region, it defaults to 0.25μm. You should be able to get similar performance by scaling it up by 10, rather than reducing the cell sizes. E.g. cyt = rxd.Region(h.allsec(), name='cyt', nrn_region='i', dx=2.5) Finitialise ...
Mon Jan 28, 2019 9:33 pm
Forum: Reaction-diffusion in NEURON
Topic: 3D Dimensional RXD/CRXD
Replies: 4
Views: 1782

Re: 3D Dimensional RXD/CRXD

1) You can reduce the number of nodes by changing dx. Also nthreads is only currently implemented for crxd extracellular reaction-diffusion. Would a radial diffusion model be sufficient? Radial diffusion can be implemented in rxd using multicompartment reactions, for example; from neuron import h, c...
Mon Jan 21, 2019 1:52 pm
Forum: Reaction-diffusion in NEURON
Topic: Different reaction rates in different sections
Replies: 3
Views: 1433

Re: Different reaction rates in different sections

Here's a working version of your code: from neuron import h, rxd from matplotlib import pyplot # needed for standard run system h.load_file('stdrun.hoc') left = h.Section(name='left') right = h.Section(name='right') left.nseg = right.nseg = 101 left.L = right.L = 101 right.connect(left) tfact0 = 137...
Thu Jan 17, 2019 2:50 pm
Forum: Reaction-diffusion in NEURON
Topic: updating Species and Rates inputs
Replies: 2
Views: 1304

Re: updating Species and Rates inputs

There are several ways of changing the initial concentration of a species, but the easiest is to use its `.initial` attribute, e.g. from neuron import h, rxd soma = h.Section('soma') cyt = rxd.Region([soma], name='cyt', nrn_region='i') ca = rxd.Species(cyt, name='ca', charge=2, initial=50e-6) # firs...
Tue Aug 28, 2018 3:38 pm
Forum: Reaction-diffusion in NEURON
Topic: Reaction-Diffusion in HOC
Replies: 5
Views: 18722

Re: Reaction-Diffusion in HOC

If python is install nrniv should find it.

Try installing the latest version of NEURON from the website https://neuron.yale.edu/neuron/download, the installer has the option to set the correct paths for you.
Sat Aug 25, 2018 9:21 am
Forum: Reaction-diffusion in NEURON
Topic: RxD in Neuron
Replies: 3
Views: 2861

Re: RxD in Neuron

Python must be installed to use rxd and is the prefered interface for specifying new models. If you are working with an existing model created in hoc, there are three ways you could include rxd in the simulation. 1] The simplest way is to specify rxd in python and load it in your hoc file with `nrnp...
Mon Jul 23, 2018 3:38 pm
Forum: Reaction-diffusion in NEURON
Topic: different results from NEURON version 7.5 and NEURON version 7.4
Replies: 1
Views: 1849

Re: different results from NEURON version 7.5 and NEURON version 7.4

Hi,

Sorry to hear that. Could you provide a minimal example of the code that is producing different results? Also how do the results differ?

Thanks.
Wed Jun 06, 2018 11:12 am
Forum: Reaction-diffusion in NEURON
Topic: Different species parameters for different regions
Replies: 7
Views: 4480

Re: Different species parameters for different regions

I was not able to reproduce the error using the current release NEURON 7.5 or development version NEURON 7.6 https://github.com/neuronsimulator/nrn . We may have already fixed this bug. Could you try running the following code; #Additional code from neuron import h, rxd h.load_file('stdrun.hoc') sec...
Fri Feb 16, 2018 4:26 pm
Forum: Reaction-diffusion in NEURON
Topic: Different species parameters for different regions
Replies: 7
Views: 4480

Re: Different species parameters for different regions

To set inhomogeneous initial concentrations you can use a function which take an rxd.Node as an argument. Node has several properties; including x (the 1D location), sec, region and segment. If you want the buffers to diffusion between the spine and dendrite you should use the same region. Here is a...
Thu Oct 05, 2017 6:21 pm
Forum: Reaction-diffusion in NEURON
Topic: Is there a model that handles Signaling Pathways in rxd?
Replies: 1
Views: 10192

Re: Is there a model that handles Signaling Pathways in rxd?

Sorry for the delay in responding. You can use NMODL for the reactions pathway and link the output to rxd using node.include_flux, as in the example you linked to; https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=185858&file=/CaHDemo/onepyr.py#tabs-2 (see the setmGLURflux function). Alte...
Wed Jun 28, 2017 1:47 pm
Forum: Anatomically detailed models
Topic: 2 Cells Sharing and Changing Same ECF Concentrations
Replies: 4
Views: 7051

Re: 2 Cells Sharing and Changing Same ECF Concentrations

Hi, We are extending the reaction-diffusion module (rxd) to support extracellular space, it’s not currently implement in the distributed version of NEURON, but the source code is available on github https://github.com/ramcdougal/nrn.git Here is a simple example of two cells in the extracellular spac...