Search found 15 matches

by adamjhn
Mon Mar 18, 2019 11:24 am
Forum: Reaction-diffusion in NEURON
Topic: Reactions only when concentration above a certain limit?
Replies: 1
Views: 622

Re: Reactions only when concentration above a certain limit?

The formulas for rxd.Rate, etc need to be continuous, but you can approximate a threshold function using a sigmoidal shaped curve. For example, you can use rxdmath.tanh to remove calcium at a constant rate when it exceeds a threshold with a narrow transition period: from neuron import h, rxd from ne...
by adamjhn
Mon Feb 18, 2019 4:30 pm
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 672

Re: diffusion intracellular->extracellular->intracellular

1) The following function will return the location of a segment e.g. 'cell1(0.5)', adapted from rxd.species._xyz; def xyz(seg): """Return the (x, y, z) coordinate of the center of the segment.""" sec = seg.sec n3d = sec.n3d() x3d = [sec.x3d(i) for i in range(n3d)] y3d = [sec.y3d(i) for i in range(n3...
by adamjhn
Sun Feb 10, 2019 1:24 pm
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 672

Re: diffusion intracellular->extracellular->intracellular

Thanks for reporting this bug, a fix has been pushed to the development branch. Currently the easiest way to do this is with mod files describing pump mechanism. The production, diffusion and accumulation are then handled by rxd. For example; from neuron import h, crxd as rxd from matplotlib import ...
by adamjhn
Mon Feb 04, 2019 3:05 pm
Forum: Reaction-diffusion in NEURON
Topic: Unexpected 3D behaviour
Replies: 2
Views: 476

Re: Unexpected 3D behaviour

This is due to a bug in reactions in 3D rxd. Thank you for identifying it. We have a fix for it, you can clone https://github.com/neuronsimulator/nrn/tree/7.6 and build from source. Alternatively replace your <neuron python library dir>/neuron/rxd/species.py with https://raw.githubusercontent.com/ne...
by adamjhn
Wed Jan 30, 2019 11:56 am
Forum: Reaction-diffusion in NEURON
Topic: 3D Dimensional RXD/CRXD
Replies: 4
Views: 640

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 ...
by adamjhn
Mon Jan 28, 2019 9:33 pm
Forum: Reaction-diffusion in NEURON
Topic: 3D Dimensional RXD/CRXD
Replies: 4
Views: 640

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...
by adamjhn
Mon Jan 21, 2019 1:52 pm
Forum: Reaction-diffusion in NEURON
Topic: Different reaction rates in different sections
Replies: 3
Views: 504

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...
by adamjhn
Thu Jan 17, 2019 2:50 pm
Forum: Reaction-diffusion in NEURON
Topic: updating Species and Rates inputs
Replies: 2
Views: 390

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...
by adamjhn
Tue Aug 28, 2018 3:38 pm
Forum: Reaction-diffusion in NEURON
Topic: Reaction-Diffusion in HOC
Replies: 5
Views: 17021

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.
by adamjhn
Sat Aug 25, 2018 9:21 am
Forum: Reaction-diffusion in NEURON
Topic: RxD in Neuron
Replies: 3
Views: 1520

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...
by adamjhn
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: 1009

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.
by adamjhn
Wed Jun 06, 2018 11:12 am
Forum: Reaction-diffusion in NEURON
Topic: Different species parameters for different regions
Replies: 7
Views: 2123

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...
by adamjhn
Fri Feb 16, 2018 4:26 pm
Forum: Reaction-diffusion in NEURON
Topic: Different species parameters for different regions
Replies: 7
Views: 2123

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...
by adamjhn
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: 8748

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...
by adamjhn
Wed Jun 28, 2017 1:47 pm
Forum: Anatomically detailed models
Topic: 2 Cells Sharing and Changing Same ECF Concentrations
Replies: 4
Views: 5882

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...