Search found 7 matches

by mgiugliano
Sun Feb 09, 2020 5:07 am
Forum: Getting started
Topic: finitialize() not working?
Replies: 2
Views: 722

Re: finitialize() not working?

Thank you for your precious answer.
by mgiugliano
Sat Feb 08, 2020 10:10 am
Forum: Getting started
Topic: finitialize() not working?
Replies: 2
Views: 722

finitialize() not working?

I am preparing a simple PYTHON-NEURON tutorial and found I am unable to use finitialize() properly. In the minimal code, below, the initial condition set by finitialize(-100) is ignored and the simulated voltage trace starts at -65mV. Why? Can anybody help me, understanding where is my mistake? Than...
by mgiugliano
Thu Aug 09, 2018 11:45 am
Forum: Adding new mechanisms and functions to NEURON
Topic: HOC kernel for Jupyter
Replies: 3
Views: 2563

Re: HOC kernel for Jupyter

Yes, it would be a terrific idea and similarly it would be nice to have the graphs appear inline.
by mgiugliano
Thu Aug 09, 2018 6:45 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Computational Optogenetics: modelling ChR2 in NMODL
Replies: 2
Views: 1859

Computational Optogenetics: modelling ChR2 in NMODL

Dear All, I implemented the channelrhodopsin model ChR2 (H134R mutant), described in a recent PLoS Comp Biology paper[1], as a nonspecific current mechanism. I have then shared this model on ModelDB (accession number 244414; to become public in the coming days). Given my limited proficiency in NEURO...
by mgiugliano
Mon Aug 06, 2018 3:11 pm
Forum: Getting started
Topic: Creation of channelrhodopsin2 using Neuron
Replies: 12
Views: 6237

[BUG FOUND!] Re: Creation of channelrhodopsin2 using Neuron

Posting in a prestigious forum as this one has strange (positive) effects: debugging occurs telepathically ;-)))))) I have now solved my (presumed) numerical instability upon removing one of the o.d.e. describing the kinetic scheme: they are NOT all independent and NEURON probably was annoyed by my ...
by mgiugliano
Mon Aug 06, 2018 12:33 pm
Forum: Getting started
Topic: Creation of channelrhodopsin2 using Neuron
Replies: 12
Views: 6237

Re: Creation of channelrhodopsin2 using Neuron

Presumably this would be a re-implementation with NEURON of a previously published model. Several such models have been published--which one do you have in mind? Are you familiar with Williams JC, Xu J, Lu Z, Klimas A, Chen X, Ambrosi CM, Cohen IS, and Entcheva E Computational Optogenetics: Empiric...
by mgiugliano
Fri Aug 18, 2006 12:19 pm
Forum: Other questions
Topic: Custom extracellular plane, Poisson equation and dft..
Replies: 2
Views: 5732

Custom extracellular plane, Poisson equation and dft..

I need to implement and simulate a network of multi-compartmental neurons, "sitting" on a conductive film (e.g. a giant substrate metallic/non-metallic microelectrode). Mathematically I know I need to solve a 2D Poisson equation, specifying ad-hoc current sources and sinks (not uniformly distributed...