Comments (7)
Couple of questions @pgleeson:
-
What's the general goal here? You need an NML file that contains the standard groups, so it works with the rest of neuroml libraries? And is the current problem here because the mitral.hoc file does not have the groups, but the existing segments can be heuristically assigned to one of the standard groups?
-
There are 4 groups in the generated NML, but only 3 standard ones (soma_group, dendrite_group, axon_group). What do you want to do with the extra group?
These are the groups present in the NML:
ModelViewParmSubset_1
ModelViewParmSubset_2
ModelViewParmSubset_3
ModelViewParmSubset_4
- Do you suggest (1) changing the group names AFTER the NML is generated with export_to_neuroml2 function, OR (2) the export_to_neuroml2 function should be modified so it generates the NML with the standard group names?
from miglioreetal14_olfactorybulb3d.
I didn't hear back in time. I'm handling the ModelViewP... groups by removing them and then replacing them with the standard all, axon, soma, and dendrite groups. See the bottom of the cell files in the above pull request.
from miglioreetal14_olfactorybulb3d.
Since the info on conductances, capacitance etc. will all be added afterwards, then yes, all of the Neuron generated groups can be removed, and the only ones needed are the "standard" ones used in NML1/2. Changing the nml file after generation in export_mitral.py was the right way to go.
Looks like this has been done correctly in the PR, though you seem to have used an older version of pyNeuroML. I'll merge and update, but you should update this (and libNeuroML) locally.
from miglioreetal14_olfactorybulb3d.
seem to have used an older version of pyNeuroML<<
Ah, maybe this explains the weird path issues I was seeing. Will update.
from miglioreetal14_olfactorybulb3d.
This is an example of how the standard group names are useful:
from miglioreetal14_olfactorybulb3d.
Oh I see, very nice
from miglioreetal14_olfactorybulb3d.
Old local version of pyNeuroML was it. I've removed the workaround in this pr: #9
from miglioreetal14_olfactorybulb3d.
Related Issues (20)
- Add channel density specifications in export_mitral.py HOT 9
- Add test script for creating and running one Mitral cell in NEURON HOT 15
- Create smaller scale version of network that can run on single processor HOT 5
- Export network structure to NML2 HOT 15
- Resolve issue of disconnected axon hillock HOT 4
- GCs do not appear to have position information HOT 1
- Create NML2/LEMS versions of synaptic mechanisms HOT 4
- Implement helper method for converting fraction along segmentGroup to fraction along segment (with id)) HOT 1
- Export or create NML2 cell file(s) for granule cell HOT 2
- Visualise/verify network connectivity as exported in NML2 HOT 17
- cell with multiple specificCapacitances OR directly connect segments of different cells together HOT 2
- Python scripts for exporting Mitral/Granule cells should be (re)added HOT 3
- Synapse conditional NET RECEIVE logic introduces delays
- running jnml -netpyne results in error related to non0-1 parentFractionAlong
- Mitral cells are not translated correctly when positioned via the network location tag
- Channel initialization contributes to conversion error
- OMV: Test Mitral cell across multiple inputs & compare to NEURON HOT 1
- Adding license info HOT 2
- Python 3 HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from miglioreetal14_olfactorybulb3d.