neuroml-python — All things Python related, particularly the Python API for NeuroML

[Neuroml-python] An object model for representing neuronal morphologies

[Michael H. <mik...@go...>]

Hi Guys,
Good to talk over skype, its really great to see upcoming developments.

I have just been thinking about the logisitics of library maintenance.

The aim is pull out the core morphology classes out of morphforge, and
into a separate package, since we want small, well encapsulated modules.
If we put the morphology class into libNeuroML, and this is intended as a
simulator independent API (i.e. more than just morphologies), then we
haven't achieved this; its the same situation that we had before, just
replace 'morphforge' for 'libNeuroML' and we still have unnessesary
dependancies if people just want to use the 'morphology' part of the library.
If we are going to pull out the morphology part of the library,
shouldn't this go in
an entirely small, separate repository, called, for example,
'neuro-morph' or something
similar, then both libNeuroML and morphforge can just import this
repository as a
submodule:

http://git-scm.com/book/en/Git-Tools-Submodules

This allows us both to use 'neuro-morph', without either side introducing
unnessessary dependancies. Github seems to support submodules.
(http://help.github.com/submodules/)

What do you think?


Mike

[Neuroml-python] Python API for multicompartmental cell models with import/export to NeuroML

[Padraig G. <p.g...@uc...>]

Hi,

One of the main outcomes of the NeuroML/CodeJam meeting was an 
initiative to try to create a common API for creating and editing 
multicompartmental neuron models in Python. This sprang from a number of 
parties who were developing applications in Python which could (or were 
planning to) create/simulate/visualise/analyse detailed neurons. 
Examples of these include Michele Mattioni's NeuronVisio, Stephan 
Gerhard's CATMAID, Mike Hull's Morphforge, Mike Vella's model 
optimisation framework... Also important in this were the provisional 
Python API for reading/writing NeuroML v2.0, and PyNN's wish to expand 
to multicompartmental neurons.

Following some initial email discussion, a repository has been set up on 
GitHub to gather ideas and test some initial implementations towards 
this API: https://github.com/NeuralEnsemble/libNeuroML.

Some initial thoughts on what should be in the API are contained in the 
ideas folder, and a proposal for the overall scope of the project is 
outlined here: 
https://github.com/NeuralEnsemble/libNeuroML/blob/master/ideas/padraig/ScopeOfProject.

While this is a "NeuroML" library, the hope is that the NeuroML 2 object 
model will sufficiently represent the objects which needed to be 
manipulated through such an API and that this library will provide a 
core with read/write functionality in XML & HDF5 which can be used as a 
basis for other interesting applications which deal with detailed 
neuronal models.

There has been a new mailing list set up, 
neu...@li... (subscribe at 
https://lists.sourceforge.net/lists/listinfo/neuroml-python), for all 
matters at the intersection of Python & NeuroML & hopefully 
multicompartmental neuron modelling in Python in general. Please 
contribute ideas to this (or fork the repository above) to give your 
feedback.

Note the NeuroML 2 pages here: http://www.neuroml.org/neuroml2 will soon 
be updated to point to this new initiative.

There will be a Skype call on Monday next week to discuss this API in a 
bit more detail, contact Andrew Davison if you'd like to be included on 
that.

Regards,
Padraig

-----------------------------------------------------
Padraig Gleeson
Room 321, Anatomy Building
Department of Neuroscience, Physiology&  Pharmacology
University College London
Gower Street
London WC1E 6BT
United Kingdom

+44 207 679 3214
p.g...@uc...
-----------------------------------------------------

[Neuroml-python] Tester

[Padraig G. <p.g...@uc...>]

Just a test mail...