I’m pleased to say that we have released Neuronvisio 0.8.5, which has several small improvements and better documentation. I’m pretty sure that there is always room to improve the documentation.
Anyway, first of all the cerebellum network rendered in Neuronvisio, with the model taken from the NeuroML website
Cerebellum Network, taken from the NeuroML example pack
The idea with this release was to demonstrate the ability of Neuronvisio to visualize also Network models which are instantiated in NEURON. To note, this ability has been there from version 0.1.0, but now we are beaming on it.
Neuronvisio is able to import 3 different files: hdf5 structured in Neuronvisio format, hoc files, and NeuroML.
The first file is our way to approach hdf5, which gives us the ability to save all the data of a simulation, plus the model itself in one single file, which can then be reloaded and moved. We do all the work here.
The other two are files format where Neuronvisio does not import directly, but let’s NEURON do the heavy-lifting, to avoid any duplication. The hoc format is classic NEURON interpreted script, while NeuroML is an effort to standardize the way neuronal model are encoded.
In particular I would like to stress the last point: Neuronvisio does not have an ad-hoc NeuroML importer, but re-use the one provided by NEURON. We now just exposing an easy way to load a NeuroML file directly in Neuronvisio with the load method from the Controls class
from neuronvisio.controls import Controls
controls = Controls() # starting the GUI
controls.load('path/to/my_model.xml') #or .h5 or .hoc
or directly launching the program, if you prefer
$ neuronvisio [path/to/my_model.xml] # or .h5 or .hoc
this gives us one powerful interface to simplify the life of a user.
Of course, if your model is in python, you can always run it within Ipython as standard python file
$ neuronvisio
In [1]: run path/to/my_model_in_python
The only problem is the NeuroML importer from NEURON does not handle properly the Network file of NeuroML, and this has been registered as issue #50 on our bug-tracker. This belong more to NEURON then Neuronvisio, but they don’t have a bug-tracker, so we logged on ours tracker and we will link any other place where the discussion will take place. NEURON has an amazing forum with quite instantaneous answers from the NEURON community, including Hines and Carnevale, and we will bring the issue over there.
So, we didn’t write our NeuroML importer, because there is no point to replicate what a software already does. That’s why we are now collaborating with the writing of the libNeuroML library, to have one good library that permits to load any NeuroML model properly, and then give the ability to the developer to map it to its own data-structure.
This is the same approach used in the SBML community, which I think is very powerful.
P.S.: So how did we manage to load the Network in NEURON and visualize it in Neuronvisio, if the NEURON (sorry, NEURON has to be written all capital to be precise…) NeuroML importer is not up to the job yet? We have used the neuroConstruct program, which is able to export a model to NEURON, and used the hoc files to load the model up.
