Thursday, May 1, 2014

PyOpenWorm and NeuroML

I'm trying to make a neuroml file from the generated rdf database in PyOpenWorm. Trying to make sense of the schema. Everything is related through integer keys and I haven't found a human description yet.

Update 1:
All of the methods read through to the a RDF graph built up in the network module. However, the neuron is not checked for existence in the databse on creation. I'm going to add a primary access method with the check.

Update 2:
Thinking about the structure of these modules. I'm guessing a config file would be good for moving the configurations around. PyOpenWorm should be a library that can be used to make the wrappers, so it shouldn't be tied to any specific database. Sounds like a job for Dependency Inversion (i.e. parametrizing the network class).

Update 3:
Learning libneuorml from Padraig G's examples in the github repo. Right now, I'm leaning towards separating the file-type specific components from PyOpenWorm proper. Eventually I want to stop opening up the library files (closely tied to the schema) and spend my time with the file-specific converters.

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