Stephen Larson

2to3

3

Upgrades c302 to work with Python 3.6.

Updates for OpenWorm 0.7 release

1

Hi guys, For the version of the [OpenWorm dockerfile](https://github.com/openworm/OpenWorm/blob/master/Dockerfile), I'd like to incorporate David's changes. This will allow us to have the dockerfile point at the CElegansNeuroML repo and therefore...

Can c302 with jNeuroML-NEURON take advantage of multiple CPU cores?

3

I'm trying to run c302 for a long session and plot the results and I'm doing it on a multi-CPU Amazon instance. Is there anyway to take advantage of multiple...

What would it take to replay a specific pattern of activity into certain c302 neurons during a simulation run?

1

Along the lines of reproducing some neuronal activity data; I'm interested in what infrastructural pieces we would need if given a raster like the following as input and trying to...

As per a model like this, based on calcium? http://www.ncbi.nlm.nih.gov/pubmed/9502792 I ask, not to overcomplicate, but potentially to simplify the process of getting c302 up to the right "dynamic set...

Go through the source and add any explanations to any public methods (those not starting with '_') that ended up undocumented.

Add summary data of system-level C. elegans to openworm/owmeta-data bundle

1

Incorporate the facts from [this spreadsheet](https://docs.google.com/spreadsheets/d/1Dc0FlreJ06cpZo_rFLTnsp4iYPUzPa0a85uMwCGjxoY/edit#gid=0) into the openworm/owmeta-data bundle. Requirements: - Must include references listed in the document as appropriate Document/Evidence - Must use DataSource / DataTranslator for translating...

Run doctests on examples in the docstrings in the source code

1

Set the doctests to run not only on the README.md but also on the examples that are now baked into the source code.

Incorporate data from gene transcription atlas

4

http://cole-trapnell-lab.github.io/projects/worm-cell-atlas/ There are many ways this could help. This should improve accuracy of several of the [data sources](https://pyopenworm.readthedocs.io/en/latest/data_sources.html), including neuropeptides, neuro receptors, and ion channels. Direct link to the getting...

Flesh out ion channel to cell spreadsheet with presence of specific channels in muscle cells

3

The linked spreadsheet contains mappings from named ion channels to a adult neurons. A similar mapping should be generated for muscle cells based on the text descriptions already given in...