Padraig Gleeson
Padraig Gleeson
c302 has recently been updated to be more owmeta compatible. This new version and a recent owmeta (as opposed to PyOpenWorm) should be used in the Dockerfile
Currently BMTK will delete all files & subfolders in the output_dir as specified of a Sonata file: ``` "output":{ "output_dir": "$OUTPUT_DIR", ... } ``` including presumably the user's home directory...
e.g. if this value for dt: https://github.com/AllenInstitute/sonata/blob/ad1d46a97029749aea835f9f016bfa1ccba1f258/examples/300_pointneurons/simulation_config.json#L10 is changed to a more realistic 0.01 ms, the following error occurs: ``` ... 2019-04-29 19:27:47,332 [INFO] Setting up output directory 2019-04-29 19:27:47,332...
A simple python script to check the local installation of (py)CUDA would be very helpful, giving info on current configuration, hardware specs etc.
In place of having to edit the herm_full_edgelist.csv file: https://github.com/openworm/CElegansNeuroML/pull/103/files#diff-0a90d206f61bd181aeabe98ef98a8887
Particularly png file here: https://github.com/openworm/CElegansNeuroML/tree/master/CElegans/pythonScripts/c302/examples/summary
A good candidate for testing OW simulations, and c302 in particular on the [SpiNNaker platform](http://apt.cs.manchester.ac.uk/projects/SpiNNaker/) would be this: [c302_A_Social.nml](https://github.com/openworm/CElegansNeuroML/blob/master/CElegans/pythonScripts/c302/examples/c302_A_Social.nml) It's the lowest level of complexity for the c302 model (params...
Being worked on here: https://github.com/openworm/CElegansNeuroML/tree/params_d - [x] Test & merge to master - [x] Incorporate in [this figure](https://github.com/openworm/CElegansNeuroML/blob/master/CElegans/pythonScripts/c302/examples/summary/README.md) - [ ] Need to load in axonal/dendritic connection locations generated from...
There is information on the neurotransmitters in each C elegans neuron here: [A cellular and regulatory map of the cholinergic nervous system of C. elegans](http://elifesciences.org/content/4/e12432v2) This should be compared with...