Neuronvisio sumatra workflow
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This document discusses using Neuronvisio and Sumatra together to run, store, search, locate, and reload neural simulation results. Neuronvisio is a graphical interface that can visualize simulation results from NEURON models and save results to HDF files. Sumatra is a tool that tracks parameters, dependencies, and details of simulations run from the command line to archive and allow searching simulations. It suggests using these tools together so that simulation results computed in NEURON can be efficiently stored, organized, and reloaded for further analysis or visualization in Neuronvisio.
![Neuronvisio and Sumatra Run, Store, Search, Locate and Reload simulations' results Michele Mattioni -- [email_address]](https://image.slidesharecdn.com/neuronvisiosumatraworkflow-100702055903-phpapp01/85/Neuronvisio-sumatra-workflow-1-320.jpg)
Neuronvisio sumatra workflow
- 1. Neuronvisio and Sumatra Run, Store, Search, Locate and Reload simulations' results Michele Mattioni -- [email_address]
- 4. Tons of Jobs executed http://www.flickr.com/photos/mmayo/6340736/
- 5. Two main areas: Computed Results Simulations Details
- 6. My current framework to handle this + Neuronvisio Sumatra
- 7. Neuronvisio -- background Graphical User Interface helper for NEURON
- 8. 3D model visualization using Mayavi
- 9. plotting of any vectors/variables
- 10. Save/Reload of simulation results http://mattions.github.com/neuronvisio/
- 11. Integrate with your existing model easily if in Python if in Hoc
- 12. Pyramidal cell in Model Db
- 13. Neuronvisio -- saving simulation results + Geometry Computed Array NeuroML HDF format
- 14. Why HDF (Hierarchical Data Format) store any kind of python list/numpy array (using PyTable)
- 15. extremely optimized for numerical data
- 16. extremely good with enourmous amount of data
- 17. hierarchic structure easy to expand
- 18. sqlite approach didn't work...
- 19. Neuronvisio HDF file structure
- 20. The tree in details - geometry geometry leaf: NeuroML rep of the model
- 21. The tree in details -- vecRef Final leaf is an array with computed data.
- 22. Every variable has its own array, with the name
- 23. Every GenericRef has an indipendent var
- 24. Loaded the results of a simulation.
- 25. Second area to tackle Neuronvisio Computed Results Simulations Details
- 26. Simulations details: Model specific: Parameters used/ Initial conditions
- 27. Stimulations applied: where, when, how?
- 28. Which kind of geometry?
- 29. ... Simulation specific: Reason: why we ran it?
- 30. Outcome: how did it go?
- 31. ... Code specific: which version of the software did I use?
- 32. which dependencies have I used?
- 33. ...
- 34. Slide from Andrew Davison (main developer), http://neuralensemble.org/meetings/talks/CodeJam3_Davison_Sumatra.pdf http://neuralensemble.org/trac/sumatra
- 35. Code under version control Accepted version control: Mercurial (hg)
- 36. Subversion (svn)
- 37. Git (git) (I patched it! Power of the opensource..) Scripts organized as Main class and parameter_file Adding git to smt supported vcs
- 38. How to run the simulation with Sumatra smt run simulator=python main=main.py default.param After Configuration smt run default.param
- 39. A part of my param file
- 41. Retrieving the simulation details
- 42. Accessing the plot from the link
- 43. Summing up To run the simulation: smt run default.param To browse ans search within the simulations smtweb To load them in Neuronvisio: run nrnvisio Data/DD-MM-YYYY/Sim_N parameters & deps automatically tracked everything is archived and searchable all the data are accessible: further analysis/modifying the plot/explore something else
- 44. Acknowledgement Nicolas Le Novère
- 45. The Computational Systems Neurobiology group @EBI
- 46. Gael Varoquaux
- 47. Andrew Davison
- 49. The end Neuronvisio Sumatra Thanks. Computed Results Simulations Details