Neuronvisio sumatra workflow

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  1. Neuronvisio and Sumatra Run, Store, Search, Locate and Reload simulations' results Michele Mattioni -- [email_address] 3. Complexity increase 4. Tons of Jobs…
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  • 1. Neuronvisio and Sumatra Run, Store, Search, Locate and Reload simulations' results Michele Mattioni -- [email_address]
  • 3. Complexity increase
  • 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 <ul><li>Graphical User Interface helper for NEURON
  • 8. 3D model visualization using Mayavi
  • 9. plotting of any vectors/variables
  • 10. Save/Reload of simulation results </li></ul>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) <ul><li>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... </li></ul>
  • 19. Neuronvisio HDF file structure
  • 20. The tree in details - geometry <ul>geometry leaf: NeuroML rep of the model </ul>
  • 21. The tree in details -- vecRef <ul><li>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 </li></ul>
  • 24. Loaded the results of a simulation.
  • 25. Second area to tackle Neuronvisio Computed Results Simulations Details
  • 26. Simulations details: <ul>Model specific: <li>Parameters used/ Initial conditions
  • 27. Stimulations applied: where, when, how?
  • 28. Which kind of geometry?
  • 29. ... </li></ul><ul>Simulation specific: <li>Reason: why we ran it?
  • 30. Outcome: how did it go?
  • 31. ... </li></ul><ul>Code specific: <li>which version of the software did I use?
  • 32. which dependencies have I used?
  • 33. ... </li></ul>
  • 34. Slide from Andrew Davison (main developer), http://neuralensemble.org/meetings/talks/CodeJam3_Davison_Sumatra.pdf http://neuralensemble.org/trac/sumatra
  • 35. <ul><li>Code under version control </li><ul><li>Accepted version control: </li><ul><li>Mercurial (hg)
  • 36. Subversion (svn)
  • 37. Git (git) (I patched it! Power of the opensource..) </li></ul></ul><li>Scripts organized as Main class and parameter_file </li></ul>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
  • 40. Sumatra web interface
  • 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 <ul><li>Nicolas Le Novère
  • 45. The Computational Systems Neurobiology group @EBI
  • 46. Gael Varoquaux
  • 47. Andrew Davison
  • 48. CodeJam4 organizers </li></ul>
  • 49. The end Neuronvisio Sumatra Thanks. Computed Results Simulations Details
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