1. Neuronvisio and Sumatra Run, Store, Search, Locate and Reload simulations' results Michele Mattioni --[email_address]

2. 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

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 asMainclass andparameter_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 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 & depsautomatically tracked everything isarchived andsearchable all the data areaccessible: further analysis/modifyingthe plot/exploresomething else 44. Acknowledgement

Nicolas Le Novre 45. The Computational Systems Neurobiology group @EBI 46. Gael Varoquaux 47. Andrew Davison 48. CodeJam4 organizers

49. The end Neuronvisio Sumatra Thanks. Computed Results Simulations Details