Neuronvisio and Sumatra Run, Store, Search, Locate and Reload simulations' results Michele Mattioni --  [email_address]
 
Complexity increase
Tons of Jobs executed http://www.flickr.com/photos/mmayo/6340736/
Two main areas: Computed Results Simulations Details
My current framework to handle this + Neuronvisio Sumatra
Neuronvisio -- background <ul><li>Graphical User Interface helper for NEURON
3D model visualization using Mayavi
plotting of any vectors/variables
Save/Reload of simulation results </li></ul>http://mattions.github.com/neuronvisio/
Integrate with your existing model easily if in Python if in Hoc
Pyramidal cell in Model Db
Neuronvisio -- saving simulation results + Geometry Computed Array NeuroML HDF format
Why HDF (Hierarchical Data Format) <ul><li>store any kind of python list/numpy array (using PyTable)
extremely optimized for numerical data
extremely good with enourmous amount of data
hierarchic structure easy to expand
sqlite approach didn't work... </li></ul>
Neuronvisio HDF file structure
The tree in details - geometry <ul>geometry leaf:  NeuroML rep of the model </ul>
The tree in details -- vecRef <ul><li>Final leaf is an array with computed data.
Every variable has its own array, with the name
Every GenericRef has an indipendent var </li></ul>
Loaded the results of a simulation.
Second area to tackle Neuronvisio Computed Results Simulations Details
Simulations details: <ul>Model specific: <li>Parameters used/ Initial conditions
Stimulations applied: where, when, how?
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Neuronvisio sumatra workflow

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A presentation which I gave at CodeJam 4 in Marseille, France.

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Neuronvisio sumatra workflow

  1. 1. Neuronvisio and Sumatra Run, Store, Search, Locate and Reload simulations' results Michele Mattioni -- [email_address]
  2. 3. Complexity increase
  3. 4. Tons of Jobs executed http://www.flickr.com/photos/mmayo/6340736/
  4. 5. Two main areas: Computed Results Simulations Details
  5. 6. My current framework to handle this + Neuronvisio Sumatra
  6. 7. Neuronvisio -- background <ul><li>Graphical User Interface helper for NEURON
  7. 8. 3D model visualization using Mayavi
  8. 9. plotting of any vectors/variables
  9. 10. Save/Reload of simulation results </li></ul>http://mattions.github.com/neuronvisio/
  10. 11. Integrate with your existing model easily if in Python if in Hoc
  11. 12. Pyramidal cell in Model Db
  12. 13. Neuronvisio -- saving simulation results + Geometry Computed Array NeuroML HDF format
  13. 14. Why HDF (Hierarchical Data Format) <ul><li>store any kind of python list/numpy array (using PyTable)
  14. 15. extremely optimized for numerical data
  15. 16. extremely good with enourmous amount of data
  16. 17. hierarchic structure easy to expand
  17. 18. sqlite approach didn't work... </li></ul>
  18. 19. Neuronvisio HDF file structure
  19. 20. The tree in details - geometry <ul>geometry leaf: NeuroML rep of the model </ul>
  20. 21. The tree in details -- vecRef <ul><li>Final leaf is an array with computed data.
  21. 22. Every variable has its own array, with the name
  22. 23. Every GenericRef has an indipendent var </li></ul>
  23. 24. Loaded the results of a simulation.
  24. 25. Second area to tackle Neuronvisio Computed Results Simulations Details
  25. 26. Simulations details: <ul>Model specific: <li>Parameters used/ Initial conditions
  26. 27. Stimulations applied: where, when, how?
  27. 28. Which kind of geometry?
  28. 29. ... </li></ul><ul>Simulation specific: <li>Reason: why we ran it?
  29. 30. Outcome: how did it go?
  30. 31. ... </li></ul><ul>Code specific: <li>which version of the software did I use?
  31. 32. which dependencies have I used?
  32. 33. ... </li></ul>
  33. 34. Slide from Andrew Davison (main developer), http://neuralensemble.org/meetings/talks/CodeJam3_Davison_Sumatra.pdf http://neuralensemble.org/trac/sumatra
  34. 35. <ul><li>Code under version control </li><ul><li>Accepted version control: </li><ul><li>Mercurial (hg)
  35. 36. Subversion (svn)
  36. 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
  37. 38. How to run the simulation with Sumatra smt run ­­simulator=python ­­main=main.py default.param After Configuration smt run default.param
  38. 39. A part of my param file
  39. 40. Sumatra web interface
  40. 41. Retrieving the simulation details
  41. 42. Accessing the plot from the link
  42. 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
  43. 44. Acknowledgement <ul><li>Nicolas Le Novère
  44. 45. The Computational Systems Neurobiology group @EBI
  45. 46. Gael Varoquaux
  46. 47. Andrew Davison
  47. 48. CodeJam4 organizers </li></ul>
  48. 49. The end Neuronvisio Sumatra Thanks. Computed Results Simulations Details

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