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SED-ML Presentation

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This presentation was held at the SBML/BioModels.net hackathon on May 1st 2010. It gives a brief overview of SED-ML and introduces a first implementation with http://libsedml.sf.net.

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SED-ML Presentation

  1. 1. The  Simulation  Experiment   Description  Markup  Language   Frank  T.  Bergmann  &  Dagmar  Waltemath     SBML  &  BioModels  Hackathon,  Seattle  2010  
  2. 2. MOTIVATION   2  
  3. 3. Motivation   J.  theor.  Biol.  (1999)  198,  445-­‐459   3   Article  No.  jtbi.1999.0924,  available  online  at  http://www.idealibrary.com  
  4. 4. Motivation   BM  22       Changes  in  model   parameterization   Use  of  a  number  of   different  models  in   one  experiment   Choice  of  correct   simulation  algorithm   Post-­‐processing  of  the   result  data,  e.g.   normalization,   logarithmic  scale     BM  86   4  
  5. 5. HOW  DOES  SED-­‐ML  HELP?   5  
  6. 6. Repeatable  simulation  experiments   Simulation  Experiment  Description    Markup   Language  (SED-­‐ML):     Is  a  language  that  aims  to  standardize  the  exchange   of  simulation  experiments,  independently  from  the   model  description  language  and  the  simulation  tool.       6  
  7. 7. Repeatable  simulation  experiments   Simulation   Model   Task   Reports   Data  Generators   7  
  8. 8. Repeatable  simulation  experiments   Simulation   Model   Model  class   Task   o reference  to   model  source   o model  type   Reports   o changes  to  be   applied  to  the   Data  Generators   model     8  
  9. 9. Repeatable  simulation  experiments   Simulation   Model   Simulation  class   o Simulation  experiment  type   Task   o Uniform  TimeCourse   o Reports   KiSAO   o Simulation  duration,  start   time....   Data  Generators   9  
  10. 10. Repeatable  simulation  experiments   Simulation   Model   Task   Task  class   Reports   o Connector  of   one  Model   Data  Generators   object  and  one   Simulation   object   10  
  11. 11. Repeatable  simulation  experiments   Simulation   Model   Task   DataGenerator     Reports   o Definition  of  how   to  generate  the   necessary  data  for   Data  Generators   the  output  from   the  simulation   results   11  
  12. 12. SED-­‐ML  Main  Concepts     o No  description  of  the   simulation  results     o SBRML     o No  description  of  the   layout  of  the  output   curves   12  
  13. 13. SED-­‐ML   13  
  14. 14. SED-­‐ML  L1  V1   SED-­‐ML  Spec  is  on   the  way   preliminary  version   available  from  Source   forge   Feel  free  to  read,  bug   report  and  start   implementing  :-­‐)   http://sourceforge.net/projects/sed-­‐ml/   14  
  15. 15. IMPLEMENTATION   15  
  16. 16. Implementation   SED-­‐ML  Script  Editor   libSedMLScript   libSedML   Other  SBW  enabled   libSedMLRunner   Simulators   RoadRunner   Simulation  Tool   http://libsedml.sf.net     16  
  17. 17. Implementation   AddTimeCourseSimulation('simulation1',  'KiSAO:0000071',  0,  50,   1000,  1000)     AddModel('model1',  'urn:miriam:biomodels.db:BIOMD0000000021')     AddModel('model2',  'model1')   AddParameterChange('model2',  'V_mT',  '0.28')   AddParameterChange('model2',  'V_dT',  '4.8')     AddTask('task1',  'simulation1',  'model1')   AddTask('task2',  'simulation1',  'model2')     AddColumn('time',  [['time',  'task1',  'time']])   AddColumn('Mt_original',  [['v1',  'task1',  'Mt']])   AddColumn('Mt_chaotic',  [['v2',  'task2',  'Mt']])   AddColumn('Mt_combined',  [['v1',  'task1',  'Mt'],  ['v2',  'task2',   'Mt'],  'v1  -­‐  v2  +  20'])     AddPlot('plot1',  'tim  mRNA  with  Oscillation  and  Chaos',   [['time',  'Mt_original'],  ['time',  'Mt_chaotic'],  ['time',   'Mt_combined']]);   http://libsedml.sf.net     17  
  18. 18. Implementation   AddTimeCourseSimulation('simulation1',  'KiSAO:0000071',  0,  50,   1000,  1000)     AddModel('model1',  'urn:miriam:biomodels.db:BIOMD0000000021')     AddModel('model2',  'model1')   AddParameterChange('model2',  'V_mT',  '0.28')   AddParameterChange('model2',  'V_dT',  '4.8')     AddTask('task1',  'simulation1',  'model1')   AddTask('task2',  'simulation1',  'model2')     AddColumn('time',  [['time',  'task1',  'time']])   AddColumn('Mt_original',  [['v1',  'task1',  'Mt']])   AddColumn('Mt_chaotic',  [['v2',  'task2',  'Mt']])   AddColumn('Mt_combined',  [['v1',  'task1',  'Mt'],  ['v2',  'task2',   'Mt'],  'v1  -­‐  v2  +  20'])     AddPlot('plot1',  'tim  mRNA  with  Oscillation  and  Chaos',   [['time',  'Mt_original'],  ['time',  'Mt_chaotic'],  ['time',   'Mt_combined']]);   http://libsedml.sf.net     18  
  19. 19. Outlook   Nested  Tasks     More  Simulation   Experiments     Advanced  Post   processing   http://dx.doi.org/10.1038/npre.2010.4257.1     19  
  20. 20. Acknowledgments   Nicolas  Le  Novére   Sven  Sahle   Henning  Schmidt   Mike  Hucka   Ion  Moraru   Fedor  Kolpakov   http://biomodels.net/sed-­‐ml   20  

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