Applying  the  Scien.fic  Method  
to  Simula.on  Experiments
Frank	
  T.	
  Bergmann,	
  PhD	
  
California	
  Ins8tute	
 ...
Outline
Background	
  &	
  Introduc8on	
  
Simula8on	
  Experiment	
  Descrip8on	
  Markup	
  Language	
  –	
  
SED-­‐ML	
...
Scien.fic  Method

Scien&fic	
  method	
  –	
  body	
  of	
  techniques	
  
for	
  inves3ga3ng	
  phenomena	
  and	
  
acqui...
Models
Models

Teusink	
  et.	
  al,	
  2003,	
  DOI:	
  10.1046/j.1432-­‐1327.2000.01527.x	
  
Adapted	
  from	
  Michael	
  Hucka	
  	
  
Model
Species

Species	
  
Reac.ons

Species	
  

Reac8ons	
  
Rate  Laws

Species	
  

Reac8ons	
  
Systems  Biology  Markup  Language  (SBML)
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/le...
SBML  SoCware  Guide

hOp://sbml.org/SBML_SoMware_Guide	
  
Journals
•  BioMedCentral	
  (all	
  journals)	
  
•  Biophysical	
  Journal	
  
•  Computa8onal	
  and	
  Mathema8cal	
  ...
Models

Teusink	
  et.	
  al,	
  2003,	
  DOI:	
  10.1046/j.1432-­‐1327.2000.01527.x	
  
Simula.on  Experiments
Simula.on  Experiments

Huang	
  et.	
  al,	
  1996,	
  DOI:	
  10.1073/pnas.93.19.10078	
  
biomodels.net/biomodels
biomodels.net/biomodels

Adapted	
  from	
  Michael	
  Hucka	
  	
  
Simula.on  Experiments

Cura8on	
  tab	
  of	
  BioModel	
  #9	
  

Curator's comment: (updated: 15 Jul 2013 13:25:23 BST)...
Simula.on  Experiments

Curator's comment: (updated: 15 Jul 2013 13:25:23 BST)#
Figure 2B of the reference publication has...
Large  scale  integra.ve  models  …  
Outline
Background	
  &	
  Introduc8on	
  
Simula8on	
  Experiment	
  Descrip8on	
  Markup	
  Language	
  –	
  
SED-­‐ML	
...
Simula.on  Experiment  
Descrip.on  Markup  Language
SED-­‐ML:  Repeatable  simula.on  experiments
Model	
  
SED-­‐ML:  Repeatable  simula.on  experiments
Simula8on	
  

Model	
  
SED-­‐ML:  Repeatable  simula.on  experiments
Model	
  

Simula8on	
  

Task	
  
SED-­‐ML:  Repeatable  simula.on  experiments
Model	
  

Simula8on	
  

Task	
  

Data	
  Generators	
  
SED-­‐ML:  Repeatable  simula.on  experiments
Model	
  

Simula8on	
  

Task	
  

Reports	
  
Data	
  Generators	
  
SED-­‐ML  Level  1  Version  1
SED-­‐ML  Level  1  Version  2
One	
  
Step	
  	
  

Model	
  

Simula8on	
  

Steady	
  	
  
State	
  

Parameters	
  

T...
SED-­‐ML  L1V2
SED-­‐ML  Future
SED-­‐ML
• Coverage	
  
• Simula8ons	
  (stochas8c	
  /	
  determinis8c	
  /	
  steady	
  state)	
  
• Parameter	
  Scans	...
Outline
Background	
  &	
  Introduc8on	
  
Simula8on	
  Experiment	
  Descrip8on	
  Markup	
  Language	
  –	
  
SED-­‐ML	
...
SED-­‐ML  Script  Editor

hOp://libsedml.sf.net	
  	
  
SED-­‐ML  Web  Tools

hOp://sysbioapps.dyndns.org/SED-­‐ML_Web_Tools	
  	
  
Systems  Biology  Workbench

hOp://sbw.sf.net	
  	
  
Systems  Biology  Workbench

hOp://sbw.sf.net	
  	
  
Systems  Biology  Workbench

hOp://sbw.sf.net	
  	
  
CellDesigner

hOp://celldesigner.org	
  	
  
hOp://pysces.sf.net	
  	
  
SBSI  –  SED  ED

hOp://sourceforge.net/projects/sbsi/	
  	
  
COPASI

hOp://www.copasi.org/	
  	
  
VCELL

hOp://www.nrcam.uchc.edu/	
  	
  
JWS  Online

hOp://jjj.biochem.sun.ac.za/	
  	
  
Libraries
•  libSedML:	
  .NET;	
  BSD	
  License	
  	
  
hOp://libsedml.sourceforge.net	
  
•  libSEDML:	
  C/C++	
  with...
Outline
Background	
  &	
  Introduc8on	
  
Simula8on	
  Experiment	
  Descrip8on	
  Markup	
  Language	
  –	
  
SED-­‐ML	
...
Conclusions
•  Opportunity:	
  Simula8on	
  Experiments	
  as	
  readily	
  exchangeable	
  as	
  
computa8onal	
  models	...
Next  Steps  …  
•  Finalize	
  SED-­‐ML	
  Level	
  1	
  Version	
  2	
  
•  Prototype	
  on	
  Version	
  3	
  

•  Expo...
Acknowledgements
	
  
•  SED-­‐ML	
  Editors:	
  Frank	
  T.	
  Bergmann,	
  Dagmar	
  Waltemath,	
  Jonathan	
  
Cooper,	...
More  Informa.on  
•  SED-­‐ML:	
  
hOp://sed-­‐ml.org	
  	
  
hOp://8nyurl.com/sed-­‐ml-­‐l1v2-­‐rc	
  	
  
hOps://lists....
Applying the Scientific Method to Simulation Experiments
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Applying the Scientific Method to Simulation Experiments

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In this talk I would like to explore on how to apply the scientific method to in silico experiments. How can we design these experiments, so that they are independent of the software tool that gave rise to them? Over the past decade we have seen the rise of model exchange formats such as the Systems Biology Markup Language (SBML), that enable us to share the models readily with colleagues and between applications.

Here I present the Simulation Experiment Description Markup Language (SED-ML) that aims to do the same thing for in silico experiments. After detailing its history, and where it currently stands, I will give a short overview of the growing tool support.

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Applying the Scientific Method to Simulation Experiments

  1. 1. Applying  the  Scien.fic  Method   to  Simula.on  Experiments Frank  T.  Bergmann,  PhD   California  Ins8tute  of  Technology   University  of  Heidelberg   Bergman@caltech.edu    
  2. 2. Outline Background  &  Introduc8on   Simula8on  Experiment  Descrip8on  Markup  Language  –   SED-­‐ML   SoMware  Support   Conclusion  
  3. 3. Scien.fic  Method Scien&fic  method  –  body  of  techniques   for  inves3ga3ng  phenomena  and   acquiring  new  knowledge,  as  well  as  for   correc&ng  and  integra&ng  previous   knowledge.   hOp://en.wikipedia.org/wiki/Scien8fic_method  
  4. 4. Models
  5. 5. Models Teusink  et.  al,  2003,  DOI:  10.1046/j.1432-­‐1327.2000.01527.x  
  6. 6. Adapted  from  Michael  Hucka    
  7. 7. Model
  8. 8. Species Species  
  9. 9. Reac.ons Species   Reac8ons  
  10. 10. Rate  Laws Species   Reac8ons  
  11. 11. Systems  Biology  Markup  Language  (SBML) <?xml version="1.0" encoding="UTF-8"?> <sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4"> <model id="BorisEJB" name="BorisEJB"> <listOfCompartments> <compartment id="compartment" size="1"/> </listOfCompartments> <listOfSpecies> <species id="MKKK" compartment="compartment" initialConcentration="90"/> <species id="MKKK_P" compartment="compartment" initialConcentration="10"/> [ . . . ] </listOfSpecies> <listOfParameters> <parameter id="J0_V1" value="2.5"/> <parameter id="J0_Ki" value="9"/> <parameter id="J0_n" value="1"/> <parameter id="J0_K1" value="10"/> [ . . . ] </listOfParameters> <listOfReactions> <reaction id="J0" reversible="false"> <listOfReactants> <speciesReference species="MKKK"/> </listOfReactants> <listOfProducts> <speciesReference species="MKKK_P"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="MAPK_PP"/> <modifierSpeciesReference species="MAPK_PP"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> [ . . . ]
  12. 12. SBML  SoCware  Guide hOp://sbml.org/SBML_SoMware_Guide  
  13. 13. Journals •  BioMedCentral  (all  journals)   •  Biophysical  Journal   •  Computa8onal  and  Mathema8cal  Biology   •  FEBS  Journal   •  IET  Systems  Biology   •  Molecular  Systems  Biology   •  Nature  (all  NPG  journals)   •  PLoS  (all  journals)   •  PNAS   •  Royal  Society  of  Chemistry  (all  journals)   •  UCSD  Molecule  Pages   hOp://sbml.org/Documents/Publica8ons_known_to_accept_submissions_in_SBML_format  
  14. 14. Models Teusink  et.  al,  2003,  DOI:  10.1046/j.1432-­‐1327.2000.01527.x  
  15. 15. Simula.on  Experiments
  16. 16. Simula.on  Experiments Huang  et.  al,  1996,  DOI:  10.1073/pnas.93.19.10078  
  17. 17. biomodels.net/biomodels
  18. 18. biomodels.net/biomodels Adapted  from  Michael  Hucka    
  19. 19. Simula.on  Experiments Cura8on  tab  of  BioModel  #9   Curator's comment: (updated: 15 Jul 2013 13:25:23 BST)# Figure 2B of the reference publication has been reproduced using Copasi 4.10 (Build 55). A logarithmic parameter scan over a range of "MAPKKK activator (Ras)" values with simultaneous calculation of the steady state was performed.# Huang  et.  al,  1996,  DOI:  10.1073/pnas.93.19.10078  
  20. 20. Simula.on  Experiments Curator's comment: (updated: 15 Jul 2013 13:25:23 BST)# Figure 2B of the reference publication has been reproduced using Copasi 4.10 (Build 55). A logarithmic parameter scan over a range of "MAPKKK activator (Ras)" values with simultaneous calculation of the steady state was performed.# Huang  et.  al,  1996,  DOI:  10.1073/pnas.93.19.10078  
  21. 21. Large  scale  integra.ve  models  …  
  22. 22. Outline Background  &  Introduc8on   Simula8on  Experiment  Descrip8on  Markup  Language  –   SED-­‐ML   SoMware  Support   Conclusion  
  23. 23. Simula.on  Experiment   Descrip.on  Markup  Language
  24. 24. SED-­‐ML:  Repeatable  simula.on  experiments Model  
  25. 25. SED-­‐ML:  Repeatable  simula.on  experiments Simula8on   Model  
  26. 26. SED-­‐ML:  Repeatable  simula.on  experiments Model   Simula8on   Task  
  27. 27. SED-­‐ML:  Repeatable  simula.on  experiments Model   Simula8on   Task   Data  Generators  
  28. 28. SED-­‐ML:  Repeatable  simula.on  experiments Model   Simula8on   Task   Reports   Data  Generators  
  29. 29. SED-­‐ML  Level  1  Version  1
  30. 30. SED-­‐ML  Level  1  Version  2 One   Step     Model   Simula8on   Steady     State   Parameters   Task   Reports   Data  Generators   Repeated  Task  
  31. 31. SED-­‐ML  L1V2
  32. 32. SED-­‐ML  Future
  33. 33. SED-­‐ML • Coverage   • Simula8ons  (stochas8c  /  determinis8c  /  steady  state)   • Parameter  Scans  (8me  course  /  steady  state  /  n-­‐ dimensional)   • Dosing  /  Pulse  experiments   • Work  in  Progress   • Accessing  Experimental  Data,     • Op8miza8on   • Parameter  Es8ma8on  
  34. 34. Outline Background  &  Introduc8on   Simula8on  Experiment  Descrip8on  Markup  Language  –   SED-­‐ML   SoMware  Support   Conclusion  
  35. 35. SED-­‐ML  Script  Editor hOp://libsedml.sf.net    
  36. 36. SED-­‐ML  Web  Tools hOp://sysbioapps.dyndns.org/SED-­‐ML_Web_Tools    
  37. 37. Systems  Biology  Workbench hOp://sbw.sf.net    
  38. 38. Systems  Biology  Workbench hOp://sbw.sf.net    
  39. 39. Systems  Biology  Workbench hOp://sbw.sf.net    
  40. 40. CellDesigner hOp://celldesigner.org    
  41. 41. hOp://pysces.sf.net    
  42. 42. SBSI  –  SED  ED hOp://sourceforge.net/projects/sbsi/    
  43. 43. COPASI hOp://www.copasi.org/    
  44. 44. VCELL hOp://www.nrcam.uchc.edu/    
  45. 45. JWS  Online hOp://jjj.biochem.sun.ac.za/    
  46. 46. Libraries •  libSedML:  .NET;  BSD  License     hOp://libsedml.sourceforge.net   •  libSEDML:  C/C++  with  bindings  for  .NET,  Java,  Perl,  Python,  R,  Ruby;   BSD  License,  hOps://github.com/Bergmann/libsedml     •  jlibsedml:  Java;  MIT  License     hOp://sourceforge.net/projects/jlibsedml/   •  clibsedml,:  C;  BSD  License   hOp://sourceforge.net/projects/clibsedml    
  47. 47. Outline Background  &  Introduc8on   Simula8on  Experiment  Descrip8on  Markup  Language  –   SED-­‐ML   SoMware  Support   Conclusion  
  48. 48. Conclusions •  Opportunity:  Simula8on  Experiments  as  readily  exchangeable  as   computa8onal  models   •  Independently  of  SoMware  tools  à  independent  verifica8on  of  results   •  Con8nue  in  another  tool  right,  where  you  leM  off  in  one  tool   •  Possibility  of  full  documenta8on  of  experiments   •  Reuse  the  precisely  same  experiment  for  different  models.     •  SoMware  Support  is  growing,  readily  available  in  a  number  of  tools.  
  49. 49. Next  Steps  …   •  Finalize  SED-­‐ML  Level  1  Version  2   •  Prototype  on  Version  3   •  Export  remaining  experiments  from  the  SBW  Simula8on  Tool     •  Finish  work  on  SED-­‐ML  exporters   •  SED-­‐ML  -­‐-­‐>  Matlab   •  SED-­‐ML  -­‐-­‐>  Jarnac  
  50. 50. Acknowledgements   •  SED-­‐ML  Editors:  Frank  T.  Bergmann,  Dagmar  Waltemath,  Jonathan   Cooper,  David  Nickerson,  Nicolas  Le  Novère,  Andrew  Miller,  Richard   Adams   •  BioModels  Support  Team   •  SED-­‐ML  Community   •  Ursula  Kummer,  Michael  Hucka,  Herbert  Sauro  
  51. 51. More  Informa.on   •  SED-­‐ML:   hOp://sed-­‐ml.org     hOp://8nyurl.com/sed-­‐ml-­‐l1v2-­‐rc     hOps://lists.sourceforge.net/lists/lis8nfo/sed-­‐ml-­‐discuss/       •  SED-­‐ML  Web  Tools:     hOp://sysbioapps.dyndns.org/SED-­‐ML_Web_Tools     •  SBML:     hOp://sbml.org/   hOp://biomodels.net/biomodels      
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