LibSedML	  h*p://libsedml.sf.net	  	        Frank	  T.	  Bergmann	                       	    HARMONY	  2012,	  Maastricht...
Repeatable	  simulaHon	  experiments	                 SimulaHon	                              Model	                      ...
LibSedML	  SED-­‐ML	  Script	  Editor	                                               libSedMLScript	                      ...
LibSedML	  script	  AddTimeCourseSimulation(simulation1,	  KiSAO:0000071,	  0,	  50,	  1000,	  1000)	  	  AddModel(model1,...
libSedML	  h*p://libsedml.sf.net	  	     5	  
Features                                       	  •  LibSedML	     –  Read,	  Create,	  Write,	  Manipulate	     –  Valida...
SED-­‐ML	  script	  editor	        h*p://libsedml.sf.net	  	     7	  
SED-­‐ML	  script	  editor	        h*p://libsedml.sf.net	  	     8	  
SBW	  SimulaHon	  Tool	  h*p://sourceforge.net/projects/sbw/files/sbw/2.9.0/	  	     9	  
SED-­‐ML	  Web	  Tools	  h*p://sysbioapps.dyndns.org/SED-­‐ML_Web_Tools	  	  	     10	  
HARMONY	  2012	  •  Tuesday	  11am:	  	      –  TroubleshooHng	  session:	  ROOM	  123	  •  Wednesday	  11am:	  	      –  ...
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libSEDML (Harmony 2012)

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LibSED-ML introduction at HARMONY 2012 in Maastricht, NL. For more details see me in the next three days

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libSEDML (Harmony 2012)

  1. 1. LibSedML  h*p://libsedml.sf.net     Frank  T.  Bergmann     HARMONY  2012,  Maastricht,  NL  
  2. 2. Repeatable  simulaHon  experiments   SimulaHon   Model   Task   Reports   Data  Generators   2  
  3. 3. LibSedML  SED-­‐ML  Script  Editor   libSedMLScript   libSedML   libSedMLRunner   SimulaHon  Tool   iBioSim   RoadRunner   h*p://libsedml.sf.net     3  
  4. 4. LibSedML  script  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]]);   h*p://libsedml.sf.net     4  
  5. 5. libSedML  h*p://libsedml.sf.net     5  
  6. 6. Features  •  LibSedML   –  Read,  Create,  Write,  Manipulate   –  Validate,  Archive   –  Resolve  models  from  FS,  Web  +  Miriam  URN   –  Applies  changes  to  models  •  Supported  Model  DescripHon  languages:     –  SBML  +  CellML   6  
  7. 7. SED-­‐ML  script  editor   h*p://libsedml.sf.net     7  
  8. 8. SED-­‐ML  script  editor   h*p://libsedml.sf.net     8  
  9. 9. SBW  SimulaHon  Tool  h*p://sourceforge.net/projects/sbw/files/sbw/2.9.0/     9  
  10. 10. SED-­‐ML  Web  Tools  h*p://sysbioapps.dyndns.org/SED-­‐ML_Web_Tools       10  
  11. 11. HARMONY  2012  •  Tuesday  11am:     –  TroubleshooHng  session:  ROOM  123  •  Wednesday  11am:     –  Nested  SimulaHons,  ROOM  147   11  

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