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. Applying the Scien.fic Method to Simula.on Experiments Frank T. Bergmann, PhD California Ins8tute of Technology University of Heidelberg Bergman@caltech.edu
- 2. Outline Background & Introduc8on Simula8on Experiment Descrip8on Markup Language – SED-‐ML SoMware Support Conclusion
- 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. Models
- 5. Models Teusink et. al, 2003, DOI: 10.1046/j.1432-‐1327.2000.01527.x
- 6. Adapted from Michael Hucka
- 7. Model
- 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> [ . . . ]
- 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. Models Teusink et. al, 2003, DOI: 10.1046/j.1432-‐1327.2000.01527.x
- 16. Simula.on Experiments Huang et. al, 1996, DOI: 10.1073/pnas.93.19.10078
- 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. 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. Large scale integra.ve models …
- 22. Outline Background & Introduc8on Simula8on Experiment Descrip8on Markup Language – SED-‐ML SoMware Support Conclusion
- 23. Simula.on Experiment Descrip.on Markup Language
- 24. SED-‐ML: Repeatable simula.on experiments Model
- 25. SED-‐ML: Repeatable simula.on experiments Simula8on Model
- 26. SED-‐ML: Repeatable simula.on experiments Model Simula8on Task
- 27. SED-‐ML: Repeatable simula.on experiments Model Simula8on Task Data Generators
- 28. SED-‐ML: Repeatable simula.on experiments Model Simula8on Task Reports Data Generators
- 29. SED-‐ML Level 1 Version 1
- 30. SED-‐ML Level 1 Version 2 One Step Model Simula8on Steady State Parameters Task Reports Data Generators Repeated Task
- 31. SED-‐ML L1V2
- 32. SED-‐ML Future
- 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. Outline Background & Introduc8on Simula8on Experiment Descrip8on Markup Language – SED-‐ML SoMware Support Conclusion
- 42. SBSI – SED ED hOp://sourceforge.net/projects/sbsi/
- 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
- 48. Outline Background & Introduc8on Simula8on Experiment Descrip8on Markup Language – SED-‐ML SoMware Support Conclusion
- 49. 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.
- 50. 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
- 51. 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
- 52. 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