SED-ML presentation given at the 2012 Sysmo-SEEK PALs meeting in Heidelberg, 28th-30th of November 2012.

1. The Simulation Experiment Description Markup
Language (SED-ML)
Dagmar Waltemath
Dept. of Systems Biology and Bioinformatics
University of Rostock
dagmar.waltemath@uni-rostock.de
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2. Standards for models, simulations and results
Fig.: Mosaic of standards, adapted from Chelliah et al., 2009 (DILS)
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3. Standards for models, simulations and results
BIOMD0000000139 , BIOMD0000000140
Simulation
Model database
Simulation results
(SBW Workbench)
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4. Basic structure of SED-ML
Fig.: SED-ML structure Waltemath et al., 2011 (BMC SysBiol)
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5. Formats for standardized simulation descriptions
• SED-ML Waltemath et al., 2011 (BMC SysBiol)
– Links to models, simulation algorithms, (result data)
– Pre- and post-processing of models
– Simulation setup
– Output specification
• KiSAO
– Classification and characterization of simulation algorithms
Courtot et al., 2011 (Nature MSB)
• NuML
– Standardized encoding of numerical data Dada et al., 2010 (Bioinformatics)
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6. SED-ML specification
• SED-ML Level 1 Version 1 Waltemath et al., 2011 (BMC SysBiol)
• Next version: SED-ML Level 1 Version 2 http://sed-ml.org
– Extended description for simulation algorithms
– Nested simulations
• Future? Parameter estimation, ...
D. Waltemath F. Bergmann D. Nickerson J. Cooper N. Le Novère
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7. SED-ML Resources/Tools
F. Bergmann
• Libraries
– jlibsedml (Java): http://sourceforge.net/projects/jlibsedml/
– Libsedml (.Net): http://libsedml.sourceforge.net
– SProS (CellML): http://www.cellml.org/tools/api
– libKiSAO Zhukova et al, 2012 (BMC Research Notes)
• Validators R. Adams
– Online: http://www.sbsi.ed.ac.uk/html/sedml/
– SED-ML Web Tools: http://sysbioapps.dyndns.org/SED-ML_Web_Tools
A. Miller
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8. SED-ML Resources/Tools
SED-ED Adams 2012 (Bioinformatics)
SED-ML Web Tools (F. Bergmann)
SED-ML support in CellDesigner
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9. SED-ML @ SEEK
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10. Demo
Reproducing simulation results in Liebal et al., 2012 (Mol Biosystem)
with SED-ML Web Tools http://sysbioapps.dyndns.org/SED-ML_Web_Tools
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11. Graph-based storage of models and simulations
Fig.: Linked storage of SBML models and SED-ML simulations setups Henkel et al., 2012 (INFORMATIK)
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12. SEMS: Methods for Model & Simulation Management
Model Version control Model Storage Model Search
• XML version control • Relational databases • Ranked model retrieval
Waltemath et al., 2011 (DBSpektrum) Henkel et al., 2010 (BMC Bioinf)
• Difference detection in XML
Waltemath et al. (submitted) • Graph-based storage • Structure- and
Henkel et al., 2012 (INFORMATIK) ontology-based search
Simulation VC Simulation Storage SimulationSearch
• Standardized encoding of simulation setups Waltemath et al., 2011 (BMC SysBiol)
• Linking models and simulation descriptions Henkel et al., 2012 (INFORMATIK)
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13. Models, models, models
And that‘s why we need model management!
http://www.cs.uofs.edu/~varrialer2/
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14. Models, models, models
Find and retrieve
And that‘s why we need model management!
http://www.cs.uofs.edu/~varrialer2/
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15. Models, models, models
Find and retrieve
Version control
And that‘s why we need model management!
http://www.cs.uofs.edu/~varrialer2/
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16. Models, models, models
Find and retrieve
Version control
Simulate
And that‘s why we need model management!
http://www.cs.uofs.edu/~varrialer2/
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17. Martin Scharm:
Ron Henkel:
model version control
graph-based
storage; retrieval
Jenny Fabian:
characterization
of cell cycle models
Olaf Wolkenhauer:
project instructor Rebekka Alm:
graph-based storage
of simulation setups
http://sems.uni-rostock.de
http://sed-ml.org
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18. References
Liebal et al., 2012 (Mol Bio System) UW Liebal, PK Sappa, T Millat, L Steil, G Homuth et al (2012) Proteolysis of beta-galactosidase following SigmaB activation in Bacillus
subtilis. Molecular BioSystems 8 (6) p. 1806-14
Henkel et al., 2012 (INFORMATIK) R Henkel, N le Novère, O Wolkenhauer, D Waltemath (2012) Considerations of graph-based concepts to manage computational biology
models and associated simulations. In: 4. Workshop über Daten in den Lebenswissenschaften: Datenbanken als Kommunikationszentrum, INFORMATIK 2012, Brunswig,
Germany.
Waltemath et al., 2011 (BMC SysBiol) D Waltemath, R Adams, FT Bergmann, M Hucka, F Kolpakov et al. (2011) Reproducible computational biology experiments with SED-
ML - The Simulation Experiment Description Markup Language BMC Systems Biology 2011, 5:198
Waltemath et al., 2011 (DBSpektrum) D Waltemath, R Henkel, H Meyer, A Heuer (2011): Das Sombi-Framework zum Ermitteln geeigneter Suchfunktionen für biologische
Modelldatenbasen. Datenbank-Spektrum
Waltemath et al. (submitted) D Waltemath et al. (under revision) On improving model reuse and result reproducibility through version control for computational models of
biological systems.
Henkel et al., 2010 (BMC Bioinf) R Henkel, L Endler, A Peters, N Le Novère, D Waltemath (2010): Ranked retrieval of Computational Biology models. BMC Bioinformatics,
11(423)
Adams 2012 (Bioinformatics) RR Adams (2012) SED-ED, a workflow editor for computational biology experiments written in SED-ML. Bioinformatics 28(8) pp. 1180-1181(2)
Zhukova et al, 2012 (BMC Research Notes) A Zhukova, R Adams, C Laibe, N Le Novere (2012): LibKiSAO: a Java Library for Querying KiSAO, BMC research notes, 2012
Courtot et al., 2011 (Nature MSB) M Courtot, N Juty, C Knüpfer, D Waltemath, A Zhukova, e al. (2011) Controlled vocabularies and semantics in systems biology. Nature
Molecular Systems Biology 7: 543
Dada et al., 2010 (Bioinformatics) JO Dada, I Spasić, N W Paton, P Mendes: SBRML: a markup language for associating systems biology data with models. Bioinformatics
(Oxford, England) 2010, 26(7):932–938
Chelliah et al., 2009 (DILS) V Chelliah, L Endler, N Juty, C Laibe, C Li, N Rodriguez, N Le Novère (2009) Data integration and semantic enrichment of systems biology models
and simulations. (English) Data integration in the life sciences. 6th international workshop, DILS 2009, Manchester
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