Presented at the 2012 PALs meeting of the Sysmo-SEEK project in Heidelberg, Germany. 28th-30th of November 2012.

1. Model and simulation management for systems biology
Dagmar Waltemath, Ron Henkel,
Martin Scharm, Olaf Wolkenhauer
Dept. of Systems Biology and Bioinformatics
University of Rostock
dagmar.waltemath@uni-rostock.de
06.12.2012 Model and simulation management | D. Waltemath

2. Models, models, models
And that‘s why we need systems biology!
http://www.cs.uofs.edu/~varrialer2/
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3. Models, models, models
And that‘s why we need model management!
http://www.cs.uofs.edu/~varrialer2/
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4. Challenge: Model reuse
On the left: Goldbeter, 1991 (Proc Natl Acad Sci) view of the cdc2 kinase. On the right:
Gardner's extension of that model with a Cyclin inhibitor, Gardner et al., 1998 (Proc Natl Acad
Sci) (Fig. taken from original publications, extended by M. Scharm)
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5. Challenge: Result reproducibility
“[..] in Biomodel database the model BIOMD0000000139 and BIOMD0000000140
are two different models and they are supposed to show different results. Unfortunately
simulating them in Copasi gives same result for both the models. [..] “
(on sbml-discuss)
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6. Challenge: Result reproducibility
“[..] in Biomodel database the model BIOMD0000000139 and BIOMD0000000140
are two different models and they are supposed to show different results. Unfortunately
simulating them in Copasi gives same result for both the models. [..] “
(on sbml-discuss)
Reply: Where is the problem?
(Figures produced by Frank Bergmann in SBW Workbench)
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7. Field of research
Management
Model Version Model Model
Control Storage Search
Simulation Simulation Simulation
Version Control Storage Search
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8. Model management: Version control
- Model history How did this model change in the past? Which parts? When?
- Difference detection What changed in this version?
- Change presentation Which parts of the model changed most frequently?
Model version control enables the study of a model’s history and
ensures long-term availability of results. (More: M. Scharm)
Model Version Control Model Storage Model Search
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9. Model management: Storage
- Annotated model code SBML, CellML, NeuroML, …, MIRIAM URNs,
identifiers.org
- Model structure
- Linked models and simulation experiments Which models on yeast
show sustained oscillations?
Graph-based storage incorporates structural information
and experiments in the search. (More: R. Henkel)
Model Version Control Model Storage Model Search
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10. Model management: Search
- Find models by annotation Which models exist about Gluconeogenesis?
- Find model by structure Which models investigate the production of
lacZ/β-Galactosidase?
- Rank models Which model is the most suitable to study glycolytic
oscillations? And why?
Ranked model retrieval supports users in quickly finding
relevant models. (More: R. Henkel)
Model Version Control Model Storage Model Search
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11. Simulation Management
- Standard formats for simulation encoding SED-ML, MIASE, KiSAO
- Linking models and simulation Which experiments are available for my
yeast metabolism model?
- Consistency checks Can I perform my analysis on this version of Ulf’s
model?
SED-ML improves result reproducibility and enables the linking
of experiments to models. (More: D. Waltemath)
Simulation VC Simulation Storage Simulation Search
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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. References
Goldbeter , 1991 (Proc Natl Acad Sci ) Goldbeter A. A minimal cascade model for the mitotic oscillator
involving cyclin and cdc2 kinase.
Gardner et al., 1998 (Proc Natl Acad Sci ) Gardner TS, Dolnik M, Collins JJ. A theory for controlling cell
cycle dynamics using a reversibly binding inhibitor.
Waltemath et al. (submitted ) Waltemath D et al. (under revision) On improving model reuse and result
reproducibility through version control for computational models of biological systems.
Waltemath et al., 2011 (BMC SysBiol) Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, et
al. (2011)Reproducible computational biology experiments with SED-ML - The Simulation Experiment
Description Markup Language BMC Systems Biology 2011, 5:198
Henkel et al., 2010 (BMC Bioinf) Henkel R, Endler L, Peters A, Le Novère N & Waltemath D (2010):
Ranked retrieval of Computational Biology models. BMC Bioinformatics, 11(423)
Henkel et al., 2012 (INFORMATIK) R. Henkel, N. le Novère, O. Wolkenhauer, D. Waltemath (2012)
Consideratons 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 (DBSpektrum) Waltemath D, Henkel R, Meyer H & Heuer A (2011): Das Sombi-
Framework zum Ermitteln geeigneter Suchfunktionen für biologische Modelldatenbasen. Datenbank-
Spektrum.
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