Sems project overview
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Sems project overview

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

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

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Sems project overview Sems project overview Presentation Transcript

  • 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.de06.12.2012 Model and simulation management | D. Waltemath
  • Models, models, models And that‘s why we need systems biology! http://www.cs.uofs.edu/~varrialer2/06.12.2012 Model and simulation management | D. Waltemath 2
  • Models, models, models And that‘s why we need model management! http://www.cs.uofs.edu/~varrialer2/06.12.2012 Model and simulation management | D. Waltemath 3
  • Challenge: Model reuse On the left: Goldbeter, 1991 (Proc Natl Acad Sci) view of the cdc2 kinase. On the right: Gardners 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)06.12.2012 Model and simulation management | D. Waltemath 4
  • 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)06.12.2012 Model and simulation management | D. Waltemath 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) Reply: Where is the problem? (Figures produced by Frank Bergmann in SBW Workbench)06.12.2012 Model and simulation management | D. Waltemath 6
  • Field of research Management Model Version Model Model Control Storage Search Simulation Simulation Simulation Version Control Storage Search06.12.2012 Model and simulation management | D. Waltemath 7
  • 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 Search06.12.2012 Model and simulation management | D. Waltemath 8
  • 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 Search06.12.2012 Model and simulation management | D. Waltemath 9
  • 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 Search06.12.2012 Model and simulation management | D. Waltemath 10
  • 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 Search06.12.2012 Model and simulation management | D. Waltemath 11
  • 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)06.12.2012 Model and simulation management | D. Waltemath 12
  • 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.06.12.2012 Model and simulation management | D. Waltemath 13