sems project overview
DESCRIPTION
Presented at the 2012 PALs meeting of the Sysmo-SEEK project in Heidelberg, Germany. 28th-30th of November 2012.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
06.12.2012 Model and simulation management | D. Waltemath
Models, models, models
2 06.12.2012 Model and simulation management | D. Waltemath
And that‘s why we need systems biology! http://www.cs.uofs.edu/~varrialer2/
Models, models, models
3 06.12.2012 Model and simulation management | D. Waltemath
And that‘s why we need model management! http://www.cs.uofs.edu/~varrialer2/
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)
4 06.12.2012 Model and simulation management | D. Waltemath
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)
5 06.12.2012 Model and simulation management | D. Waltemath
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)
(Figures produced by Frank Bergmann in SBW Workbench)
Reply: Where is the problem?
6 06.12.2012 Model and simulation management | D. Waltemath
Field of research
Management
Model Version
Control
Simulation
Version Control
Model
Storage
Simulation
Storage
Model
Search
Simulation
Search
7 06.12.2012 Model and simulation management | D. Waltemath
Model Version Control Model Search Model Storage
Model version control enables the study of a model’s history and ensures long-term availability of results. (More: M. Scharm)
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?
8 06.12.2012 Model and simulation management | D. Waltemath
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)
9 06.12.2012 Model and simulation management | D. Waltemath
Model Version Control Model Search Model Storage
Ranked model retrieval supports users in quickly finding relevant models. (More: R. Henkel)
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?
10 06.12.2012 Model and simulation management | D. Waltemath
Model Version Control Model Search Model Storage
SED-ML improves result reproducibility and enables the linking of experiments to models. (More: D. Waltemath)
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?
11 06.12.2012 Model and simulation management | D. Waltemath
Simulation VC Simulation Search Simulation Storage
SEMS: Methods for Model & Simulation Management
• XML version control
• Difference detection in XML Waltemath et al., submitted
• Ranked model retrieval Henkel et al., 2010 (BMC Bioinf)
• Structure- and
ontology-based search
Simulation VC SimulationSearch Simulation Storage
• Relational databases Waltemath et al., 2011 (DBSpektrum)
• Graph-based storage Henkel et al., 2012 (INFORMATIK)
• Standardized encoding of simulation setups Waltemath et al., 2011 (BMC SysBiol)
• Linking models and simulation descriptions Henkel et al., 2012 (INFORMATIK)
Model Search Model Version control Model Storage
12 06.12.2012 Model and simulation management | D. Waltemath
References
06.12.2012 Model and simulation management | D. Waltemath 13
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.