simulation experiment descriptions and management

The Simulation Experiment Description Markup Language (SED-ML)

Dagmar Waltemath

Dept. of Systems Biology and Bioinformatics

University of Rostock

[email protected]

06.12.2012 Simulation experiment description | D. Waltemath

mailto:[email protected]



Fig.: Mosaic of standards, adapted from Chelliah et al., 2009 (DILS)

Standards for models, simulations and results

2 06.12.2012 Simulation experiment description | D. Waltemath

06.12.2012 Simulation experiment description | D. Waltemath 3 3

Simulation

Model database

Simulation results

(SBW Workbench)

BIOMD0000000139 , BIOMD0000000140

Standards for models, simulations and results

Basic structure of SED-ML

Fig.: SED-ML structure Waltemath et al., 2011 (BMC SysBiol)


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)


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, ...

6

F. Bergmann N. Le Novère D. Nickerson J. Cooper D. Waltemath 06.12.2012 Simulation experiment description | D. Waltemath

http://sed-ml.org/

http://sed-ml.org/

http://sed-ml.org/

http://sed-ml.org/

SED-ML Resources/Tools

• 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 – Online: http://www.sbsi.ed.ac.uk/html/sedml/

– SED-ML Web Tools: http://sysbioapps.dyndns.org/SED-ML_Web_Tools

F. Bergmann

R. Adams

A. Miller


http://sourceforge.net/projects/jlibsedml/

http://sourceforge.net/projects/jlibsedml/

http://libsedml.sourceforge.net/

http://libsedml.sourceforge.net/

http://www.cellml.org/tools/api

http://www.cellml.org/tools/api

http://www.sbsi.ed.ac.uk/html/sedml/

http://www.sbsi.ed.ac.uk/html/sedml/

http://sysbioapps.dyndns.org/SED-ML_Web_Tools




SED-ML Resources/Tools

SED-ML Web Tools (F. Bergmann)

SED-ED Adams 2012 (Bioinformatics)

SED-ML support in CellDesigner






http://www.ncbi.nlm.nih.gov/pubmed/22368254




http://www.celldesigner.org/

SED-ML @ SEEK


Demo

06.12.2012 Simulation experiment description | D. Waltemath 10

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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Graph-based storage of models and simulations

Fig.: Linked storage of SBML models and SED-ML simulations setups Henkel et al., 2012 (INFORMATIK)


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


Models, models, models

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And that‘s why we need model management!


http://www.cs.uofs.edu/~varrialer2/


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Find and retrieve





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Find and retrieve Version control




Simulate


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Find and retrieve Version control



Ron Henkel: graph-based storage; retrieval

Martin Scharm: model version control

Rebekka Alm: graph-based storage of simulation setups

Jenny Fabian: characterization of cell cycle models

http://sems.uni-rostock.de

http://sed-ml.org

Olaf Wolkenhauer: project instructor


http://sems.uni-rostock.de/



http://sed-ml.org/

http://sed-ml.org/

http://sed-ml.org/

References

06.12.2012 Model and simulation management | D. Waltemath 18

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

http://www.ingentaconnect.com/content/oup/cabios;jsessionid=3lahp2701938m.alice


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