e:Bio Kick-Off Meeting, SEMS

Tools and Methods for Improved Result Reproducibility in

Systems Biology (SEMS)

Department of Systems Biology and Bioinformatics

University of Rostock

Dagmar Waltemath, Martin Scharm, Ron Henkel, Olaf Wolkenhauer

e:Bio Kick-Off Meeting, 23-25 September 2013, Mainz

24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 1


Reuse existing models.

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Annotation

+ 140.811 derived models

(Models in BioModels Database; Figure courtesy Ron Henkel)


Reproduce published results.

“[..] in Biomodels database the model BIOMD0000000139 and

BIOMD0000000140 are two different models and they are supposed to show

different results. Unfortunately simulating them [..] gives same result for

both the models. [..] “ (Quote: arvin mer on sbml-discuss)

(Figures produced in COPASI)


SEMS – Improving result reproducibility


"Quantitative models will be only as useful as

their access and reuse is easy for all scientists”

(Nicolas Le Novère, 2006)

Standard representation formats

(Fig. adapted from: Courtot, Waltemath et al. Nature MSB, 2011)



NuML

SBRML




MAMO

NuML

SBRML



Data links

MAMO

NuML

SBRML



Data links

MAMO

NuML

SBRML



Project goals

1. Specify and establish a standard for the description of

simulation experiments (SED-ML) Waltemath et al. BMC Sys Biol (2011)

2. Develop methods for simulation management with focus on

model provenance Waltemath et al. Bioinformatics (2013)

3. Establish links between model-related data on storage level Henkel et al. INFORMATIK2012 (2012)

4. Promote reproducible science


http://co.mbine.org/

Standard representation of simulation experiments

http://sed-ml.org/


http://sed-ml.org/

http://sed-ml.org/

http://sed-ml.org/

Model provenance

(Figure courtesy Martin Scharm)


Model provenance: BiVeS & BudHat

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

VANTED


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



ModelGraphs:Linking model-related data

(Fig.: Henkel et al. INFORMATIK2012 (2012))

(Figure courtesy Ron Henkel, COMBINE2013)


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




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dealing with the Cell Cycle and

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Summary


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http://sbml.org

http://sbml.org/

Thank you for your attention!

SEMS group

Martin Scharm

Martin Peters

Markus Wolfien

Rebekka Alm

Olaf Wolkenhauer

Associated member

Ron Henkel

Collaborators

Falk Schreiber (IPK Gatersleben)

Christian Rosenke (University of Rostock)

Jon Olav Vik (UMB)

Jonathan Cooper (University of Oxford)

Tommy Yu (University of Auckland)

COMBINE

SED-ML Editors

biomodels.net

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

@SemsProject HERMES-

Forschungsförderung

der Universität Rostock

http://biomodels.net/




Technology

e:Bio Kick-Off Meeting, SEMS