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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NumberofAnnotations
NumberofModels
Models
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

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

Standard representation of simulation experiments
http://sed-ml.org/

Model provenance
(Figure courtesy Martin Scharm)

Model provenance: BiVeS & BudHat
http://budhat.sems.uni-rostock.de
VANTED

ModelGraphs:Linking model-related data
(Fig.: Henkel et al. INFORMATIK2012 (2012))
(Figure courtesy Ron Henkel, COMBINE2013)
Document
Tyson1991
Cell Cycle 6
var
C2 pM CellReaction3 CP
Uniprot:P04551 Uniprot:P04551 GO:0005623
Interpro:
IPR006670
isVersionOf
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hasPart
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asProduct
asReactant isContainedIn
Pubmed:
1831270
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isDescribedBy
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3.1.3.16
isVersionOf
Document
Tyson1991
Cell Cycle 6
var
Interpro:
IPR006670
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isVersion
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is
asProduct
Pubmed:
1831270
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isDescribedBy
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EC-Code:
3.1.3.16
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SEDML
Modelrefere
nce
Output
Datagenera
tor
Simulation Task
Variable
Variable
Document
Tyson_1991
C2 CP
time
environment
isDescribedBy Pubmed:
1831270
time timeCPC2 CP C2
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Ontology
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isA
SBO:064 SBO:545SBO:004 SBO:003
http://sems.uni-rostock.de/projects/morre/

ModelGraphs:Linking model-related data
Document
Tyson1991
Cell Cycle 6
var
Interpro:
IPR006670
isVersionOf
isVersion
hasPart
is
asProduct
Pubmed:
1831270
Kegg Pathway
sce04111
isDescribedBy
is
EC-Code:
3.1.3.16
isVersionOf
Document
SEDML
Modelrefere
nce
Output
Datagenera
tor
Simulation Task
Variable
Variable
Document
Tyson_1991
C2 CP
time
environment
isDescribedBy Pubmed:
1831270
time timeCPC2 CP C2
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Ontology
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Model
Publication
Annotation
Person
Simulation
Show me models by Tyson,
dealing with the Cell Cycle and
simulating concentration of cdc2!

Summary
track development
store retrieve
rank
Retrieval
Ranking
Δ
Δ
Version 1
Version 2
latest
Version Control
Do
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on
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Storage
Docu
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SEDM
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refere
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Docu
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SEDM
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refere
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Outpu
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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

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