Research Seminar BBT Braunschweig 2014

1. Reproducibility, dissemination,
and management of modeling results
17 February 2014, Braunschweig
Dagmar Waltemath
http://sems.uni-rostock.de

2. Nature Blogs: Of Schemes and Dreams (2014) Nine Worrying Stats on the Effect of Poor Scientific Data Management
http://sems.uni-rostock.de
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3. Nature Blogs: Of Schemes and Dreams (2014) Nine Worrying Stats on the Effect of Poor Scientific Data Management
http://sems.uni-rostock.de
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4. “We’ve been hearing a common theme from
the academic community – researchers are
having difficulty managing and accessing their
data. It seems to be an ongoing problem for
research scientists, at any stage of their
careers.”
(Nature Blogs: Of Schemes and Dreams (2014) Nine Worrying Stats on the Effect of Poor Scientific Data
Management)
http://sems.uni-rostock.de
4

5. Outline
reproducibility
dissemination
http://sems.uni-rostock.de
management
5

6. Outline
reproducibility
dissemination
management
“People can’t share knowledge if they don’t
speak a common language”
Tom Davenport, Lawrence Prusak (2000) Working Knowledge
http://sems.uni-rostock.de
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7. Reproducible modeling results :: Standards
Model
Entities, network
of reactions, math
Fig: Goldbeter (1991),
http://www.ncbi.nlm.nih.
gov/pubmed/1833774
Annotations
Compartment: Cell GO:0005623
Publication: Goldbeter
PMID:1833774
M = inactive CDCD2 Kinase:
UniProt:CDK1a_XENIA
Fig.: BioModels Database
Behavior: Oscillation
TEDDY_0000006
Algorithm: Gillespie
KiSAO:000029
Protocols
Fig.: BioModels Database
http://sems.uni-rostock.de
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8. Reproducible modeling results :: Towards publication
1
3
2
+
4
5
Following: Waltemath et al (2013) Reproducibility of model-based results in systems biology. Springer
http://sems.uni-rostock.de
8

9. Outline
reproducibility
dissemination
management
[Quantitative] models will be only as useful as their access and reuse
is easy for all scientists.
Nicolas Le Novère (2006) Model storage, exchange and integration. BMC Neuroscience
http://sems.uni-rostock.de
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10. Dissemination :: Model curation and annotation
Fig.: Li et al (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic
models. BMC Systems Biology
http://sems.uni-rostock.de
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11. Dissemination :: Public model repositories
1.
2.
3.
4.
Higher visibility of research
Long-term availability
Link to other resources
Quality-checks
Fig.: Piwowar and Vision (2013) Data reuse and the open
data citation advantage. PeerJ
http://sems.uni-rostock.de
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12. Dissemination :: Quality checks with functional curation
Fig.: Example for functional curation on heart model, http://travis.cs.ox.ac.uk/FunctionalCuration/db.html
Fig.: Cooper et al (under review) Through models to knowledge with virtual experiments
http://sems.uni-rostock.de
Martin Scharm
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13. Outline
reproducibility
dissemination
management
“And that’s why we need model Management.“
Following: http://www.indiana.edu/~hperp200/images/WhyWeNeedComputer_thumb.png
http://sems.uni-rostock.de
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14. Management :: Integration of model-related data
“Which models are annotated with ‘Adenosine tri-phosphate’?”
Document
”Which models contain reactions with
ATP as reactant and ADP as product?“
C2
CP
Pubmed:
1831270
Kegg Pathway
sce04111
is
pM
Cell
asProduct
asReactant
EC-Code:
3.1.3.16
Uniprot:P04551
Uniprot:P04551
Interpro:
IPR006670
is
hasPart
isContainedIn
isVersion
isVersionOf
• Relations between entities
• Links to concepts in bio-ontologies
Reaction3
isVersionOf
• Graph store (Neo4J database)
isDescribedBy
Tyson1991
Cell Cycle 6
var
GO:0005623
Fig.: Henkel et al (2012) Considerations of graph-based
concepts to manage of computational biology models and
associated simulations INFORMATIK2012, Braunschweig
Ron Henkel
http://sems.uni-rostock.de
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15. Management :: Integration of model-related data
Document
Document
SEDML
Pubmed:
1831270
isDescribedBy
Tyson_1991
Modelreference
C2
is_connected
is_connected
environment
Simulation
Task
Datagenerator
Output
CP
Variable
is_connected
Variable
C2
CP
time
time
time
CP
KISAO:
Ontology
C2
KISAO:097
is_mapped_to
KISAO:000
KISAO:201
isA
Document
isDescribedBy
KISAO:433
Tyson1991
Cell Cycle 6
var
Reaction3
C2
CP
pM
KISAO:352
KISAO:20
KISAO:019
Kegg Pathway
sce04111
is
KISAO:273
KISAO:447
SBO:
Ontology
Cell
asProduct
isContainedIn
is
hasPart
isA
ha
f
nO
sP
art
isVersionOf
SBO:0000
is
sio
er
EC-Code:
3.1.3.16
isV
isVersionOf
asReactant
SBO:064
Uniprot:P04551
Interpro:
IPR006670
GO:0005623
SBO:544
SBO:004
SBO:231
SBO:003
SBO:236
SBO:545
SBO:000064
Fig.: Henkel et al (in preparation)
http://sems.uni-rostock.de
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16. Management :: Combination of methods
Keywords describing a
model of interest.
Rank
isVersion
Of
CP
Unipr
ot:P0
4551
is
pM
3.
Maex‘98
SEDM
L
Tyso
n_19
91
Inte
rpro
:
IPR
006
670
Pubm
isDescribedBy
Cel
l
envi
ron
men
t
ed:
Pubm
183127
0 ed:
183127
0
Model
refere
nce
CP
Simul
ation
Task
Outpu
t
Datag
enera
tor
Varia
ble
GO:0
0056
23
C2
CP
time
time
time
CP
C2
Varia
ble
ID:
BIOMD000000005
Authors:
Tyson JJ.
Date:
13 Sep 2005 12:31:08
Publication: pubmed:1831270
Species:
cdc2k, cyclin …
Reaction: cyclin_cdc2k_dissociation, …
Tyson‘91
Tyson‘91 ODE plot
simulate
Tyson‘91
Doc
ume
nt
Pub
med:
Kegg
1831
Path
270
way
sce04
111
is
hasPart
isVersion
Unipr
ot:P0
4551
Novak‘97
Docu
ment
isDescrib
edBy
C2
ECCode:
3.1.3.
16
Format
retrieve
select simulation
description
compare with paper
search
C2
isVersion
Of
19
91
Cel
l
Cy
cle
6
var
1.
2.
Do
cu
me
Tys
nt
on
Re
act
ion
3
Name
Tyson’91 ODE plot
Model: BIOMD000000005
add simulation
Algorithm:
ODE solver
description to
Type:
time course
simulation software Output:
plot
Fig.: Following Waltemath et al (2013) Reproducibility of model-based results in systems biology. Springer.
Henkel et al (2010) Ranked retrieval of Computational Biology models. BMC bioinformatics
http://sems.uni-rostock.de
Ron Henkel
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17. Management :: Provenance
“Give me the best matching model published on the Cell Cycle
and considering cdk1.”
Lucene: species:cdk1, compartment:cell, …
Fig.: Waltemath et al (2013) Improving the reuse of computational models through version control.Bioinformatics
http://sems.uni-rostock.de
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18. Management :: Model version control
Fig.: courtesy Martin Scharm, BudHat, http://sems.uni-rostock.de/budhat
http://sems.uni-rostock.de
Martin Scharm
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19. Summary :: SEMS projects & Contributions
foster
dissemination
improve
management
Document
isDescribedBy
Tyson1991
Cell Cycle 6
var
Reaction3
C2
CP
Pubmed:
1831270
Kegg Pathway
sce04111
is
pM
Cell
asProduct
EC-Code:
3.1.3.16
http://sems.uni-rostock.de
Uniprot:P04551
Uniprot:P04551
Interpro:
IPR006670
is
hasPart
isContainedIn
isVersion
isVersionOf
asReactant
isVersionOf
ensure
reproducibility
GO:0005623
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20. Thank you for your attention.
Collaborators
Nicolas Le Novère
Christian Rosenke
David Nickerson
Wolfgang Müller
Jonathan Cooper
Falk Schreiber
Jon Olav Vik
SED-ML Editorial Board
Tommy Yu
SBML Editorial Board
HARMONY 2015
Wittenberg
HERMESForschungsförderung
HERMES-Forschungsförderung
der
der Universität RostockUniversität Rostock
http://sems.uni-rostock.de
@SemsProject
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