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Research Seminar BBT Braunschweig 2014
Citation preview
http://sems.uni-rostock.de
Dagmar Waltemath 17 February 2014, Braunschweig
Reproducibility, dissemination,
and management of modeling results
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 3
Nature Blogs: Of Schemes and Dreams (2014) Nine Worrying Stats on the Effect of Poor Scientific Data Management
http://sems.uni-rostock.de
“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)
4
http://sems.uni-rostock.de
reproducibility dissemination management
Outline
5
http://sems.uni-rostock.de
reproducibility dissemination management
Outline
6
“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
Reproducible modeling results :: Standards
7
Model
Entities, network
of reactions, math
Fig: Goldbeter (1991),
http://www.ncbi.nlm.nih.
gov/pubmed/1833774
Annotations
Fig.: BioModels Database
Protocols
Fig.: BioModels Database
Behavior: Oscillation
TEDDY_0000006
Algorithm: Gillespie
KiSAO:000029
Compartment: Cell GO:0005623
Publication: Goldbeter
PMID:1833774
M = inactive CDCD2 Kinase:
UniProt:CDK1a_XENIA
http://sems.uni-rostock.de
Reproducible modeling results :: Towards publication
8
+
1 2
3 4 5
Following: Waltemath et al (2013) Reproducibility of model-based results in systems biology. Springer
http://sems.uni-rostock.de
reproducibility dissemination management
Outline
9
[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
Dissemination :: Model curation and annotation
10
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
Dissemination :: Public model repositories
11
1. Higher visibility of research
2. Long-term availability
3. Link to other resources
4. Quality-checks
Fig.: Piwowar and Vision (2013) Data reuse and the open
data citation advantage. PeerJ
http://sems.uni-rostock.de
Dissemination :: Quality checks with functional curation
12
Fig.: Example for functional curation on heart model, http://travis.cs.ox.ac.uk/FunctionalCuration/db.html
Martin Scharm Fig.: Cooper et al (under review) Through models to knowledge with virtual experiments
http://sems.uni-rostock.de
reproducibility dissemination management
Outline
13
“And that’s why we need model Management.“ Following: http://www.indiana.edu/~hperp200/images/WhyWeNeedComputer_thumb.png
http://sems.uni-rostock.de
Management :: Integration of model-related data
14
• Graph store (Neo4J database)
• Relations between entities
• Links to concepts in bio-ontologies
Document
Tyson1991
Cell Cycle 6
var
C2 pM CellReaction3 CP
Uniprot:P04551 Uniprot:P04551 GO:0005623Interpro:
IPR006670
isV
ers
ion
Of
isV
ers
ion
ha
sP
art
is
asProduct
asReactant isContainedIn
Pubmed:
1831270
Kegg Pathway
sce04111
isDescribedBy
is
EC-Code:
3.1.3.16
isV
ers
ion
Of
Fig.: Henkel et al (2012) Considerations of graph-based
concepts to manage of computational biology models and
associated simulations INFORMATIK2012, Braunschweig
”Which models contain reactions with
ATP as reactant and ADP as product?“
“Which models are annotated with ‘Adenosine tri-phosphate’?”
Ron Henkel
http://sems.uni-rostock.de
Management :: Integration of model-related data
15
Fig.: Henkel et al (in preparation)
SBO:
Ontology
SBO:0000
SBO:544 SBO:236SBO:231
isA
SBO:064 SBO:545SBO:004 SBO:003
KISAO:
Ontology
KISAO:000
KISAO:019
KISAO:352
KISAO:20
KISAO:097 KISAO:201
KISAO:433 KISAO:273
isA
KISAO:447
Document
SEDML
Modelref-
erenceOutput
Data-
generatorSimulation Task
Variable
Variable
Document
Tyson1991
Cell Cycle 6
var
C2 pM CellReaction3 CP
Uniprot:P04551 GO:0005623Interpro:
IPR006670
isVersionO
f
isV
ers
ion
Of
ha
sP
art
is
asProduct
asReactant isContainedIn
Kegg Pathway
sce04111
isDescribedBy
is
EC-Code:
3.1.3.16
isV
ers
ion
Of
hasP
art
Document
Tyson_1991
C2 CP
time
environment
isDescribedByPubmed:
1831270
time timeCPC2 CP C2
is_connected is_connected
is_mapped_to
is_connected
SBO:000064
is
http://sems.uni-rostock.de
Management :: Combination of methods
16
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
Keywords describing a model of interest.
Tyson‘91Tyson‘91 ODE plot
search retrieve
add simulation description to
simulation software
simulate
com
par
e w
ith
pap
er
Rank Name Format
1. Novak‘97
2. Tyson‘91
3. Maex‘98ID: BIOMD000000005Authors: Tyson JJ.Date: 13 Sep 2005 12:31:08Publication: pubmed:1831270Species: cdc2k, cyclin …Reaction: cyclin_cdc2k_dissociation, …
Tyson’91 ODE plot
select simu
lation
d
escriptio
n
Model: BIOMD000000005Algorithm: ODE solverType: time courseOutput: plot
DocumentTyson1991 Cel
l Cycle 6
var
C2 pMCel
l
Reaction
3
CP
Uniprot:P04551
Uniprot:P04551
GO:00056
23
Interpro
: IPR006670
isV
ersi
on
Of
isV
ersi
on
has
Par
t
is
Pubmed:1831270
Kegg Pathway
sce04111
isDescribedBy
is
EC-Code: 3.1.3.
16
isV
ersi
on
Of
Document
SEDML
Modelrefere
nce
Output
Datagenera
tor
Simulation
Task
Variable
Variable
Docume
nt
Tyson_19
91
C2 CP
time
environ
ment
isDescribedByPubm
ed:183127
0
Pubmed:
1831270
time timeCPC2 CP C2
Ron Henkel
http://sems.uni-rostock.de
Management :: Provenance
17
Fig.: Waltemath et al (2013) Improving the reuse of computational models through version control.Bioinformatics
“Give me the best matching model published on the Cell Cycle
and considering cdk1.”
Lucene: species:cdk1, compartment:cell, …
http://sems.uni-rostock.de
Management :: Model version control
18
Fig.: courtesy Martin Scharm, BudHat, http://sems.uni-rostock.de/budhat Martin Scharm
http://sems.uni-rostock.de
ensure reproducibility
foster dissemination
improve management
Summary :: SEMS projects & Contributions
19
Document
Tyson1991
Cell Cycle 6
var
C2 pM CellReaction3 CP
Uniprot:P04551 Uniprot:P04551 GO:0005623Interpro:
IPR006670
isV
ers
ion
Of
isV
ers
ion
ha
sP
art
is
asProduct
asReactant isContainedIn
Pubmed:
1831270
Kegg Pathway
sce04111
isDescribedBy
is
EC-Code:
3.1.3.16
isV
ers
ion
Of
http://sems.uni-rostock.de
Thank you for your attention.
20
HERMES-
Forschungsförderung
der Universität Rostock HERMES-Forschungsförderung
der Universität Rostock
HARMONY 2015
Wittenberg
Christian Rosenke
Wolfgang Müller
Falk Schreiber
SED-ML Editorial Board
SBML Editorial Board
Collaborators
Nicolas Le Novère
David Nickerson
Jonathan Cooper
Jon Olav Vik
Tommy Yu
@SemsProject