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)

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reproducibility dissemination management

Outline

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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

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Reproducible modeling results :: Standards

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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

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Reproducible modeling results :: Towards publication

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+

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

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[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

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Fig.: Li et al (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic

models. BMC Systems Biology

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Dissemination :: Public model repositories

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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

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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

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“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

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• 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

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Pubmed:

1831270

Kegg Pathway

sce04111

isDescribedBy

is

EC-Code:

3.1.3.16

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ion

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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

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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

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Tyson_1991

C2 CP

time

environment

isDescribedByPubmed:

1831270

time timeCPC2 CP C2

is_connected is_connected

is_mapped_to

is_connected

SBO:000064

is

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Management :: Combination of methods

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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

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CP

Uniprot:P04551

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23

Interpro

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Document

SEDML

Modelrefere

nce

Output

Datagenera

tor

Simulation

Task

Variable

Variable

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Tyson_19

91

C2 CP

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environ

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ed:183127

0

Pubmed:

1831270

time timeCPC2 CP C2

Ron Henkel

http://sems.uni-rostock.de

Management :: Provenance

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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, …

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Management :: Model version control

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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

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Document

Tyson1991

Cell Cycle 6

var

C2 pM CellReaction3 CP

Uniprot:P04551 Uniprot:P04551 GO:0005623Interpro:

IPR006670

isV

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ion

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isV

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ha

sP

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asProduct

asReactant isContainedIn

Pubmed:

1831270

Kegg Pathway

sce04111

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is

EC-Code:

3.1.3.16

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Of

http://sems.uni-rostock.de

Thank you for your attention.

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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