Improving the Management of Computational Models · GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var Reaction3 C2 CP pM Cell Uniprot:P04551 Uniprot:P04551 GO:0005623

SYSTEMS BIOLOGY

BIOINFORMATICS

ROSTOCKS E Ssimulation experiment management system

Improving the Management ofComputational Modelsstorage – retrieval & ranking – version control

MARTIN SCHARM1,2 , RON HENKEL1 , DAGMAR WALTEMATH1 ,OLAF WOLKENHAUER1,31Department of Systems Biology & Bioinformatics, University of Rostock2Department of Computer Science, University of Oxford3Stellenbosch Institute for Advanced Study, South Africa

http://sems.uni-rostock.de

European Bioinformatics InstituteUK 2013

Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 1

http://www.sbi.uni-rostock.de/team/single/martin-scharm/http://www.sbi.uni-rostock.de/team/single/ron-henkel/http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/http://www.sbi.uni-rostock.de/team/single/prof-olaf-wolkenhauer/http://sems.uni-rostock.dehttp://www.sbi.uni-rostock.de/team/single/martin-scharm/http://www.sbi.uni-rostock.de/team/single/ron-henkel/http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/http://www.sbi.uni-rostock.de/team/single/prof-olaf-wolkenhauer/

Introduction

time

#mod

els

2013-06-18

462

+50

1+x·1

03

216

+19

6

2009-06-1631

2005-04-11

• Number of models is steadily increasing• Models tend to get more complex• Continuous development


http://www.sbi.uni-rostock.de/team/single/martin-scharm/http://www.sbi.uni-rostock.de/team/single/ron-henkel/http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/http://www.sbi.uni-rostock.de/team/single/prof-olaf-wolkenhauer/

Introduction

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tions

mod

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06

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2013• Number of models is steadily increasing• Models tend to get more complex• Continuous development



Introduction

time

#Ver

sions

• Number of models is steadily increasing• Models tend to get more complex• Continuous development



IntroductionTasks

• Storage & Availability

• Search & Retrieval

• Version Control



IntroductionTasks



• Version Control?



IntroductionTasks



• Version Controlversion x-1 version x version x+1



IntroductionSolutions

Several projects developmethods to support thecommunity

ModelRepository



SYSTEMS BIOLOGY

BIOINFORMATICS

ROSTOCKS E Ssimulation experiment management system

track development

store retrieve

rank

Retrieval

Ranking

ΔΔ

Version 1

Version 2

latest

Version Control

DocumentTyson1991 Cell

Cycle 6

varC2 pM Cell

Reaction3

CP

Uniprot:P04551

Uniprot:P04551

GO:0005623

Interpro

: IPR006670

isVe

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Pubmed:1831270

Kegg Pathway

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isDescribedBy

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EC-Code: 3.1.3.16

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SEDML

Modelreference

Output

Datagenerator

Simulation Task

Variable

Variable

Document

Tyson_1991

C2 CP

time

environmen

t

isDescribedByPubmed:

1831270

time timeCPC2 CP C2


Cycle 6

varC2 pM Cell

Reaction3

CP

Uniprot:P04551

Uniprot:P04551

GO:0005623

Interpro

: IPR006670

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hasP

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Pubmed:1831270

Kegg Pathway

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isDescribedBy

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EC-Code: 3.1.3.16

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Cycle 6

varC2 pM Cell

Reaction3

CP

Uniprot:P04551

Uniprot:P04551

GO:0005623

Interpro

: IPR006670

isVe

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Pubmed:1831270

Kegg Pathway

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isDescribedBy

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EC-Code: 3.1.3.16

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Cycle 6

varC2 pM Cell

Reaction3

CP

Uniprot:P04551

Uniprot:P04551

GO:0005623

Interpro

: IPR006670

isVe

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hasP

art

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Pubmed:1831270

Kegg Pathway

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isDescribedBy

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EC-Code: 3.1.3.16

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Document

Tyson_1991

C2 CP

time

environmen

t


1831270

time timeCPC2 CP C2


Cycle 6

varC2 pM Cell

Reaction3

CP

Uniprot:P04551

Uniprot:P04551

GO:0005623

Interpro

: IPR006670

isVe

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nOf

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hasP

art

is

Pubmed:1831270

Kegg Pathway

sce04111

isDescribedBy

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EC-Code: 3.1.3.16

isVe

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Cycle 6

varC2 pM Cell

Reaction3

CP

Uniprot:P04551

Uniprot:P04551

GO:0005623

Interpro

: IPR006670

isVe

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nOf

isVe

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n

hasP

art

is

Pubmed:1831270

Kegg Pathway

sce04111

isDescribedBy

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EC-Code: 3.1.3.16

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Document

Tyson_1991

C2 CP

time

environmen

t


1831270

time timeCPC2 CP C2

Graph Database

Document

SEDML

Modelreference

Output

Simulation

Task

Document

SEDML

Modelreference

Output

Datagenerator

Simulation Task

Variable

Variable

Document

SEDML

Modelreference

Output

Datagenerator

Simulation Task

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


http://sems.uni-rostock.de/http://www.sbi.uni-rostock.de/team/single/martin-scharm/http://www.sbi.uni-rostock.de/team/single/ron-henkel/http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/http://www.sbi.uni-rostock.de/team/single/prof-olaf-wolkenhauer/

StorageGraphDB

Taken from: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.174.8830&rep=rep1&type=pdf



StorageAvailable Data

Model & Simulation Annotation & Ontologies A model’s network

• Constituent names• XML encoded

representation

• Biochemicalbackground

• Synonyms

• Model structure• Aggregation values• Model related data



StorageGraphDB

Document

Tyson1991 Cell Cycle 6

var

C2 pM CellReaction3 CP

Uniprot:P04551 Uniprot:P04551 GO:0005623Interpro: IPR006670

isVe

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hasP

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asProductasReactant isContainedIn

Pubmed:1831270

Kegg Pathwaysce04111

isDescribedBy

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EC-Code: 3.1.3.16

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Tyson 1991 - SBML

Model

Entities

Annotations

fig. courtesy R. HenkelDec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 8


StorageGraphDB

Document

Model

sodium channel

sodium channel m

gate

time

envmt

has_annotation Pubmed:12991237

time timevm v m

is_connected is_connected

is_mapped_to

Tyson 1991 - CellML

Model

Component

Variable



StorageGraphDB

Document

SEDML

Modelreference Output

DatageneratorSimulation Task

Variable

Variable

Tyson 1991 - SED-ML

Simulation

Entity

Variable



StorageGraphDB

SBO:Ontology

SBO:0000

SBO:544 SBO:236SBO:231

isA

SBO:064 SBO:545SBO:004 SBO:003

Systems Biology Ontology

Root

1. Level

All Ontologies available in OWL can be added easily

fig. courtesy R. Henkel



StorageGraphDB

Models Model related data



StorageGraphDB


Document


var



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Pubmed:1831270


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EC-Code: 3.1.3.16

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StorageGraphDB


Document


var



isVe

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hasP

art

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Pubmed:1831270


isDescribedBy

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EC-Code: 3.1.3.16

isVe

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Document

Model

sodium channel

sodium channel m

gate

time

envmt


time timevm v m


is_mapped_to



StorageGraphDB


Document


var



isVe

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nOf

isVe

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hasP

art

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Pubmed:1831270


isDescribedBy

is

EC-Code: 3.1.3.16

isVe

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Document

Model

sodium channel

sodium channel m

gate

time

envmt


time timevm v m


is_mapped_to

Document

SEDML



Variable

Variable



StorageGraphDB


Document


var



isVe

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nOf

isVe

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hasP

art

is


Pubmed:1831270


isDescribedBy

is

EC-Code: 3.1.3.16

isVe

rsio

nOf

Document

Model

sodium channel

sodium channel m

gate

time

envmt


time timevm v m


is_mapped_to

Document

SEDML



Variable

Variable

SBO:Ontology

SBO:0000


isA




StorageGraphDB


Document


var



isVe

rsio

nOf

isVe

rsio

n

hasP

art

is


Pubmed:1831270


isDescribedBy

is

EC-Code: 3.1.3.16

isVe

rsio

nOf

Document

Model

sodium channel

sodium channel m

gate

time

envmt


time timevm v m


is_mapped_to

Document

SEDML



Variable

Variable

SBO:Ontology

SBO:0000


isA


Henkel et al. 2013, Graph-based storage of computational biology models and associated simulations, in preparation



StorageGraphDB


Document


var



isVe

rsio

nOf

isVe

rsio

n

hasP

art

is


Pubmed:1831270


isDescribedBy

is

EC-Code: 3.1.3.16

isVe

rsio

nOf

Document

Model

sodium channel

sodium channel m

gate

time

envmt


time timevm v m


is_mapped_to

Document

SEDML



Variable

Variable

SBO:Ontology

SBO:0000


isA


Index

Model

IdNameComponentVariableSpeciesReactionCompartment



StorageGraphDB


Document


var



isVe

rsio

nOf

isVe

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n

hasP

art

is


Pubmed:1831270


isDescribedBy

is

EC-Code: 3.1.3.16

isVe

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nOf

Document

Model

sodium channel

sodium channel m

gate

time

envmt


time timevm v m


is_mapped_to

Document

SEDML



Variable

Variable

SBO:Ontology

SBO:0000


isA


Index

Model

Publication

TitleJournalAbstractAuthors



StorageGraphDB


Document


var



isVe

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Pubmed:1831270


isDescribedBy

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EC-Code: 3.1.3.16

isVe

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Document

Model

sodium channel

sodium channel m

gate

time

envmt


time timevm v m


is_mapped_to

Document

SEDML



Variable

Variable

SBO:Ontology

SBO:0000


isA


Index

Model

Publication

Person

First nameLast nameOrganizationEmail



StorageGraphDB


Document


var



isVe

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Pubmed:1831270


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EC-Code: 3.1.3.16

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Document

Model

sodium channel

sodium channel m

gate

time

envmt


time timevm v m


is_mapped_to

Document

SEDML



Variable

Variable

SBO:Ontology

SBO:0000


isA


Index

Model

Publication

Person

Annotation

URIDescription



StorageGraphDB


Document


var



isVe

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Document

Model

sodium channel

sodium channel m

gate

time

envmt


time timevm v m


is_mapped_to

Document

SEDML



Variable

Variable

SBO:Ontology

SBO:0000


isA


Index

Model

Publication

Person

Annotation

Simulation

IdName



retrieval & rankingExample

Document


var



isVe

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EC-Code: 3.1.3.16

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Show me models byTyson describing the cellcycle and have cdc2!

Person

Annotation



retrieval & rankingExample

Document


var



isVe

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hasP

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Pubmed:1831270


isDescribedBy

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EC-Code: 3.1.3.16

isVe

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Thank you!

Person

Annotation

1. (0.859) Tyson1991 - Cell Cycle 6 var2. (0.854) Tyson2001_Cell_Cycle_Regulation3. (0.477) Chen2004 - Cell Cycle Regulation

Henkel et al. 2010: Ranked retrieval of Computational Biology modelsDec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13


Version Control

version x-1 version x version x+1

what happened ?

track versions Ø



Version Control

version x-1 version x version x+1

track versions Ø

what happened ?



Model EvolutionExample: Cell Cycle

CyclinCdc2 P

CyclinCdc2 P

Modeling the cell division...

John J Tyson, 1991

muell




Cyclin

Cdc2 P

Cyclin

Cdc2 P

Cdc25Cdc25∗ Wee1 Wee1∗

Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte

Bela Novak and John J Tyson, 1993

Cyclin

Cdc2 P

Cyclin

Cdc2 P


John J Tyson, 1991

muell




Cyclin

Cdc2 P

Cyclin

Cdc2 P




Cyclin

Cdc2 P

Cyclin

Cdc2 P

Cdc25Cdc25∗

Mik1 Mik1∗

Wee1 Wee1∗

Quantitative analysis of a molecular model of mitotic control in Fission yeast


Cyclin

Cdc2 P

Cyclin

Cdc2 P


John J Tyson, 1991

muell




Cyclin

Cdc2 P

Cyclin

Cdc2 P




Cyclin

Cdc2 P

Cyclin

Cdc2 P

Cdc25Cdc25∗

Mik1 Mik1∗

Wee1 Wee1∗

Quantitative analysis of a molecular model of mitotic control in Fission yeast


Cyclin

Cdc2 P

Cyclin

Cdc2 P


John J Tyson, 1991

Cyclin

Cdc2 P

Cyclin

Cdc2 P

Cdc25Cdc25∗

Mik1 Mik1∗

Wee1 Wee1∗

Cyclin

Cdc2 P

Rum1

Modeling the control of DNA replication in fission yeast


muell



Version Controlgood news

A r C

B

D

cycE/cdk2

RB/E2F

RB-Hypo

free E2F

A r

B

C

D

E s

RB/E2F

RB-Hypo

free E2F

cycE/cdk2

RB-Phos

new insights

Waltemath et al.: Improving the reuse of computational models through versioncontrol. Bioinformatics (2013) 29(6): 742-728;


http://bioinformatics.oxfordjournals.org/content/29/6/742.longhttp://bioinformatics.oxfordjournals.org/content/29/6/742.longhttp://www.sbi.uni-rostock.de/team/single/martin-scharm/http://www.sbi.uni-rostock.de/team/single/ron-henkel/http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/http://www.sbi.uni-rostock.de/team/single/prof-olaf-wolkenhauer/

BiVeSDifference Detection

A r C

B

D

cycE/cdk2

RB/E2F

RB-Hypo

free E2F

A r

B

C

D

E s

RB/E2F

RB-Hypo

free E2F

cycE/cdk2

RB-Phos

A

r

BC

D

A

r

B

C

D

E

s

Biochemical Model Version Control System

• compares models encoded in standadizedformats (currently: and )

• maps hierarchically structured contentmapping



BiVeSDifference Detection

A r C

B

D

cycE/cdk2

RB/E2F

RB-Hypo

free E2F

A r

B

C

D

E s

RB/E2F

RB-Hypo

free E2F

cycE/cdk2

RB-Phos

A

r

BC

D

A

r

B

C

D

E

s

Biochemical Model Version Control System

• compares models encoded in standadizedformats (currently: and )

• maps hierarchically structured content• constructs a diff (in XML format)• is able to interprete this diff

Diff

movesproduct of r: C

deletesproduct of r: B

insertsspecies: Eproduct of r: Ereaction s

mapping

diff construction



BudHatDiff Visualization

A r C

B

D

cycE/cdk2

RB/E2F

RB-Hypo

free E2F

A r

B

C

D

E s

RB/E2F

RB-Hypo

free E2F

cycE/cdk2

RB-Phos

A

r

BC

D

A

r

B

C

D

E

s

Diff

movesproduct of r: C

deletesproduct of r: B

insertsspecies: Eproduct of r: Ereaction s

• calls BiVeS to construct the diff• displays the result in various formats

• the XML diff• a reaction network highlighting the

changes using• a human readable report

A r B

C

D

E s



ApplicationsCommunicating Changes

Novak & Tyson ’93: Numerical analysis of a comprehensive model of M-phase control in Xenopusoocyte extracts and intact embryos

Biomodels Database BIOMD0000000107:


http://www.ebi.ac.uk/biomodels-main/BIOMD0000000107http://www.sbi.uni-rostock.de/team/single/martin-scharm/http://www.sbi.uni-rostock.de/team/single/ron-henkel/http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/http://www.sbi.uni-rostock.de/team/single/prof-olaf-wolkenhauer/


Fixed the model→ How to communicate the changes?

Unix diff?

1c1< --->

287 lines...





BiVeS Diff?

much smarter, but still 24 lines..Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 21




BiVeS Diff: Highlighted chemical reaction network





BiVeS Diff: Report



ApplicationsBiomodelsDatabase / PMR2

Biomodels Database CellML Model Repository

963 # Models 158910193 # Versions 128789148 # prod. Diffs 12936

BiVeS Unix’ Diff BiVeS Unix’ Diff2233 1890 # empty Diffs 10113 10043

434.825 1977.210 ∅ #ops 349.5282 480.249

6915 non-empty diffs following 2823 non-empty diffs



ApplicationsBiomodelsDB / PMR2

Biomodels Database

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Documents

Improving the Management of Computational Models · GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var Reaction3 C2 CP pM Cell Uniprot:P04551 Uniprot:P04551 GO:0005623