The CellML models’ walk through the repository

SYSTEMS BIOLOGY

BIOINFORMATICS

ROSTOCKS E Ssimulation experiment management system

The CellML models’ walkthrough the repositoryA retrospective study

MARTIN SCHARM, DAGMAR WALTEMATHDepartment of Systems Biology & Bioinformatics, University of Rostock

http://sems.uni-rostock.de

8th International CellML WorkshopAuckland, New Zealand 2014

Apr 14, 2014 SEMS | Martin Scharm, Dagmar Waltemath 1

http://www.sbi.uni-rostock.de/team/single/martin-scharm/

http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/




SYSTEMS BIOLOGY

BIOINFORMATICS


S E Ssimulation experiment management system

Graph Database

Version Control

∆ ∆

Retrieval

Ranking

retrieve

rank

track development

store

Version 1

Version 2

latest

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


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



The CellML Model Repository

2007 2008 2009 2010 2011 2012 2013

050

010

0015

0020

0025

00

Number of models in the repository




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.long

http://bioinformatics.oxfordjournals.org/content/29/6/742.long



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

B

C

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 delta (in XML format)

• is able to interprete this diff

<XML>Diff

movesproduct of r: C

deletesproduct of r: B

insertsspecies: Eproduct of r: Ereaction s

</XML>

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

B

C

D

A

r

B

C

D

E

s

<XML>Diff

movesproduct of r: C

deletesproduct of r: B

insertsspecies: Eproduct of r: Ereaction s

</XML>

• 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





for r in $repositories

do

hg clone $r

done

∅CellML Files 2702





M1

1M

1

2M

1

3

M2

2M

2

3

M3

3

∅CellML Files 2702∅Versions 18329





M1

1M

1

2M

1

3

M2

2M

2

3

M3

3

∆ ∆

∆


∅#Deltas 15626





M1

1M

1

2M

1

3

M2

2M

2

3

M3

3

∆ ∆

∆


∅#Deltas 15626∅#relevant 2833∅#operations 355.31




The CellML Model RepositoryGrowth

2007 2008 2009 2010 2011 2012 2013

050

010

0015

0020

0025

00

Number of models in the repository





2007 2008 2009 2010 2011 2012 2013

050

010

0015

0020

0025

00

Number of models in the repositoryAvg number of nodes in an XML tree





2007 2008 2009 2010 2011 2012 2013

050

010

0015

0020

0025

00


Dec 3rd, 2010: about 800 models with

mean size of ≈56 nodes per model

in repositories SVP_0000*





2007 2008 2009 2010 2011 2012 2013

050

010

0015

0020

0025

00


Dec 3rd, 2010: about 800 models with

mean size of ≈56 nodes per model

in repositories SVP_0000*

“Here we describe the development of an online re-pository of Standard Virtual Biological Parts (SVPs)– mathematical model components describing thefunction of SBPs [(Standard Biological Parts)] whichcan be downloaded, extended and recombined to aidthe design, in silico, of synthetic biological systems.”





2007 2008 2009 2010 2011 2012 2013

05

1015

20

units

,impo

rts,

com

pone

nts

mean num unitsmean num importsmean num componentsmean num variables

050

100

150

varia

bles




The CellML Model RepositoryTypes of Operation

A

B

C D

E

F

A

B

G D

E

C

x=“y” x=“z”

● ●●●● ●●●● ●●●● ●● ●● ●●● ● ●●●●● ●● ● ●●● ● ●●●●●●● ●●●● ●●●● ●●●● ●● ●● ●

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1 5 10 50 100 500 1000

updates

deletes

inserts

moves

median50%




The CellML Model RepositoryModification Targets

<component name=“Template_Species”><variable name=“time” units=“second” public_interface=“in”/><variable name=“concentration” units=“nM” initial_value=“concInit” public_interface=“out”/><variable name=“JGain” units=“nM_per_s” public_interface=“in”/><math xmlns=“http://www.w3.org/1998/Math/MathML”>

<apply><eq/><apply>

<diff/><bvar>

<ci>time</ci></bvar><ci>concentration</ci>

</apply><ci>JGain</ci>

</apply></math>

</component>

● ●● ●● ●● ●● ●●● ●● ● ●●● ●●● ●●●● ● ● ●●●●● ●●● ●● ●● ●● ●● ●●● ●●● ● ●● ●● ●● ●● ●●●●● ●● ● ●● ●●● ●●●● ●● ●●●● ●●● ●● ●●●● ●●● ●●●● ● ● ●●●● ●● ●●● ●●●● ●● ●● ● ●● ●●●● ●● ●●● ●● ●●● ●● ●● ● ●● ●● ●●● ●● ●● ●●●●●●● ●●● ●●● ● ●● ●●●● ●● ●● ●● ●● ●●●● ●● ●●●● ●

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1 5 10 50 100 500 1000

document nodes

attributes

text nodes




The CellML Model RepositoryOperations

Novak1993 12 updates 20 moves 80 inserts 20 deletes




SYSTEMS BIOLOGY

BIOINFORMATICS


Thank you for your attention!

SEMS group

Dagmar WaltemathRon HenkelMartin PetersMarkus WolfienRebekka AlmOlaf Wolkenhauer

@SemsProject



https://twitter.com/semsproject




Science

The CellML models’ walk through the repository