standardized visualisation of differences between model versions

1

Standardized visualization of differences between model versions

Tom Gebhardt, Martin Scharm, Vasundra Touré, Dagmar Waltemath, Olaf WolkenhauerDepartment of Systems Biology and Bioinformatics, University of Rostock

COMBINE 2016 Newcastle upon Tyne

23rd of September 2016

m nthe

computational modeling in biology network

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Motivation: models are evolving

Biological models are constantly evolving implying that several versions of a model can exist.

Scharm et al. (2015) An algorithm to detect and communicate the differences in computational models describing biological systems - Bioinformatics.

Figure courtesy: Tom Gebhart

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Motivation: models are evolving

Biological models are constantly evolving implying that several versions of a model can exist.

Statistics based on two repositories of computational models: Physiome and Biomodels.

Number of models: 3237

Number of model versions: 14439

Number of deltas: 10662


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

1

3

7

20

55

148

403

1097

2981

8103

22026

59874

162755

Cha

nges

Figure courtesy: Tom Gebhart

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

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Motivation: visualizing models

Plus, it is common to have a visual representation of biological networks…

Systems Biology Tools for Integrated Omics Analysis - M. Hugues

H. Kim (2015), Nature Chemical Biology

Brown et al. (1999), Trends in Microbiology

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Motivation: visualizing models

Plus, it is common to have a visual representation of biological networks…

… but understanding them depends on the reader’s knowledge …

Ras recruits

RafRas

translocates Raf

Ras activates

Raf

Systems Biology Tools for Integrated Omics Analysis - M. Hugues

H. Kim (2015), Nature Chemical Biology

Brown et al. (1999), Trends in Microbiology

Ras Raf

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The Systems Biology Graphical Notation

… unless the Systems Biology Graphical Notation is used.

SBGN webpage: http://sbgn.github.io/sbgn/

standardized glyphs and arcs and semantics specific to each.

sinksource


http://sbgn.github.io/sbgn/


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sinksource

Process DescriptionBiochemistry

Activity FlowMolecular biology

Entity RelationshipPhysiology, Genetics

Three languages are defined.



http://journal.imbio.de/article.php?aid=263




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sinksource

Process DescriptionBiochemistry

Activity FlowMolecular biology

Entity RelationshipPhysiology, Genetics

Three languages are defined.







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Objective: standardize diffs visualization

Highlighting of the differences between two model versions using SBGN.

RAF

ERK

MEK MEK

2P

ERK

MEK

P

ERK

P

RAF

P

ERK

2P

ADPATP

ATP ADP

ATP

ATP ADP

ADP

Version 1

MEK

2P

RAF

P

ERK

P

RAS

active

ERKERK

2P

ERK

RAS

MEK

P

RAF

ADP

ADP

ATP ATP

ATP

ADPATP

ADP

Version 2

10

Objective: standardize diffs visualization

Highlighting of the differences between two model versions using SBGN.

MEK

2P

RAS

ERK

RAF

P

RAF

RAS

active

ERK

2P

ERK

MEK

P

ERK

P

MEK

ATP

ATP

ATP ADP

ADP ADP

ADP

ATPADP

ATP

RAF

ERK

MEK MEK

2P

ERK

MEK

P

ERK

P

RAF

P

ERK

2P

ADPATP

ATP ADP

ATP

ATP ADP

ADP

Version 1

MEK

2P

RAF

P

ERK

P

RAS

active

ERKERK

2P

ERK

RAS

MEK

P

RAF

ADP

ADP

ATP ATP

ATP

ADPATP

ADP

Version 2Transition version

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What are the steps?


1) Generate a tool to compare differences between two versions

The description of a model’s evolution is performed by the BiVeS library.

Biochemical Model Version Control System

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

C

D

H E

com

mun

icatio

n pb

A

B

C D E

F

G

A

B

D H E

F

Gev

alua

tion p

b

A

B

C D E

F

G

A

B

D H E

F

Gprop

agat

ion p

b

A

B

C D E

F

G

A

B

D H E

F

Gid=“species1” id=“species1”

initi

alm

appi

ng p

b

A

B

C D E

F

G

A

B

D H E

F

G

model version 1model version 2

list of species list of reactions

C + D E D + H E

pre-

proc

essin

g pb

pre-

proc

essi

ngco

mm

un

ica

tion

eval

uatio

npr

opag

atio

nin

itial

map

ping

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

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What are the steps?


1) Generate a tool to compare differences between two versions2) Generate a visual of the differences

Differences are colour coded:

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

U. Liebal - “Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis” (Mol. BioSyst)Model Versions: laczsynth-2012-11-10 and laczsynth-2012-11-11

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

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What are the steps?

1) Generate a tool to compare differences between two versions2) Generate a visual of the differences3) Make the visual SBGN-compliant

Differences VisuaLization

https://github.com/Gebbi8/DiVil

U. Liebal - “Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis” (Mol. BioSyst)Model Versions: laczsynth-2012-11-10 and laczsynth-2012-11-11

https://github.com/Gebbi8/DiVil

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Preliminary workflow

BiVeSBioModels

CellML

highlighted network

SBGN-MLPNG

JPEG

SVG

m odels v ersionsv ersion

transition

d ifferences

visualization

library

compute

d ifferences

s pecies B

s pecies A

1

2 3 4

5

89

10

11 12

highlighted

reaction

network

6

report of

changes

diff encoded in

XML

SBGN PD

compliant JSON

DOT language

Graph-ML

JSON

7

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BiVeSBioModels

CellML

highlighted network

SBGN-MLPNG

JPEG

SVG


transition

d ifferences

visualization

library

compute

d ifferences

s pecies B

s pecies A

1

2 3 4

5

89

10

11 12

highlighted

reaction

network

6

report of

changes

diff encoded in

XML

SBGN PD

compliant JSON

DOT language

Graph-ML

JSON

7

16


BiVeSBioModels

CellML

highlighted network

SBGN-MLPNG

JPEG

SVG


transition

d ifferences

visualization

library

compute

d ifferences

s pecies B

s pecies A

1

2 3 4

5

89

10

11 12

highlighted

reaction

network

6

report of

changes

diff encoded in

XML

SBGN PD

compliant JSON

DOT language

Graph-ML

JSON

7

17


BiVeSBioModels

CellML

highlighted network

SBGN-MLPNG

JPEG

SVG


transition

d ifferences

visualization

library

compute

d ifferences

s pecies B

s pecies A

1

2 3 4

5

89

10

11 12

highlighted

reaction

network

6

report of

changes

diff encoded in

XML

SBGN PD

compliant JSON

DOT language

Graph-ML

JSON

7

18


BiVeSBioModels

CellML

highlighted network

SBGN-MLPNG

JPEG

SVG


transition

d ifferences

visualization

library

compute

d ifferences

s pecies B

s pecies A

1

2 3 4

5

89

10

11 12

highlighted

reaction

network

6

report of

changes

diff encoded in

XML

SBGN PD

compliant JSON

DOT language

Graph-ML

JSON

7

19


BiVeSBioModels

CellML

highlighted network

SBGN-MLPNG

JPEG

SVG


transition

d ifferences

visualization

library

compute

d ifferences

s pecies B

s pecies A

1

2 3 4

5

89

10

11 12

highlighted

reaction

network

6

report of

changes

diff encoded in

XML

SBGN PD

compliant JSON

DOT language

Graph-ML

JSON

7

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Importance of SBO terms

without SBO terms with SBO terms

cell

u

z

cell

u

EmptySet

z

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cell

u

z

cell

u

EmptySet

z

Annotate your models !

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cell

u

z

cell

u

EmptySet

z

SBGN workshop: still time to join us!

Annotate your models !

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Conclusion

Necessary improvements:● The SBGN output● Colour information● User interface

Opportunity for a student internship in Rostock (2-4 months project)More information: www.sems.uni-rostock.de

Prototype: SBGN map showing differences between model versions

● Extension of BiVeS library → information for generating SBGN map● Automatic force-based layout● Generation of an SBGN-ML file and graphical exports

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

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Thank you for your attention!

Contact: [email protected]

Martin ScharmBiVeS and Budhat

Tom GebhardtDiViL

The SEMS team

Funded by

standardized visualisation of differences between model versions

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