Talk at the IPK in Gatersleben to initiate collaborations with the VANTED/e!Dal crews. The slides are also available at our website http://sems.uni-rostock.de/2013/05/research-visit-at-the-ipk-gatersleben/

1. SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCK
S E Ssimulation experiment management system
BiVeS & BudHat
Version Control for Computational Models
MARTIN SCHARM
Department of Systems Biology & Bioinformatics
Faculty of Computer Science & Electrical Engineering
University of Rostock
http://sems.uni-rostock.de
Gatersleben 2013
June 11, 2013 Bives & Budhat | Martin Scharm 1 / 13

2. SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCK
S E Ssimulation experiment management system
track development
store retrieve
rank
Management
Δ
Δ
Version 1
Version 2
latest
Format-independent,
graph-based storage
Information Retrieval-based
search and ranking
Diff-based
version control
http://sems.uni-rostock.de/
June 11, 2013 Bives & Budhat | Martin Scharm 2 / 13

3. Version Control
Intro
• many models
• multiple versions of each model
• several repositories
time
#models
June 11, 2013 Bives & Budhat | Martin Scharm 3 / 13

4. Version Control
Intro
• many models
• multiple versions of each model
• several repositories
version x-1 version x version x+1
June 11, 2013 Bives & Budhat | Martin Scharm 3 / 13

5. Version Control
Intro
• many models
• multiple versions of each model
• several repositories
June 11, 2013 Bives & Budhat | Martin Scharm 3 / 13

6. Version Control
Intro
• many models
• multiple versions of each model
• several repositories
version x-1 version x version x+1
track versions
what happened ?
June 11, 2013 Bives & Budhat | Martin Scharm 3 / 13

7. Version Control
good 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 version
control. Bioinformatics (2013) 29(6): 742-728;
June 11, 2013 Bives & Budhat | Martin Scharm 4 / 13

8. BiVeS
Difference 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 standadized
formats (currently: and )
• maps hierarchically structured content
mapping
June 11, 2013 Bives & Budhat | Martin Scharm 5 / 13

9. BiVeS
Mapping
• input: 2 XML documents
• map unambiguos
nodes/subtrees
• propagate mapping up/down
• exploit further knowledge of
biological systems
same ID
same
subtree
hash
...
... ...... ...
...
... ...... ...
June 11, 2013 Bives & Budhat | Martin Scharm 6 / 13

10. BiVeS
Mapping
• input: 2 XML documents
• map unambiguos
nodes/subtrees
• propagate mapping up/down
• exploit further knowledge of
biological systems
eq. netw....
... ...... ...
...
... ...... ...
June 11, 2013 Bives & Budhat | Martin Scharm 6 / 13

11. BiVeS
Mapping
• input: 2 XML documents
• map unambiguos
nodes/subtrees
• propagate mapping up/down
• exploit further knowledge of
biological systems
A B
C
D E
A B
C
D E
A B
C
D E
June 11, 2013 Bives & Budhat | Martin Scharm 6 / 13

12. BiVeS
Difference 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 standadized
formats (currently: and )
• maps hierarchically structured content
• constructs a diff (in XML format)
• is able to interprete this diff
<XML>
Diff
moves
product of r: C
deletes
product of r: B
inserts
species: E
product of r: E
reaction s
</XML>
mapping
di construction
June 11, 2013 Bives Budhat | Martin Scharm 7 / 13

13. BudHat
Diff 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
moves
product of r: C
deletes
product of r: B
inserts
species: E
product of r: E
reaction 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
June 11, 2013 Bives Budhat | Martin Scharm 8 / 13

14. BiVeS BudHat
DEMO
The Power of BudHat!
http://budhat.sems.uni-rostock.de
June 11, 2013 Bives Budhat | Martin Scharm 9 / 13

15. Rostock goes Gatersleben
Our Aim
VANTED BiVeS
June 11, 2013 Bives Budhat | Martin Scharm 10 / 13

16. Rostock goes Gatersleben
Our Aim
VANTED BiVeS
June 11, 2013 Bives Budhat | Martin Scharm 10 / 13

17. Rostock goes Gatersleben
Our Aim
VANTED BiVeS
let’s collaborate!
We VANT BiVeS!
June 11, 2013 Bives Budhat | Martin Scharm 10 / 13

18. BiVeS
Integration
jvm network cmd
import de.unirostock.sems.bives.api.SBMLDiff;
[...]
SBMLDiff differ = new SBMLDiff (sbmlFileA, sbmlFileB);
differ.mapTrees ();
String graph = differ.getGraphML ();
[...]
June 11, 2013 Bives Budhat | Martin Scharm 11 / 13

19. BiVeS
Integration
jvm network cmd
curl -d file1=http://some.server/model/version1
-d file2=http://other.server/model/version2
-d get=graphml bives.server/api
June 11, 2013 Bives Budhat | Martin Scharm 11 / 13

20. BiVeS
Integration
jvm network cmd
java -jar BiVeS.jar path/to/version1 path/to/version2
git diff 88fea1cddf b64477d742 model.file
June 11, 2013 Bives Budhat | Martin Scharm 11 / 13

21. BiVeS BudHat
Summary
• BiVeS = Difference detection for hierarchically structured content
• BudHat = Prototype to demonstrate the capabilities
• Both tools are open source
• Our goal is to extend existing models repositories with a valuable version
control mechanism
June 11, 2013 Bives Budhat | Martin Scharm 12 / 13

22. SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCK
S E Ssimulation experiment management system
That’s it! Stay tuned ;-)
@SemsProject
http://sems.uni-rostock.de
http://budhat.sems.uni-rostock.de
Questions? Suggestions? Recommendations? Drop me an email:
martin.scharm@uni-rostock.de
June 11, 2013 Bives Budhat | Martin Scharm 13 / 13