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/
How to Troubleshoot Apps for the Modern Connected Worker
BiVeS & BudHat: Invited Talk @ 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
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