Download - BiVeS & BudHat: Version Control for Computational Models @ 7th International CellML Workshop
SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCKS E Ssimulation experiment management system
BiVeS & BudHatVersion Control for Computational Models
MARTIN SCHARMDepartment of Systems Biology & BioinformaticsFaculty of Computer Sciences & Electrical EngineeringUniversity of Rostock
http://sems.uni-rostock.de
7th International CellML Workshop
March 25, 2013 Bives & Budhat | Martin Scharm 1 / 10
SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCKS E Ssimulation experiment management system
track development
store retrieve
rank
Management
Δ
Δ
Version 1
Version 2
latest
Format-independent, graph-basedmodel storage
Information Retrieval-basedmodel search and ranking
Diff-based modelversion control
http://sems.uni-rostock.de/
March 25, 2013 Bives & Budhat | Martin Scharm 2 / 10
Version ControlVersion Control
A r C
B
D
cycE/cdk2
RB/E2F
RB-Hypo
free E2F
March 25, 2013 Bives & Budhat | Martin Scharm 3 / 10
Version ControlVersion Control
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
March 25, 2013 Bives & Budhat | Martin Scharm 4 / 10
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
• maps hierarchically structured content
• compares models encoded in standadizedformats (currently: and )
• constructs a diff (in XML format)
<XML>Diff
movesproduct of r: C
deletesproduct of r: B
insertsspecies: Eproduct of r: Ereaction s
</XML>
mapping
di� construction
March 25, 2013 Bives & Budhat | Martin Scharm 5 / 10
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
March 25, 2013 Bives & Budhat | Martin Scharm 6 / 10
BiVeS & BudHatDEMO
lets take a look at our tools in action!
http://budhat.sems.uni-rostock.de
March 25, 2013 Bives & Budhat | Martin Scharm 7 / 10
BiVeS & BudHatIntegration
BiVeS & BudHat can be integrated in extisting repositories!
Requirements:
• Models must be encoded in standadized formats (e.g. CellML or SBML)
• Each version of a model must be accessible for BudHat (either physically orthrough an API)
• Java based web server (e.g. tomcat), may run on a seperate node
If you are interested in using our tools feel free to contact us.
March 25, 2013 Bives & Budhat | Martin Scharm 8 / 10
BiVeS & BudHatSummary
• BiVeS = Difference detection for hierarchical structures
• BudHat = Visualization of changes
• Both tools are open source
• We do not want to establish yet another platform
• Our goal is to extend existing models repositories with a valuable versioncontrol mechanism
March 25, 2013 Bives & Budhat | Martin Scharm 9 / 10
SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCKS 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:[email protected]
March 25, 2013 Bives & Budhat | Martin Scharm 10 / 10
