bives & budhat: version control for computational models @ 7th international cellml workshop
DESCRIPTION
Introduction to BiVeS and BudHat at the 7th International CellML Workshop on Waiheke Island by Martin Scharm, member of the SEMS group at the University of Rostock. The slides are also available at our website http://sems.uni-rostock.de/2013/03/sems-at-the-7th-international-cellml-workshop/TRANSCRIPT
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