BiVeS & BudHat @ Harmony2013
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SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCKS E Ssimulation experiment management system
BiVeS & BudHatVersion Control for Computational Models
MARTIN SCHARMDepartment of Systems Biology & BioinformaticsFaculty of Computer Science & Electrical EngineeringUniversity of Rostock
http://sems.uni-rostock.de
HARMONY 2013Farmington, CT, USA
May 20, 2013 Bives & Budhat | Martin Scharm 1 / 13
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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-based storage
Information Retrieval-basedsearch and ranking
Diff-basedversion control
http://sems.uni-rostock.de/
May 20, 2013 Bives & Budhat | Martin Scharm 2 / 13
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Version ControlIntro
• many models
• multiple versions of each model
• several repositories
time
#mod
els
May 20, 2013 Bives & Budhat | Martin Scharm 3 / 13
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Version ControlIntro
• many models
• multiple versions of each model
• several repositories
version x-1 version x version x+1
May 20, 2013 Bives & Budhat | Martin Scharm 3 / 13
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Version ControlIntro
• many models
• multiple versions of each model
• several repositories
May 20, 2013 Bives & Budhat | Martin Scharm 3 / 13
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Version ControlHow to get versions
• the FTP way
• the VCS way
usr@srv % ftp ftp.ebi.ac.ukConnected to ftp.gslb.ebi.ac.uk.220-[...]230 Login successful.Remote system type is UNIX.Using binary mode to transfer files.ftp> cd pub/databases/biomodels/releases/2012-08-11/250 Directory successfully changed.ftp> get BioModels_Database-r24_pub-sbml_files.tar.bz2local: BioModels_Database-r24_pub-sbml_files.tar.bz2 remote:
BioModels_Database-r24_pub-sbml_files.tar.bz2200 PORT command successful. Consider using PASV.150 Opening BINARY mode data connection for BioModels_Database-r24_pub-
sbml_files.tar.bz2 (91772 bytes).226 Transfer complete.
May 20, 2013 Bives & Budhat | Martin Scharm 4 / 13
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Version ControlHow to get versions
• the FTP way
• the VCS way
usr@srv % hg clone http://models.cellml.org/w/andre/nickerson-2008destination directory: nickerson-2008requesting all changesadding changesetsadding manifestsadding file changesadded 2 changesets with 131 changes to 131 filesupdating to branch default131 files updated, 0 files merged, 0 files removed, 0 files unresolvedusr@srv % hg log path/to/model[...]
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Version ControlHow to get versions
• the FTP way
• the VCS way
version x-1 version x version x+1
track versions X
what happened ?
May 20, 2013 Bives & Budhat | Martin Scharm 4 / 13
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Version Controlgood 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 versioncontrol. Bioinformatics (2013) 29(6): 742-728;
May 20, 2013 Bives & Budhat | Martin Scharm 5 / 13
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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
• compares models encoded in standadizedformats (currently: and )
• maps hierarchically structured contentmapping
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BiVeSMapping
• input: 2 XML documents• map unambiguos
nodes/subtrees• propagate mapping up/down• exploit further knowledge of
biol. systems
same ID
samesubtree
hash
...
... ...... ...
...
... ...... ...
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BiVeSMapping
• input: 2 XML documents• map unambiguos
nodes/subtrees• propagate mapping up/down• exploit further knowledge of
biol. systems
eq. netw....
... ...... ...
...
... ...... ...
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BiVeSMapping
• input: 2 XML documents• map unambiguos
nodes/subtrees• propagate mapping up/down• exploit further knowledge of
biol. systems
A B
C
D E
A B
C
D E
A B
C
D E
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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
• compares models encoded in standadizedformats (currently: and )
• maps hierarchically structured content
• 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
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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
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BiVeS & BudHatDEMO
lets take a look at our tools in action!
http://budhat.sems.uni-rostock.de
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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.
May 20, 2013 Bives & Budhat | Martin Scharm 11 / 13
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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
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SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCKS E Ssimulation experiment management system
That’s it! Stay tuned ;-)
@SemsProjecthttp://sems.uni-rostock.dehttp://budhat.sems.uni-rostock.de
Questions? Suggestions? Recommendations? Drop me an email:<[email protected]>
May 20, 2013 Bives & Budhat | Martin Scharm 13 / 13