BiVeS & BudHat -- Version Control for Computational Models @ All hands PALs Meeting
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Transcript of BiVeS & BudHat -- Version Control for Computational Models @ All hands PALs Meeting
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SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCKS E Ssimulation experiment management system
BiVeS & BudHatVersion Control for Computational Models
MARTIN SCHARM, RON HENKEL, DAGMAR WALTEMATH
Department of Systems Biology & BioinformaticsFaculty of Computer Sciences & Electrical EngineeringUniversity of Rostock
http://sems.uni-rostock.de
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 1 / 19
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Table of contents
Motivation
Detecting Differences
Visualizing Differences
Conclusions
Done
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 2 / 19
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Motivation
Motivation
Detecting Differences
Visualizing Differences
Conclusions
Done
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 3 / 19
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Version Control for ModelsMotivation
metabolic and gene regulation network model in C. acetobutylicum
Haus et. al. 2011
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 4 / 19
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Version Control for ModelsMotivation
timeinternal Version Release
PapoutsakisEquations and calculations for fermentations of butyric acid bacteria1984 in Biotechnology and bioengineering
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 5 / 19
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Version Control for ModelsMotivation
timeinternal Version Release
Papoutsakis
ShintoKinetic modeling and sensitivity analysis of acetone–butanol–ethanol production2007 in Journal of biotechnology
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 5 / 19
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Version Control for ModelsMotivation
timeinternal Version Release
Papoutsakis
Shinto
COSMIC IA systems biology approach to investigate the effect of pH-induced gene regulationon solvent production by Clostridium acetobutylicum in continuous culture2011 in BMC systems biology
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 5 / 19
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Version Control for ModelsMotivation
timeinternal Version Release
Papoutsakis
Shinto
COSMIC I
COSMIC II
A shift in the dominant phenotype governsthe pH-induced switch in C. acetobutylicumpending
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 5 / 19
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Version Control for ModelsMotivation
timeinternal Version Release
Papoutsakis
Shinto
COSMIC I
COSMIC II
???
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 5 / 19
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Version Control for ModelsMotivation
timeinternal Version Release
Papoutsakis
Shinto
COSMIC I
COSMIC II
???
some title20?? in some journal
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 5 / 19
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Version Control for ModelsMotivation
timeinternal Version Release
Papoutsakis
Shinto
COSMIC I
COSMIC II
???
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 5 / 19
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Version Control for ModelsMotivation
timeinternal Version Release
Papoutsakis
Shinto
COSMIC I
COSMIC II
???
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 5 / 19
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Version Control for ModelsRequirements
• Unambiguously identifiable models
• Robust difference detection
• Interpretation and justification of identified changes
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 6 / 19
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Detecting Differences
Motivation
Detecting Differences
Visualizing Differences
Conclusions
Done
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 7 / 19
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SBMLlet’s take a short look at our models
Model
species reactions...
A B C D B+C−→DA−→B
Model is encoded in XML
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 8 / 19
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SBMLlet’s take a short look at our models
Model
species reactions...
A B C D B+C−→DA−→BE A+E−→B
We are interested in changes of the entities!
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 8 / 19
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Conventional Diffing
Generating a diff using Unix’ diff-tool is very useful for various things:
• text (notes, latex etc)• source code• ...
22 def s a l u t e23 p u t s " H e l l o ? "24 end
vs22 def s a l u t e23 p u t s " H e l l o ! "24 end
23 c 2 3< p u t s " H e l l o ? "−−−> p u t s " H e l l o ! "
⇒ content that is line-based
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 9 / 19
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Conventional Diffing
Generating a diff using Unix’ diff-tool is very useful for various things:
• text (notes, latex etc)• source code• ...
22 def s a l u t e23 p u t s " H e l l o ? "24 end
vs22 def s a l u t e23 p u t s " H e l l o ! "24 end
23 c 2 3< p u t s " H e l l o ? "−−−> p u t s " H e l l o ! "
⇒ content that is line-based
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 9 / 19
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Diff for XMLAppropriate for SBML versioning?
version A<reaction id="StoP" fast="false">
<listOfReactants >
<speciesReference species="S"/>
</listOfReactants >
<listOfProducts >
<speciesReference species="P"/>
</listOfProducts >
</reaction >
S P
version B<reaction fast="false" id="StoP">
<listOfReactants >
<speciesReference species="S"/>
</listOfReactants >
<listOfProducts >
<speciesReference species="M"/>
</listOfProducts >
</reaction >
S M
What does a resulting diff of these models reveal?
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 10 / 19
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Diff for XMLAppropriate for SBML versioning?
usr@srv ~ $ diff A B
1,7c1 ,7
< <reaction id="StoP" fast="false">
< <listOfReactants >
< <speciesReference species="S"/>
< </listOfReactants >
< <listOfProducts >
< <speciesReference species="P"/>
< </listOfProducts >
---
> <reaction fast="false" id="StoP">
> <listOfReactants >
> <speciesReference species="S"/>
> </listOfReactants >
> <listOfProducts >
> <speciesReference species="M"/>
> </listOfProducts >
A
B
⇒ interesting parts arecovered up in lots ofirrelevant changes
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 11 / 19
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Our taskDifference detection between models
How to identify changes in XML-encoded computational models?
How to interprete detected changes?
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 12 / 19
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BivesIdentifikation of differences
Bives = Biochemical Model Versioning SystemLibrary to identify and classify changes between SBML-encoded models
• Adaptation of XyDiff (in collaboration with Robert Hälke)
• Input: 2 SBML models
• Output: Diff in XML format containing Diff operations:
• Deletes
• Inserts
• Updates
• Moves
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 13 / 19
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Visualizing Differences
Motivation
Detecting Differences
Visualizing Differences
Conclusions
Done
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 14 / 19
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Visualizing DifferencesChanges in action
Budhat: Prototype for Version Control
• Display of the generated Diff
• Visualization of the model (in collaboration with Steffen Hadlak)
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 15 / 19
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Real-World-Example
DEMO of BudHat using models from
Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilisLiebal et. al. 2012
http://budhat.sems.uni-rostock.de
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 16 / 19
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Conclusions
Motivation
Detecting Differences
Visualizing Differences
Conclusions
Done
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 17 / 19
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Conclusions
• Version control is beneficial
• We do not want to establish yet another platform for users
• Can SysMO/SEEK be improved by our tools?
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 18 / 19
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SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCKS E Ssimulation experiment management system
That’s it! Stay tuned ;-)
http://sems.uni-rostock.de
http://budhat.sems.uni-rostock.de
Questions? Suggestions? Recommendations? Drop me an email:[email protected]
29. November 2012 Bives & Budhat | Martin Scharm, Ron Henkel, Dagmar Waltemath 19 / 19