SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCK
S E Ssimulation experiment management system
BiVeS & BudHat
Difference Detection fo...
SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCK
S E Ssimulation experiment management system
track development
store retrieve
rank
...
Provenance
Provenance represents the seven W’s (Who, What, Where, Why, When, Which, (W)how).
– Goble 2002
G ˇ
ĽĽ
ˇ ˇ
ŤŤŤŤ
...
Provenance
Requirements
X1 X2
Y1
Y2
Y3
Availability & Identity
I O
-vs-
I
M
O
Difference
Detection
I
M
O
updated
reaction
...
Provenance
Requirements
X1 X2
Y1
Y2
Y3
Availability
& Identity
I O
-vs-
I
M
O
Difference Detection
I
M
O
updated
reaction
...
Provenance
Requirements
X1 X2
Y1
Y2
Y3
Availability
& Identity
I O
-vs-
I
M
O
Difference
Detection
I
M
O
updated
reaction
...
Provenance
Requirements
X1 X2
Y1
Y2
Y3
Availability
& Identity
I O
-vs-
I
M
O
Difference
Detection
I
M
O
updated
reaction
...
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-P...
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-...
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-P...
BiVeS  BudHat
DEMO
BudHat in action!
http://budhat.sems.uni-rostock.de
Sep 19, 2013 Bives  Budhat | Martin Scharm 8
BiVeS
Integration
jvm network cmd
import de.unirostock.sems.bives.api.SBMLDiff;
[...]
SBMLDiff differ = new SBMLDiff (sbml...
BiVeS
Integration
jvm network cmd
curl -d ’{
get:
[
documentType,
xmlDiff
],
files:
{
versionA:http://your.db/path/to/vers...
BiVeS
Integration
jvm network cmd
java -jar BiVeS.jar path/to/versionA path/to/versionB
git diff 88fea1cddf b64477d742 mod...
BiVeS  BudHat
Summary
• BiVeS = Difference detection for hierarchically structured content
• BudHat = Prototypic web inter...
SYSTEMS BIOLOGY
BIOINFORMATICS
ROSTOCK
S E Ssimulation experiment management system
That’s it! Stay tuned ;-)
@SemsProject...
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BiVeS & BudHat @ Combine2013 in Paris

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Talk by Martin Scharm at the COMBINE meeting September 2013 in Paris.
Find more information and download the slides at http://sems.uni-rostock.de/2013/09/sems-at-the-combine-2013/

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BiVeS & BudHat @ Combine2013 in Paris

  1. 1. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK S E Ssimulation experiment management system BiVeS & BudHat Difference Detection for Computational Models MARTIN SCHARM Department of Systems Biology & Bioinformatics Faculty of Computer Science & Electrical Engineering University of Rostock http://sems.uni-rostock.de COMBINE 2013 Sep 19, 2013 Bives & Budhat | Martin Scharm 1
  2. 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 Difference detection and provenance http://sems.uni-rostock.de/ Sep 19, 2013 Bives & Budhat | Martin Scharm 2
  3. 3. Provenance Provenance represents the seven W’s (Who, What, Where, Why, When, Which, (W)how). – Goble 2002 G ˇ ĽĽ ˇ ˇ ŤŤŤŤ ˇ ˇ šššš ˇ 2 ˇ ˇ ŁŁ ˇ Music and Arts BiVeS library. M.S. extended BiVeS and implemented the online application BudHat. Funding: This work has been funded by the German Federal Ministry of Education and Research (e:Bio program). Conflict of Interest: none declared. REFERENCES Beard,D.A. et al. (2009) CellML metadata standards, associated tools and reposi- tories. Philos. Transact. A Math. Phys. Eng. Sci., 367, 1845–1867. Chawathe,S. et al. (1996) Change detection in hierarchically structured information. ACM SIGMOD Rec, 25, 493–504. Cooper,J. et al. (2011) High-throughput functional curation of cellular electrophysi- ology models. Prog. Biophys. Mol. Biol, 107, 11–20. Cuellar,A. et al. (2006) The CellML metadata 1.0 specification. http://www.cellml. org/specifications/metadata/cellml_metadata_1.0 (30 January 2013, date last accessed). Cuellar,A.A. et al. (2003) An overview of CellML 1.1, a biological model descrip- tion language. Simulation, 79, 740–747. Finkelstein,A. et al. (2004) Computational challenges of systems biology. IEEE Comp., 37, 26–33. Gleeson,P. et al. (2010) NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Comput. Biol., 6. e1000815þ. Henkel,R. et al. (2010) Ranked retrieval of computational biology models. BMC Bioinformatics, 11. 423þ. Henkel,R. et al. (2012) Considerations of graph-based concepts to manage compu- tational biology models and associated simulations. In: Goltz,U. et al. (ed.) Workshop on data in the life sciences. ‘‘INFORMATIK 2012’’, Lecture Notes in Informatics 208, 1545–1551. Herrga˚ rd,M. et al. (2008) A consensus yeast metabolic network reconstruction ob- tained from a community approach to systems biology. Nat. Biotechnol., 26, 1155–1160. Hines,M.L. et al. (2004) ModelDB: a database to support computational neurosci- ence. J. Comput. Neurosci., 17, 7–11–11. Hirschberg,D. (1977) Algorithms for the longest common subsequence problem. J. ACM, 24, 664–675. Hoehndorf,R. et al. (2011) Integrating systems biology models and biomedical ontologies. BMC Syst. Biol., 5, 124. Hucka,M. et al. (2003) The systems biology markup language (sbml): a medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524–531. Hucka,M. et al. (2010) The Systems Biology Markup Language (SBML): Language specification for level 3 version 1 core. http://iweb.dl.sourceforge.net/project/ sbml/specifications/Level%203%20Ver.%201/sbml-level-3-version-1-core-rel-1. pdf (30 January 2013, date last accessed). Juty,N. et al. (2012) Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res., 40 (D1), D580–D586. Krause,F. et al. (2010) Annotation and merging of SBML models with semanticSBML. Bioinformatics, 2, 421. Lassila,O. et al. (1998) Resource description framework (RDF) model and syntax specification. W3C Recommendation. http://www.w3.org/TR/REC-rdf-syntax/ (30 January 2013, date last accessed). Le Nove` re et al. (2005) Minimum Information Requested In the Annotation of biochemical Models (MIRIAM). Nature Biotechnol., 23, 1509–1515. Le Nove` re,N. et al. (2009) The systems biology graphical notation. Nature Biotechnol., 27, 735–741. Li,C. et al. (2010) Biomodels database: an enhanced, curated and annotated re- source for published quantitative kinetic models. BMC Syst. Biol., 4, 92. Miller,A. et al. (2010) An overview of the cellml api and its implementation. BMC Bioinformatics, 11, 178. Miller,A. et al. (2011) Revision history aware repositories of computational models of biological systems. BMC Bioinformatics., 12, 22. Ro¨ nnau,S. et al. (2005) Towards xml version control of office documents. In: Proceedings of the 2005 ACM symposium on Document engineering. ACM, New York, NY, USA, pp. 10–19. Ro¨ nnau,S. et al. (2009) Efficient and reliable merging of xml documents. In: Proceedings of the 18th ACM conference on Information and knowledge manage- ment (CIKM 09). ACM, New York, NY, pp. 2105–2106. Rosado,A.L. et al. (2009) An XQuery-based version extension of an XML Native Database. In: Proceedings of the 2009 EDBT/ICDT Workshops. ACM, New York, NY, USA, pp. 99–106. Saffrey,P. and Owen,R. (2009) Version control of pathway models using xml patches. BMC Syst. Biol., 3, 34. Tyson,J.J. (1991) Modeling the cell division cycle: cdc2 and cyclin interactions. Proc. Natl Acad. Sci. USA, 88, 7328–7332. Waltemath,D. et al. (2011) Reproducible computational biology experiments with SED-ML—the simulation experiment description markup language. BMC Syst. Biol., 5, 198. Wittig,U. et al. (2006) Sabio-rk: integration and curation of reaction kinetics data. In: Data Integration in the Life Sciences. Springer, Berlin Heidelberg, pp. 94–103. Yu,T. et al. (2011) The physiome model repository 2. Bioinformatics, 27, 743–744. D.Waltemath et al. atUniversitaetsbibliothekRostockonJuly18,2013http://bioinformatics.oxfordjournals.org/Downloadedfrom Literature Code Sep 19, 2013 Bives & Budhat | Martin Scharm 3
  4. 4. Provenance Requirements X1 X2 Y1 Y2 Y3 Availability & Identity I O -vs- I M O Difference Detection I M O updated reaction introduced new modifier Interpretation Sep 19, 2013 Bives & Budhat | Martin Scharm 4
  5. 5. Provenance Requirements X1 X2 Y1 Y2 Y3 Availability & Identity I O -vs- I M O Difference Detection I M O updated reaction introduced new modifier Interpretation Sep 19, 2013 Bives & Budhat | Martin Scharm 4
  6. 6. Provenance Requirements X1 X2 Y1 Y2 Y3 Availability & Identity I O -vs- I M O Difference Detection I M O updated reaction introduced new modifier Interpretation Sep 19, 2013 Bives & Budhat | Martin Scharm 4
  7. 7. Provenance Requirements X1 X2 Y1 Y2 Y3 Availability & Identity I O -vs- I M O Difference Detection I M O updated reaction introduced new modifier Interpretation Sep 19, 2013 Bives Budhat | Martin Scharm 4
  8. 8. 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; Sep 19, 2013 Bives Budhat | Martin Scharm 5
  9. 9. 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 Sep 19, 2013 Bives Budhat | Martin Scharm 6
  10. 10. 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 Sep 19, 2013 Bives Budhat | Martin Scharm 7
  11. 11. BiVeS BudHat DEMO BudHat in action! http://budhat.sems.uni-rostock.de Sep 19, 2013 Bives Budhat | Martin Scharm 8
  12. 12. BiVeS Integration jvm network cmd import de.unirostock.sems.bives.api.SBMLDiff; [...] SBMLDiff differ = new SBMLDiff (sbmlFileA, sbmlFileB); differ.mapTrees (); String graph = differ.getCRNGraphML (); [...] Sep 19, 2013 Bives Budhat | Martin Scharm 9
  13. 13. BiVeS Integration jvm network cmd curl -d ’{ get: [ documentType, xmlDiff ], files: { versionA:http://your.db/path/to/versionA.sbml, versionB:http://your.db/path/to/versionA.sbml } }’ http://bives.server.tld Sep 19, 2013 Bives Budhat | Martin Scharm 9
  14. 14. BiVeS Integration jvm network cmd java -jar BiVeS.jar path/to/versionA path/to/versionB git diff 88fea1cddf b64477d742 model.file Sep 19, 2013 Bives Budhat | Martin Scharm 9
  15. 15. BiVeS BudHat Summary • BiVeS = Difference detection for hierarchically structured content • BudHat = Prototypic web interface to demonstrate how BiVeS can be used to communicate the differences Sep 19, 2013 Bives Budhat | Martin Scharm 10
  16. 16. 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 Sep 19, 2013 Bives Budhat | Martin Scharm 11

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