Characterising differences between model versions
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The document discusses characterizing differences between versions of computational models. It describes a system called BiVeS that identifies changes by mapping elements between two model versions hierarchically, then evaluating the mapping to find inserts, deletes, updates and moves. An ontology called COMODI is being built to classify model changes by type, target, reason, intention and more to help understand how and why models evolve.
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Characterising differences between model versions
- 1. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK S E Ssimulation experiment management system Characterising differences between model versions MARTIN SCHARM, DAGMAR WALTEMATH Department of Systems Biology & Bioinformatics, University of Rostock http://sems.uni-rostock.de e:Bio Status Seminar 2015 University of Duisburg-Essen September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 1
- 2. Model Evolution Example: Cell Cycle Romond1999 Goldbeter1991 Tyson1991 Novak1993 Marlovits1998 Novak1995Novak1997 Moriya2011 Calzone2007 Novak1998 Tyson2001 Chen2000 Chen2004 Queralt2006 Vinod2011 Novak2001 Sriram2007 Csikasz-Nagy2006 Hatzimanikatis1999 Swat2004 Qu2003 Ciliberto2003 mammalian R-point (G1/S-transition) Srividyha2006 Mitotic exit Budding Yeast Not in biomodels database minimal oscillator Novak1995 Gardner1998 Ibrahim2008a Ibrahim2008b Ibrahim2009 Mitosis Obeyesekere1997 Conradie2010 Obeyesekere1999 Bai2003 Aguda&Tang1999 Novak2004 Haberichter2007 (G-Phase) September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 2
- 3. Model Evolution Example: Cell Cycle Romond1999 Goldbeter1991 Tyson1991 Novak1993 Marlovits1998 Novak1995Novak1997 Moriya2011 Calzone2007 Novak1998 Tyson2001 Chen2000 Chen2004 Queralt2006 Vinod2011 Novak2001 Sriram2007 Csikasz-Nagy2006 Hatzimanikatis1999 Swat2004 Qu2003 Ciliberto2003 mammalian R-point (G1/S-transition) Srividyha2006 Mitotic exit Budding Yeast Not in biomodels database minimal oscillator Novak1995 Gardner1998 Ibrahim2008a Ibrahim2008b Ibrahim2009 Mitosis Obeyesekere1997 Conradie2010 Obeyesekere1999 Bai2003 Aguda&Tang1999 Novak2004 Haberichter2007 (G-Phase) September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 2
- 4. Model Evolution Example: Cell Cycle Cyclin Cdc2 P Cyclin Cdc2 P Modeling the cell division... John J Tyson, 1991 September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 3
- 5. Model Evolution Example: Cell Cycle Cyclin Cdc2 P Cyclin Cdc2 P Cdc25Cdc25∗ Wee1 Wee1∗ Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte Bela Novak and John J Tyson, 1993 Cyclin Cdc2 P Cyclin Cdc2 P Modeling the cell division... John J Tyson, 1991 September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 3
- 6. Model Evolution Example: Cell Cycle Cyclin Cdc2 P Cyclin Cdc2 P Cdc25Cdc25∗ Wee1 Wee1∗ Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte Bela Novak and John J Tyson, 1993 Cyclin Cdc2 P Cyclin Cdc2 P Cdc25Cdc25∗ Mik1 Mik1∗ Wee1 Wee1∗ Quantitative analysis of a molecular model of mitotic control in Fission yeast Bela Novak and John J Tyson, 1995 Cyclin Cdc2 P Cyclin Cdc2 P Modeling the cell division... John J Tyson, 1991 September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 3
- 7. Model Evolution Example: Cell Cycle Cyclin Cdc2 P Cyclin Cdc2 P Cdc25Cdc25∗ Wee1 Wee1∗ Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte Bela Novak and John J Tyson, 1993 Cyclin Cdc2 P Cyclin Cdc2 P Cdc25Cdc25∗ Mik1 Mik1∗ Wee1 Wee1∗ Quantitative analysis of a molecular model of mitotic control in Fission yeast Bela Novak and John J Tyson, 1995 Cyclin Cdc2 P Cyclin Cdc2 P Modeling the cell division... John J Tyson, 1991 Cyclin Cdc2 P Cyclin Cdc2 P Cdc25Cdc25∗ Mik1 Mik1∗ Wee1 Wee1∗ Cyclin Cdc2 P Rum1 Modeling the control of DNA replication in fission yeast Bela Novak and John J Tyson, 1997 September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 3
- 8. BiVeS identifies differences in versions of computational models 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 standadised formats (currently: and ) • maps hierarchically structured content • evaluates and communicates the differences <XML> Diff moves product of r: C deletes product of r: B inserts species: E product of r: E reaction s </XML> mapping diff construction September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 4
- 9. BiVeS identifies differences in versions of computational models A B C D E F G A B D H E F G model version 1 model version 2 list of species list of reactions C + D = E D + H = E take two versions of a computational model September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 5
- 10. BiVeS identifies differences in versions of computational models A B C D E F G A B D H E F G id=“species1” id=“species1” connect entities which are for sure the same September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 6
- 11. BiVeS identifies differences in versions of computational models A B C D E F G A B D H E F G propagate this initial mapping into the rest of the tree September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 7
- 12. BiVeS identifies differences in versions of computational models A B C D E F G A B D H E F G evaluate the mapping and identify inserts, deletes, updates, and moves September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 8
- 13. BiVeS identifies differences in versions of computational models C D H E communicate the differences to the user September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 9
- 14. BiVeS identifies differences in versions of computational models <?xml version="1.0" encoding="UTF-8" standalone="no"?> <bives type="fullDiff"> <update/> <delete> [...] <node id="6" oldChildNo="1" oldParent="../listOfModifiers[1]" oldPath="../listOfModifiers[1]/modifierSpeciesReference[1]" oldTag="modifierSpeciesReference" triggeredBy="5"/> <attribute id="7" name="species" oldPath="../modifierSpeciesReference[1]" oldValue="cdc2" triggeredBy="6"/> </delete> <insert> [...] <node id="12" newChildNo="2" newParent="../listOfReactants[1]" newPath="../listOfReactants[1]/speciesReference[2]" newTag="speciesReference"/> <attribute id="13" name="species" newPath="../speciesReference[2]" newValue="cdc2" triggeredBy="12"/> <attribute id="14" name="metaid" newPath="../speciesReference[2]" newValue=" 818337" triggeredBy="12"/> </insert> [...] </bives> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 Scharm et. al. BIOINFORMATICS 2015, accepted for publication September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 10
- 15. What do these changes look like? analysis of more than 150 diffs study of modifications derivation of a vocabulary A B C D E F G A B D H E F G Change affectedhadReason intended changeType appliedTo September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 11
- 16. What do these changes look like? insertion <species name=“Gulcose-6-Phosphate” initialConcentration=“0.6” /> Type: new node Affects: the reaction network Intention: probably an extension of the model September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 12
- 17. What do these changes look like? insertion <species name=“Gulcose-6-Phosphate” initialConcentration=“0.6” /> update <parameter name=“ka” value=“0.3” /> <parameter name=“ka” value=“0.1” /> Type: updated attribute Affects: the mathematical model Intention: correction Reason: mismatch with publication dcdc25 dt = ka×dimer_p×(total_cdc25−cdcs5p) Ka+total_cdc25−cdcs5p September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 12
- 18. What do these changes look like? insertion <species name=“Gulcose-6-Phosphate” initialConcentration=“0.6” /> update <parameter name=“ka” value=“0.3” /> <parameter name=“ka” value=“0.1” /> <species name=“Gulcose-6-Phosphate” initialConcentration=“0.6” /> <species name=“Glucose-6-Phosphate” initialConcentration=“0.6” /> Type: updated attribute Reason: typo September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 12
- 19. What do these changes look like? insertion <species name=“Gulcose-6-Phosphate” initialConcentration=“0.6” /> update <parameter name=“ka” value=“0.3” /> <parameter name=“ka” value=“0.1” /> <species name=“Gulcose-6-Phosphate” initialConcentration=“0.6” /> <species name=“Glucose-6-Phosphate” initialConcentration=“0.6” /> deletion <reaction id=“r23”> ... </reaction> Type: deletion of node and attributes Affects: reaction network and mathematical model Intention: simplification September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 12
- 20. COMODI Characterising model differences We’re building an ontology, because COmputational MOdels DIffer. Change Target affected Reason hadReason Intention intended Type changeType Entity appliedTo September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 13
- 21. COMODI Characterising model differences Entity Node ModelId EntityIdentifier Attribute ModelName EntityName Text September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 14
- 22. What do these changes look like? is_a comodi:Change comodi:changeType comodi:Insertion comodi:affected comodi:ReactionNetwork comodi:intended comodi:Extension Masymos September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 15
- 23. Summary Questions we’d like to help answering • How did my collaborator change our model? • Did someone update the model that I retrieved from the database? • Weird behaviour since the last update..!? Show me all versions that changed the kinetics of reaction r23. • Who changed reaction r23? When and why did they do that!? September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 16
- 24. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK S E Ssimulation experiment management system Thank you for your attention! SEMS group Dagmar Waltemath Martin Scharm Martin Peters Mariam Nassar Fabienne Lambusch Olaf Wolkenhauer @SemsProject http://sems.uni-rostock.de September, 2015 COMODI | Martin Scharm, Dagmar Waltemath 17