Improving the management of computational models.

1. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK S E Ssimulation experiment management system Improving the Management of Computational Models storage – retrieval & ranking – version control MARTIN SCHARM 1,2 , RON HENKEL 1 , DAGMAR WALTEMATH 1 , OLAF WOLKENHAUER 1,3 1 Department of Systems Biology & Bioinformatics, University of Rostock 2 Department of Computer Science, University of Oxford 3 Stellenbosch Institute for Advanced Study, South Africa http://sems.uni-rostock.de European Bioinformatics Institute UK 2013 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 1

2. Introduction time #models 2013-06-18 462+501+x·103 216+196 2009-06-16 31 2005-04-11 • Number of models is steadily increasing • Models tend to get more complex • Continuous development Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 2

3. Introduction reactions model ~27.06 curated ~288.91 noncurated 2013 • Number of models is steadily increasing • Models tend to get more complex • Continuous development Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 2

4. Introduction time #Versions • Number of models is steadily increasing • Models tend to get more complex • Continuous development Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 2

5. Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 3

6. Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 3

7. Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control ? Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 3

8. Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control version x-1 version x version x+1 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 3

9. Introduction Solutions Several projects develop methods to support the community Model Repository Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 4

10. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK S E Ssimulation experiment management system track development store retrieve rank Retrieval Ranking Δ Δ Version 1 Version 2 latest Version Control Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Docu ment SEDM L Model refere nce Outpu t Datag enera tor Simul ation Task Varia ble Varia ble Doc ume nt Tyso n_19 91 C2 CP time envi ron men t isDescribedBy Pubm ed: 183127 0 time timeCPC2 CP C2 Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Doc ume nt Tyso n_19 91 C2 CP time envi ron men t isDescribedBy Pubm ed: 183127 0 time timeCPC2 CP C2 Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Doc ume nt Tyso n_19 91 C2 CP time envi ron men t isDescribedBy Pubm ed: 183127 0 time timeCPC2 CP C2 Graph Database Docu ment SEDM L Model refere nce Outpu t Simul ation Task Docu ment SEDM L Model refere nce Outpu t Datag enera tor Simul ation Task Varia ble Varia ble Docu ment SEDM L Model refere nce Outpu t Datag enera tor Simul ation Task http://sems.uni-rostock.de/ Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 5

11. Storage GraphDB Taken from: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.174.8830&rep=rep1&type=pdf Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 6

12. Storage Available Data Model & Simulation Annotation & Ontologies A model’s network • Constituent names • XML encoded representation • Biochemical background • Synonyms • Model structure • Aggregation values • Model related data Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 7

13. Storage GraphDB Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Tyson 1991 - SBML Model Entities Annotations ﬁg. courtesy R. Henkel Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 8

14. Storage GraphDB Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Tyson 1991 - CellML Model Component Variable ﬁg. courtesy R. Henkel Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 9

15. Storage GraphDB Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable Tyson 1991 - SED-ML Simulation Entity Variable ﬁg. courtesy R. Henkel Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 10

16. Storage GraphDB SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Systems Biology Ontology Root 1. Level All Ontologies available in OWL can be added easily ﬁg. courtesy R. Henkel Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 11

17. Storage GraphDB Models Model related data Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12

18. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12

19. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12

20. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12

21. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12

22. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12

23. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Henkel et al. 2013, Graph-based storage of computational biology models and associated simulations, in preparation Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12

24. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Index Model Id Name Component Variable Species Reaction Compartment Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12

25. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Index Model Publication Title Journal Abstract Authors Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12

26. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Index Model Publication Person First name Last name Organization Email Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12

27. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Index Model Publication Person Annotation URI Description Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12

28. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Index Model Publication Person Annotation Simulation Id Name Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12

29. retrieval & ranking Example Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Show me models by Tyson describing the cell cycle and have cdc2! Person Annotation Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13

35. retrieval & ranking Example Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Thank you! Person Annotation 1. (0.859) Tyson1991 - Cell Cycle 6 var 2. (0.854) Tyson2001_Cell_Cycle_Regulation 3. (0.477) Chen2004 - Cell Cycle Regulation Henkel et al. 2010: Ranked retrieval of Computational Biology models Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13

36. Version Control version x-1 version x version x+1 what happened ? track versions Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 14

37. Version Control version x-1 version x version x+1 track versions what happened ? Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 14

38. Model Evolution Example: Cell Cycle Cyclin Cdc2 P Cyclin Cdc2 P Modeling the cell division... John J Tyson, 1991 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 15

39. 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 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 15

40. 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 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 15

41. 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 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 15

42. 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; Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 16

43. 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 mapping Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 17

44. 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 diff construction Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 18

45. 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 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 19

46. Applications Communicating Changes Novak & Tyson ’93: Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos Biomodels Database BIOMD0000000107: Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 20

47. Applications Communicating Changes Fixed the model → How to communicate the changes? Unix diff? 1c1 < <?xml version=’1.0’ encoding=’UTF-8’ standalone=’no’?> --- > <?xml version="1.0" encoding="UTF-8" standalone="no"?> 287 lines... Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 21

48. Applications Communicating Changes Fixed the model → How to communicate the changes? BiVeS Diff? <?xml version="1.0" encoding="UTF-8" standalone="no"?> <bives type="fullDiff"> <update/> <delete> <node id="1" oldChildNo="1" oldParent="/listOfReactions[1]/reaction[ <attribute id="2" name="rdf:resource" oldPath="/listOfReactions[1]/r <node id="5" oldChildNo="4" oldParent="/listOfReactions[1]/reaction[ <node id="6" oldChildNo="1" oldParent="/listOfReactions[1]/reaction[ <attribute id="7" name="species" oldPath="/listOfReactions[1]/reacti </delete> <insert> <attribute id="3" name="metaid" newPath="/listOfReactions[1]/reactio <attribute id="4" name="metaid" newPath="/listOfReactions[1]/reactio <attribute id="9" name="metaid" newPath="/listOfReactions[1]/reactio <node id="10" newChildNo="1" newParent="/listOfReactions[1]/reaction much smarter, but still 24 lines.. Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 21

49. Applications Communicating Changes Fixed the model → How to communicate the changes? BiVeS Diff: Highlighted chemical reaction network Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 21

50. Applications Communicating Changes Fixed the model → How to communicate the changes? BiVeS Diff: Report Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 21

51. Applications BiomodelsDatabase / PMR2 Biomodels Database CellML Model Repository 963 # Models 1589 10193 # Versions 12878 9148 # prod. Diffs 12936 BiVeS Unix’ Diff BiVeS Unix’ Diff 2233 1890 # empty Diffs 10113 10043 434.825 1977.210 ∅ #ops 349.5282 480.249 6915 non-empty diffs following 2823 non-empty diffs Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 22

54. Applications BiomodelsDB / PMR2 Biomodels Database q qqq q qq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqq q qqqqqqqqq qq qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq qqqqqqqqqqqq qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qq q qq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q q q qqqqqqqqqqqqq q qqqqqq q qqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqq q q q qqqqqqq q q q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqq q qq q qqqqqqq q qqqqqqqqqq q qqqqqqqqqqqqqqqq q qqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqq q qqqqqq q qqqqqq q qqqqq q qqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q q q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q q q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqq q qq qq q qqqq 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qqqq q qqqqqqqqqq q qq q qqqqq q qqqqqqqqqq q qqq q qqqqqqq qq qqqqqqq q q q q q q qqqqqqqqqqq q q qq q q qqqqqqqqq q q q qq q q qqq q qqqqqqqqqq q qqqqq q qqq q qq qqqq qq qq q q q qqqqqqq q qq q qqq q qq q qqqq q q q q q q q q q qqqqq qq qq q qq q q q q q q q q q qq qqqqq q qqqqq q qq q qqq qq q q qqqqqqqqqqqqqqqqqqq qq q qq q q q q qqqqq q qq qq qq qqqqqqqq q qqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqq q qqqq q qq q q q qqqq q q qq q q qq q q q q q q q q q qq q q qqq q qqq q q q qq q q qqq q qq q q q q qq q q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqq qq qq q q q qqqqq q q q qqqq q q q q qqq q qqqqqqqqqqqqqq qqqqq q qqq q q q qqqq qq qqqqqqqqqq q q qq q q qqq q qqq q q q q q q qq qq q q qq q q qqqqqq q q qqqq q qqqqqqqqqq q qqq q qqq q qq qqqqqqqqqqq qqq q q qqqqq q q qqqqqq q q qq qqq qqq q qqqqqq q qq qq q q q qqqqqq q qq q qqqq q qqq q qq q qq qqqqqqqqq q qqqqq q qqqq q q qqq q qqq q qqqqqqq q qqqqqqqq q qqqqq q qqqqqqqqqqqqqqqqqqqqqq q qqqqqqq q q q qqqqqqq qqq q qqqqq q qqqq q q qqq q q q q qqqqq q q qqq q q qq q q q q q q q qqq 0 5000 10000 15000 20000 25000 0500010000150002000025000 #operations needed by BiVeS #operationsneededbyUnix'diff #operations Unix' diff == #operations BiVeS Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 23

55. Applications BiomodelsDB / PMR2 qq q q qq qq q qq qq qqqq qq q qq qq q qqqq qq qq qqq qqqqq q qq qq qq q qq qq qqq qq q qqq q qqq qq qqq q qq qq q qq qqqqq qq q q qq q qqq qqq qqqqqq qqq qq qq q qq qqqq q q qq qq qq q q qq qqq qq qq qq q q qq q q qq qq qq q q qqqq qqq q qqqq q qqqq q q qq qq qq qqq qqqq qq qq qq qqq qqq qq q q qq qqqq qqq q qqqq qqqqq qqq qqqq q q qqqqq q q qqqq q qq qqqqq q qqq qqq qq q qq q qqqq qqq qqqq qqqq q q qq qqq q q q qqqqqq qq q qqq q qqqqqqq qqqq qqq qqq q q q qqq qqq qq qqq qq qq qq qq qq q qqq qq qqqq q q qqq qq qq qq qqq q qqq qq qq qqqq qqq q qq qqq q qqq qq qqqq qq qq q qqq qq qq qqqqqq qqqqqq q qqqq q qq q qqq qqq q qqq qq qqqqqqq qqqqqq qq qqq q qqqqq qq qqqq q qqq qqq q qqqqqq q q q qq qqq q qqq qqqq q q q qqq qqq qqq qqq qqq q q qqq qqqqqq qq qqqq q qqq q qq qq qq qqq qqqq qqq qqq qqq q q qqq qqqq q qq q qq q qq qq qqqq qq qq q qqq qqqq q qqq qqq q qq q q qqq qq qqq q q qq qqq qqq qqqq qqqqq qq qqqqqq q qqqqqq q q qq q qq qq qq qq qq qqqqqq qq q qqqq qqq qqq q qqqq qqqqqqqq qq q qqq qqq qq qq qqqqqq q q qq qqqqqq qq qqqqq qq q qqqqq qq qq qqqq qqq qqqqq q qq qq qq qq qq qqqq qqq qq qqqq qqq q qqq qq qqqqq qqqq q qq qq qqqqqqq q qqq qqq qq q qqqqqq qqq qqq qq qqqq qq qqq q qqqqq q qq qqq qqq qqq qqq q qqqqqqqq qqq q q q qqq q q q qqq qqqq q qqq qqq qqqq qq q qqq qq q qq q qq qq q qqq qq q q qq qq qq qqqq q qq qq q qqqq qqqqq qq qq qqq qq qq q qqqq qq qqq qqqqqqqq q qqq q qq q qqqq qq qq qqq qq q qq qqq q qq qq qqq qq qqqqq qqq qq qqq qq qqqqqq qqqq q qq qqqq qq qqq q qqq q qq q q qqqq q qqqqq qqq qq qq qq q qq qqq qqq qq qq q qqqqq qqqqq qq qqqqq q qqq qqq q q qqqqqq qqq qq qqq q qq q qq qq q qqqqq q qq q qqq qqq q qq qq qq q qq q qq qq qqqqq qq qq qqqq qqqq qq qq q qqq qqq qq qq qqq qqqq qqq qq q qq qqq qq qqq q qq qqq q q qq q qqq qq qqq qq qq qq q q qqqqqq qqqq qqqqq qqq qqq q qqqqqq qqq qq qq qqq qq qqq qqq qq qq qq qqq q qqqq q qqqq q qqqqq qq qq qqq qq qqqq qqq q qqq qqq qq qqqqq qqq q qqqqq qq qqq qqq qqqq qqqq qq qqq q qqq qq q q qqqq qqqq qqq q qq qq qqq qq qqq qqqq qq qq qqq qqq qqqqq qq qqq q qq qq qq qqqq qqqq q qq qq qqq q q qqq qq qq q qqq qqqqqq qqq qqqq qq q qqq qqq q qqq qqqq qqqq qqqq q qq qqqq q qqq qqqqq qqq qq qqqqq qq qq q qqq q qqq qq qq q qq qq qq qq qq q qqqq q qq qqq q q qqqq qq qqqqq qq qqqq qqq q q qq qqq q q qqqq qq qqqqq qqq q qqq q q qqqq qq qqqq q qq qq qqq qqq q qq qq qqq qqqqqqqqq q qqq qq qq qq qqq qqqqq qq qq qq qq qqq q q qq qq q qq qqqq qqq qq qq qq qqq q qqq qqqqqq qq qqqq qqq q q qqqqq qqqq qqq qqq q qq qqqq q qq qq qq qq qq qq qqqq q qqqq qqqq qqq qq qqqq qq qqq qqq qq q qq qqqqq qqq qqqq qqq q q q qq qq qqqqq q qqq qqq qqq qqq qqqqq q qq qqq q qqqqq qqqqqq qqq qqq qqqqq q qqq qq qqq qqq qqq qqq qq qqq qqqq qq qqqqq q qq q q qqq q qqq qq q qq q qq qqqq qq qq qqqq qqqqq qq q qqq qqqq q qqq q qqqqq qq qq qq qqqqq q qq qq qqqq qqq qq qq q q qqqqq q q q qq qqq qqq q qq qq q qq qq qqqq q qq qqqq qq qqqq q q q qqq qqq qq qq qqqq q qq qqq qq qq qq qqqqqq q qqq q qq qq q qq q qqq q qq qqq qq q qq qqq q qqqq q q qqq q q qqq qqq qqqq qqqq qqq q qq qqq qq qqq qqq qq qqqqqqq qqq qqqq qq qqq qq qqq q qqq qq qqqq q qq q qqq qq qqq qq qq qqqqq qqq q qq q q qqq qq qq q q qq qq q q qqq qqqq qq q qqqq qq qqq qq q qq qq qq q qqq qqq qq qq qqqq q qqq qqqqq qqqq qqq qq qq qqq q qq qq q qq qqq q qqq qqqqq q q qq qqq q qqq qq qq q qqqqq qq qqq qqq qqqq qqqqq q qq qqqq qqqq q q qqqq q qq qqq qq q q q qq q qqqq q qqq q q updatesinserts 1 5 10 50 100 500 1000 qqq q qqq q qq q qqqqq qq q qq qq qqq qq qqq q qq qq qq qqq q q qqqqqqqqqq qq qqq q q qqqqq q qqq qqq qq q q qqq qqqqqq qq qqqq qqqqqqq qqq qq qq qqq qqqq qq qqq qqq q qqq qq qqqq q q qq qqq q qqqqqq qq qqqq qqq q qq qq qq q qqq q qqq qqq qq qqq qqq qq qq qq qq qq q qqqqq qqqqq q qqq qqqq qq qqqqq qq q qq qq qqq qq qqqq qqq qqq qqqq q qq qq qqq q q qq qq qq q qq qq q qq qqq q qq q qqq q qq qqq qq qq qqq qq qqq q q qq qq qq qq qq qq qqq qqq qqq qqq qqq qqq qq q q qq q qqqq qq qq q qq q qq qq qq q qqqq qqq q qq qqq qq qq qq qqqqq qq q qq qq qqq qq qq qqq q qqqq qqqq q q q qq qq q qqqq q qqq qq qqq qqq qqq qqqqqqqq qqqq qqqqq qqq qq qqq qqq qqq qq qqq qqqq qqqqq q qqq qqqq qqqqq qqqqq q qqq qqq qqq qq qq q qq qq qq qqqq qq qq qqq qq qqqq qq qqqq q qqq q q qq qq qq qqqq qqq q qq qq q q qq q qqqqq qq q q qq qqq qqq qq q qq q qqq q qqq qqqq qqq qqqq qq q qq qq qq qqqqq qq qq qq q qq qq q qqq qqqqqq qqq q qqqqq q qqq qqq qqqq qqq qq qqqqq q qqq qq qqqq qqqqqqqq qq qq q q qqqqq q qqqq qq q q qqq qqq qq qqq qqq q qq qqq qqq qqq qqqqqq qq q qqqqq q qq qq qqq qqqqq q qqqq qqqq qq qqq qqqq qqq q qq qqq qqq qqqq q q qqqq qq q qq q qqq q q qqq qq qqq qqq qq qq qqqqqq qq qq qqq qqqqqqqqqq qqq qqqqq qqq qqqqqqq qqq qqq qq qqq qqqqqq q updatesinserts 1 5 10 50 100 500 1000 Biomodels Database CellML Model Repository move insert delete update move insert delete update Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 24

56. Applications BiomodelsDB / PMR2 qqq qqq q q qqq qq q qq q qq qqqq q qq qq qq qq qq q qq qqq qq qq q qq q qq qq qqqqqqqq q qqq qqq qq qqq q q qqq q qq qq qq qq q qqq qq qqq qq qqq q qqq q qqqqq qq qq qqq qq qq q qq qq qq qqqq qq q qqqq qqq q qqq qq qq qqq qq q qqq qq qqq qqq qq qq qq q qq q qqq q qqqq qqq qq q q q qqq qq qq q qqq qqqq qq qq qqq q qq qq qq qqq qqq qq qqq qq q qqq qqq qq q q qqq q qq q q qqqqq q qq qqq q qq q qq qq qqq q qq q q qq qq qq qqq qqq qq q qqq qq qq q qq q qq qq q q qqq q qq q qq qqqq q qqqqqq qqq qq qq qq q q qq qqq qqq qq qqq qqq q q qqqq qq qq q qq qqq qqqq q qq qqqqq q qqq qq qqq qqq qq q qqqqqqqq q qq qq qq q qq qqq qqq qq qqq q qq qq qqq q q qq q qqqq qqq qq qqq qqq qq q qqq q qq qqq qq qqqq qq qq qq qqq q qq q qqq qq qq qq q qq qqq q qqq qq q q q qqqqqq qqqqqq q qq qq qq qq q qq qqq qq qq qqq qqqqqq q q qqqq qqq q q qqq q qqq qqq qqq qq q q q qqq qq qq qqq qqqq q qqqq qq qq q qq qq qq qqqq qq q qq qqqq q q qqq q qqq qq qq q qqq qqq qqq q qq qqq qq q qq qqqq q qq qqqq qqq qq qq q qqq qq qqq q q qq qq q qq qqq q qq qqq qq qqqq qqqq qq q qq qq qqqq q qq q q qqq q qqqq q qq qq q qqq q qq q q qq qqq qq qq q qq q qq qq qqq qqq qq q q qq qqq qqqqq q qq q q q qq qqq qq qqq q qqq qq qq qqqq qq qqq qq qq q qqqq qq q q q qq q qqq qq qq qqq q q qq q qqq qq q q qq qqq qq q qqq qqqqq qqqqqq qqq qq q qqq qqq qq q qq qq qqq q q qq qq q qqqqq qqq qqq q qqq qq qqqq q qq q q qq q qq qq q qq qq qqq qq q qq qqqq q qq qq qq q qq q q qqq qq q qq qqqq qq qqq qq qq qqqq qqq qqq qq q qqq qq q qqqq qq q q q qq q qqqq qq q q qqq qq qq qqqq q qq qqq qq qqqqq q q qqq q qq qq qqq qq q qq qq qqq qq qqq q qq qqq qqq q qq q qqqqq q qqq qq q qq qq qq q qq q qq qqq qq q qqqqq qq q qq qqqq qqq q qqq q q q q qq q qq qqqq q qq qqq qqqqq qq qqqq qq qq q qqq q qqq qq q q qq qq qqq qqq qqq qq qqq qqq q qqqq q qq qqq qq qq q qq q qq qqqq q q qq qqq qqq q qq q q qqq q q qqq qq q qq qq qq qq q q q qqq qqq qqq qqq qq q qq qqq qqq qqq qq q q qq qq qq q qqq qqq qq qq qq qq q qq qqq q qq qqqq qq q qq qq qq qq qq qqqq qqq qq q q qqq q qqq qq qqq q q qqqq qq qq qq qq qq q qqq qqq q qqq q qqq q qq qq q qq qq qq qqq q qqq qqqq qqqq qq qq qqq qqq qqq qqq q qqq q qq q qqqq q qq q q qq qq qq qq qq qq q qqq qqqq qq qq q qqq q q q qqq q qqq q q qq q qq qqq qqq q qqq qq qq attrnodetext 1 5 10 50 100 500 1000 q qq qq q q qq q qq q q q qqqqq qq qq q q qqq qqq q qq qq qqq q qq qqq qq qq qq qqqqq qqqqq q q qq qqqq q qq qqqq q q qqq q qqqq qq q q qqq qq qq qqq qqq qqq qqqq qq qqqqqq q q qqq qqq q qq qq qq qqq q qqq qq qqqq qqq q qqqqq qqq q q qqq qq qqq qqq qqqqq q q qq q qqq qqq qqq qq q qqq qq qqq q qq qq qqq qqqqq qqq qqq q qqq qq qqq q qqqqq q q qqq q qq qq q qqqqqq q qqqq qq qqqqqqqq qqqqqq qq qqq qqqqqqq q qqqq qqqq q qqq qq qqqqqqq qq qq q qqq qq qqqq qqqqq q qqqq qqq qq qq qq qqqq qq qqqq qqqq qq q q qqqqqq qqq qqqqqq qq qqqqqq q q qqqq q qq q qq qq qq q qqq qq qqqq qq qqq q q qq qq qq q qqq q q qqqqqq qq qqqq q qqq qqqq qqq qq qq qqqq qq qq qqq q qqqq qqq qqq qqq q qq qqq q qq qqq qq qqq qqq q qq qqqqqq qq qqq q qqq qq qqqqq qq qq qq qqq qqq qq qq qq qqq qq qqqq qqq q qq qqq qq qqqq qq qqq qqq q q q qqq qqqq q qqqq qq q qq qqqq qq q q qqqq qqq qq q qq qqq qq qqq q qq q qq qq q qq q qqq qq q qq q qq qq q q qq qqq q qqq qqq qqq q qq q q qqq qq q q q qqqq qq q qqqq qq qqqqq qq attrnodetext 1 5 10 50 100 500 1000 Biomodels Database CellML Model Repository Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 25

57. Summary • SEMS develops methods for improved model management • Storage • Retrieval & Ranking • Version Control • ... and implements these methods in tools that are • modularly designed • open source • easy to integrate Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 26

58. Future • Support for further standards • PharmML • CombineArchive • SBGN • respect further ontologies in storage/search • Improved version control • mapping w/ respect to biological meaning • scoring schemes for differences • ﬁlter for changes • Improved availability and analyzability of data Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 27

59. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK S E Ssimulation experiment management system Thank you for your attention! SEMS group Dagmar Waltemath Ron Henkel Martin Peters Markus Wolﬁen Rebekka Alm Olaf Wolkenhauer @SemsProject http://sems.uni-rostock.de Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 28

60. BiVeS Integration jvm network cmd import de.unirostock.sems.bives.api.SBMLDiff; [...] SBMLDiff differ = new SBMLDiff (sbmlFileA, sbmlFileB); differ.mapTrees (); String graph = differ.getCRNGraphML (); [...] Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 29

61. 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 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 29

62. BiVeS Integration jvm network cmd java -jar BiVeS.jar path/to/versionA path/to/versionB git diff 88fea1cddf b64477d742 model.file Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 29

63. BiVeS -vs- Unix’ Diff Artifacts delete a single line in an XML: <variable name="T" units="kelvin" initial_value="295" public_interface="out"/> for Unix’ diff it is 1 operation. Bives detects 5 operations (delete node variable and 4 attributes). Worse if multiple nodes on the same line: <para><emphasis><ulink url="caffeine.zip">Caffeine</ulink></emphasis> - Caffeine-induced Ca2+ transients from 18 i And worst if whole document only 1 line → max. 2 operations for the Unix diff tool. Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 30

64. CombineArchive Single ﬁle containing models and model related data: • simulation experiment descriptions in SED-ML • graphical representations in SBGN-ML necessary for the description of a model and all associated data and procedures → simpliﬁes exchange Proposal by Nicolas Le Novère, Frank Bergmann, and Richard Adams http://co.mbine.org/documents/archive We developed a JAVA library to create/read/manipulate CombineArchives http://sems.uni-rostock.de/projects/combinearchive/ → database import/export, difference detection between whole archives Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 31

65. BiVeS Mapping • input: 2 XML documents • map unambiguos nodes/subtrees • propagate mapping up/down • exploit further knowledge of biological systems same ID same subtree hash ... ... ...... ... ... ... ...... ... Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 32

66. BiVeS Mapping • input: 2 XML documents • map unambiguos nodes/subtrees • propagate mapping up/down • exploit further knowledge of biological systems eq. netw.... ... ...... ... ... ... ...... ... Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 32

67. BiVeS Mapping • input: 2 XML documents • map unambiguos nodes/subtrees • propagate mapping up/down • exploit further knowledge of biological systems A B C D E A B C D E A B C D E Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 32

68. Applications Investigating BiomodelsDB / PMR2 qqqq qq q q q qqq qq q q qqq qq qq qqq qqqq q q q qq qq qqq q qq qq qqq qq qq qq qq qqqq qqq q qqq qq qqq q qqqq qq qqq qq qqq qqqq qq qq qqq qqq qqqq qq qq qq qqq q qqqq qqqqq qq qqqq qqq q q qq q qqqq qqq q qqqqq q qqq qqqq qqqqq qq qq qqq qqq qqq q q qq qqq qqq qqq q qqqqq qqq qq qq qq qq q qqqq qqqq qqq qq q qqq qqqq qqq qq qqqq q qqqqq qq q qq qq qqqqq q qq qqq qqq qqqq q qqq qqq q qqq qq q qq qq qq qqq q qq qqqq q qq qq qqqq qqqq qqq qq qqq qqqq q q qq qqq q qq q qqqqq qq q q qq qq qq qq qq q qqq qq q qqq q qqqq qq qq qqq q qqq qq qq qqq qqqq qqq qqqq q qqqqq qqq qq qqq q qq qqqq qq qq qq qqq qq q q qq q qq q q qqq qq qqq qqq qqq qq qq qq qqqq qq q q q qq q qq qqq q qqq q qqqq qqqqq qqqq qqq qqqqq qq qq q qqq q qqqq q qq qq qq qq qqq q qqqqq q qqq qq q qq q qq qqqqq q qq qq qq qq qqq q qqqq qqq q q qqqqq qqqq qqq q qq q qqq qq qqqq qqqq q q q qqqq qqqq q qq qqq q q qqq q qq qq qq q qq qq q qq qqq qq qq qqq qq qqqq qq q bivesunix 0 500 1000 1500 qq qq q qq q qq qq q qqqq qqq q qqq q qq q qqqq qqq q qqq qq q qqq qqq qq q qqqq qqqq q q qq qqqq q q qq qqq q qqqq qq q qq qq qqq q qq qq q qqq qq qq qq qq q q qqqq qqq qq qq qq qqq qq qq qqqq q qq q q qqq q qq qqq qqq qqqq qq q qq q qqqqqq qqqqq qq qq qqq q q qq qqqqqq qq qqq qq qqqqqqqq qq qq q qq q q qqq qq qqqq q qq qqq q q qq qq qq qqq qq qqqq bivesunix 0 500 1000 1500 Biomodels Database CellML Model Repository Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 33

69. Applications Investigating BiomodelsDB / PMR2 q q qqqq q qqqq qq q qqq qqqq q q qqq qqq qq qq qqq qq q qqq q qqqq qq qqq qqqq qq qqqqq qqq qq q q qqq q q qqq qqq qq qq q qqq q qq qq qqq qqq qq qqq qqq qq qq q qq qqq q qq qqq q qq qq q qqq q qqq q qq qq qq qqq qq qq qq q qqqqq q qqqqq qq qq qqq q qqq qq q qqqqq qq q qqqqq qqq qqq qq qq q q qqq qqqq q q qqq qq qqq q qq qq q q qq qq q qq qq qqq q q qqqq q qq qq qq qq qq qq q qq qq q qqqq qqq q bivesunix 0 500 1000 1500 2000 2500 3000 3500 q qqqq qqqqq q qqq qq qqqq qqq qqq qq q qqq qq qqq q qq q qqqq qq q qq qqq q qqq qqq qqq q q qqq qq qq qq qq qq qq qqqq qq qqq qq qq qqq q qq qqq q qqqq qq qqq qq qq qq q qqq qq qqq q qqq q qqqqq q qq qqq q qq qq qq qqqqq q qq q q q q qq qqqq q qq q bivesunix 0 500 1000 1500 2000 2500 3000 3500 Biomodels Database CellML Model Repository Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 34

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