Improving the Management of Computational Models -- Invited talk at the EBI
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Improving the Management of Computational Models: storage – retrieval & ranking – version control More information and slides to download at http://sems.uni-rostock.de/2013/12/martin-visits-the-ebi/
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- 1. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK SE S simulation
experiment management system Improving the Management of
Computational Models storage retrieval & ranking version
control M AR TIN S CHARM1,2 , R ON H ENKEL1 , DAGMAR WALTEMATH1 , O
LAF W OLKENHAUER1,3 1 2 3 Department of Systems Biology &
Bioinformatics, University of Rostock Department of Computer
Science, University of Oxford 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. 31 462 + 501 + x 103 216 + 196 #models Introduction
2013-06-18 Number of models is steadily increasing Models tend to
get more complex Continuous development 2009-06-16 2005-04-11 time
Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath,
Olaf Wolkenhauer 2
- 3. Introduction ~288.91 ~27.06 reactions model 2013 noncurated
Number of models is steadily increasing Models tend to get more
complex Continuous development curated Dec 4, 2013 SEMS | Martin
Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 2
- 4. Introduction #Versions Number of models is steadily
increasing Models tend to get more complex Continuous development
time 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 x-1 version x version x+1 Version Control Dec 4,
2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf
Wolkenhauer 3
- 9. Introduction Solutions Several projects develop methods to
support the community Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel,
Dagmar Waltemath, Olaf Wolkenhauer Model Repository 4
- 10. SE S SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK simulation
experiment management system Retrieval is CP isVersion Pubm ed:
183127 0 envi ron men t Model refere nce Simul ation CP T ask Outpu
t store Datag enera tor V aria ble Inte rpro : IPR 006 670 GO:0
0056 23 CP time time time CP V aria ble C2 Do cu me T ys nt on 19
91 Cel l Cy cle 6 var C2 CP 19 91 Cel l Cy cle 6 var Unipr ot:P0
4551 Unipr ot:P0 4551 is Pub med: Kegg 1831 Path 270 way sce04 111
Cel l ECCode: 3.1.3. 16 Unipr ot:P0 4551 Unipr ot:P0 4551 hasPart
isVersion pM GO:0 0056 23 Inte rpro : IPR 006 670 Inte rpro : IPR
006 670 GO:0 0056 23 Doc ume nt isDescrib edBy is pM Pub med: Kegg
1831 Path 270 way sce04 111 T yso n_19 91 Cel l Inte rpro : IPR 006
670 isDescribedBy envi ron men t C2 ECCode: 3.1.3. 16 isDescrib
edBy CP is C2 is Re act ion 3 Cel l isVersion Of isVersion Unipr
ot:P0 4551 Do cu me T ys nt on Pub med: Kegg 1831 Path 270 way
sce04 111 pM hasPart isVersion Of Unipr ot:P0 4551 isVersion Of C2
ECCode: 3.1.3. 16 Re act ion 3 is isVersion Of isDescribedBy Cel l
pM Unipr ot:P0 4551 hasPart isVersion Of Unipr ot:P0 4551 retrieve
SEDM L T yso n_19 91 C2 ECCode: 3.1.3. 16 isVersion Of Doc ume nt
Pub med: Kegg 1831 Path 270 way sce04 111 is hasPart C2 Docu ment
isDescrib edBy isVersion Re act ion 3 19 91 Cel l Cy cle 6 var
isDescrib edBy CP isVersion Of Do cu me T ys nt on 19 91 Cel l Cy
cle 6 var C2 isVersion Of Do cu me T ys nt on Re act ion 3 Pubm ed:
183127 0 CP is Graph Database C2 GO:0 0056 23 CP time time time CP
C2 rank Do cu me T ys nt on T ask Outpu t Unipr ot:P0 4551 Unipr
ot:P0 4551 Do cu me T ys nt on 19 91 Cel l Cy cle 6 var Docu ment
Model refere nce SEDM L Re act ion 3 T ask Inte rpro : IPR 006 670
GO:0 0056 23 Outpu t isVersion Unipr ot:P0 4551 Unipr ot:P0 4551
Pub med: Kegg 1831 Path 270 way sce04 111 isDescrib edBy is Cel l
pM Datag enera tor is isVersion Of T ask hasPart isVersion Of
ECCode: 3.1.3. 16 Simul ation Simul ation CP Cel l pM Outpu t Docu
ment SEDM L Model refere nce C2 is is ECCode: 3.1.3. 16 Datag enera
tor Pub med: Kegg 1831 Path 270 way sce04 111 isDescrib edBy CP
isVersion Simul ation C2 isVersion Of track development SEDM L
Model refere nce 19 91 Cel l Cy cle 6 var Re act ion 3 hasPart Docu
ment isVersion Of Version 2 Inte rpro : IPR 006 670 GO:0 0056 23
Doc ume nt V aria ble latest V aria ble T yso n_19 91 C2 Version
Control CP isDescribedBy envi ron men t C2 Version 1 time time Pubm
ed: 183127 0 CP time CP C2 Ranking 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 Dec 4, 2013
Constituent names XML encoded representation Annotation &
Ontologies Biochemical background Synonyms SEMS | Martin Scharm,
Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer A models network
Model structure Aggregation values Model related data 7
- 13. Storage GraphDB Tyson 1991 - SBML Document Model Tyson1991
Cell Cycle 6 var isDescribedBy Entities Reaction3 C2 is CP Pubmed:
1831270 Kegg Pathway sce04111 pM Cell asProduct Annotations
EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 Interpro: IPR006670
is hasPart isContainedIn isVersion isVersionOf isVersionOf
asReactant GO:0005623 g. courtesy R. Henkel Dec 4, 2013 SEMS |
Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer
8
- 14. Storage GraphDB Tyson 1991 - CellML Document Model Model
Component Variable sodium channel m v is_connected time envmt
has_annotation is_connected time time Pubmed: 12991237 sodium
channel m gate v m is_mapped_to g. courtesy R. Henkel Dec 4, 2013
SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf
Wolkenhauer 9
- 15. Storage GraphDB Tyson 1991 - SED-ML Document Simulation
Entity SEDML Modelrefere nce Simulation Task Output Datagenera tor
Variable Variable Variable g. courtesy R. Henkel Dec 4, 2013 SEMS |
Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer
10
- 16. Storage GraphDB Systems Biology Ontology SBO: Ontology Root
SBO:0000 isA 1. Level SBO:064 SBO:544 SBO:004 SBO:231 SBO:003
SBO:236 SBO:545 All Ontologies available in OWL can be added easily
g. courtesy R. Henkel Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel,
Dagmar Waltemath, Olaf Wolkenhauer 11
- 17. Storage GraphDB Models Dec 4, 2013 Model related data SEMS
| Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer
12
- 18. Storage GraphDB Models Model related data Document
isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed:
1831270 Kegg Pathway sce04111 is pM Cell asProduct EC-Code:
3.1.3.16 Dec 4, 2013 Uniprot:P04551 Uniprot:P04551 Interpro:
IPR006670 is hasPart isContainedIn isVersion isVersionOf
isVersionOf asReactant GO:0005623 SEMS | Martin Scharm, Ron Henkel,
Dagmar Waltemath, Olaf Wolkenhauer 12
- 19. Storage GraphDB Models Model related data Document
isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed:
1831270 Kegg Pathway sce04111 is pM Cell asProduct asReactant
Uniprot:P04551 Uniprot:P04551 is hasPart isVersion isVersionOf
isVersionOf EC-Code: 3.1.3.16 isContainedIn Interpro: IPR006670
GO:0005623 Document Model sodium channel m v is_connected time
envmt time has_annotation is_connected time Pubmed: 12991237 sodium
channel m gate v m is_mapped_to Dec 4, 2013 SEMS | Martin Scharm,
Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
- 20. Storage GraphDB Models Model related data Document Document
isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed:
1831270 SEDML Kegg Pathway sce04111 is pM Cell Modelrefere nce
Simulation Task Output Datagenera tor asProduct asReactant
isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 is
hasPart isVersionOf isVersionOf isVersion Variable Interpro:
IPR006670 GO:0005623 Variable Document Model sodium channel m v
is_connected time envmt time has_annotation is_connected time
Pubmed: 12991237 sodium channel m gate v m is_mapped_to Dec 4, 2013
SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf
Wolkenhauer 12
- 21. Storage GraphDB Models Model related data Document Document
isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed:
1831270 SEDML Kegg Pathway sce04111 is pM Cell Modelrefere nce
Simulation Task Datagenera tor Output asProduct asReactant
isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 is
hasPart isVersionOf isVersionOf isVersion Variable Interpro:
IPR006670 Variable GO:0005623 Document Model has_annotation SBO:
Ontology Pubmed: 12991237 SBO:0000 sodium channel is_connected
envmt is_connected sodium channel m gate isA SBO:064 m v time time
time v SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m
is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar
Waltemath, Olaf Wolkenhauer 12
- 22. Storage GraphDB Models Model related data Document Document
isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed:
1831270 SEDML Kegg Pathway sce04111 is pM Cell Modelrefere nce
Simulation Task Datagenera tor Output asProduct asReactant
isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 is
hasPart isVersionOf isVersionOf isVersion Variable Interpro:
IPR006670 Variable GO:0005623 Document Model has_annotation SBO:
Ontology Pubmed: 12991237 SBO:0000 sodium channel is_connected
envmt is_connected sodium channel m gate isA SBO:064 m v time time
time v SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m
is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar
Waltemath, Olaf Wolkenhauer 12
- 23. Storage GraphDB Models Model related data Document Document
isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed:
1831270 SEDML Kegg Pathway sce04111 is pM Modelrefere nce Cell
Simulation Task Datagenera tor Output asProduct asReactant
isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 is
hasPart isVersionOf isVersionOf isVersion Variable Interpro:
IPR006670 Variable GO:0005623 Document Model has_annotation SBO:
Ontology Pubmed: 12991237 SBO:0000 sodium channel is_connected
envmt is_connected sodium channel m gate isA SBO:064 m v time time
time v SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m
is_mapped_to 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 Index Model related data Document
Document Model isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3
C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Cell
asProduct asReactant Uniprot:P04551 Uniprot:P04551 is hasPart
isVersion isVersionOf isVersionOf EC-Code: 3.1.3.16 isContainedIn
Interpro: IPR006670 GO:0005623 Document Model has_annotation Id
Name Component Variable Species Reaction Compartment Modelrefere
nce Simulation Task Datagenera tor Output Variable Variable SBO:
Ontology Pubmed: 12991237 SBO:0000 sodium channel is_connected
envmt is_connected sodium channel m gate isA SBO:064 m v time time
time v SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m
is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar
Waltemath, Olaf Wolkenhauer 12
- 25. Storage GraphDB Models Index Model related data Document
Document Model isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3
C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Cell
Publication Modelrefere nce Simulation Task Datagenera tor Output
asProduct asReactant isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551
Uniprot:P04551 is hasPart isVersionOf isVersionOf isVersion
Variable Interpro: IPR006670 GO:0005623 Document Model
has_annotation Title Journal Abstract Authors Variable SBO:
Ontology Pubmed: 12991237 SBO:0000 sodium channel is_connected
envmt is_connected sodium channel m gate isA SBO:064 m v time time
time v SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m
is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar
Waltemath, Olaf Wolkenhauer 12
- 26. Storage GraphDB Models Index Model related data Document
Document Model isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3
C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Cell
Publication Modelrefere nce Simulation Task Datagenera tor Output
asProduct asReactant isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551
Uniprot:P04551 is hasPart isVersionOf isVersionOf isVersion
Variable Interpro: IPR006670 Person Variable GO:0005623 Document
Model sodium channel is_connected envmt has_annotation is_connected
First name Last name Organization Email Pubmed: 12991237 sodium
channel m gate SBO: Ontology SBO:0000 isA SBO:064 m v time time
time v SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m
is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar
Waltemath, Olaf Wolkenhauer 12
- 27. Storage GraphDB Models Index Model related data Document
Document Model isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3
C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Cell
Publication Modelrefere nce Simulation Task Datagenera tor Output
asProduct asReactant isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551
Uniprot:P04551 is hasPart isVersionOf isVersionOf isVersion
Variable Interpro: IPR006670 Person Variable GO:0005623 Document
Annotation Model has_annotation SBO: Ontology Pubmed: 12991237
SBO:0000 sodium channel is_connected envmt is_connected sodium
channel m gate URI Description isA SBO:064 m v time time time v
SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m is_mapped_to Dec
4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf
Wolkenhauer 12
- 28. Storage GraphDB Models Index Model related data Document
Document Model isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3
C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Cell
Publication Modelrefere nce Simulation Task Datagenera tor Output
asProduct asReactant isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551
Uniprot:P04551 is hasPart isVersionOf isVersionOf isVersion
Variable Interpro: IPR006670 Person Variable GO:0005623 Document
Annotation Model sodium channel is_connected envmt has_annotation
is_connected SBO: Ontology Pubmed: 12991237 SBO:0000 Simulation
sodium channel m gate isA SBO:064 m v time time is_mapped_to Dec 4,
2013 time v m SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 Id
Name SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf
Wolkenhauer 12
- 29. retrieval & ranking Example Show me models by Tyson
describing the cell cycle and have cdc2! Document isDescribedBy
Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg
Pathway sce04111 is pM Cell asProduct asReactant isContainedIn is
hasPart isVersionOf isVersionOf EC-Code: 3.1.3.16 isVersion Person
Annotation Uniprot:P04551 Dec 4, 2013 Uniprot:P04551 Interpro:
IPR006670 GO:0005623 SEMS | Martin Scharm, Ron Henkel, Dagmar
Waltemath, Olaf Wolkenhauer 13
- 30. retrieval & ranking Example Show me models by Tyson
describing the cell cycle and have cdc2! Document isDescribedBy
Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg
Pathway sce04111 is pM Cell asProduct asReactant isContainedIn is
hasPart isVersionOf isVersionOf EC-Code: 3.1.3.16 isVersion Person
Annotation Uniprot:P04551 Dec 4, 2013 Uniprot:P04551 Interpro:
IPR006670 GO:0005623 SEMS | Martin Scharm, Ron Henkel, Dagmar
Waltemath, Olaf Wolkenhauer 13
- 31. retrieval & ranking Example Show me models by Tyson
describing the cell cycle and have cdc2! Document isDescribedBy
Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg
Pathway sce04111 is pM Cell asProduct asReactant isContainedIn is
hasPart isVersionOf isVersionOf EC-Code: 3.1.3.16 isVersion Person
Annotation Uniprot:P04551 Dec 4, 2013 Uniprot:P04551 Interpro:
IPR006670 GO:0005623 SEMS | Martin Scharm, Ron Henkel, Dagmar
Waltemath, Olaf Wolkenhauer 13
- 32. retrieval & ranking Example Show me models by Tyson
describing the cell cycle and have cdc2! Document isDescribedBy
Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg
Pathway sce04111 is pM Cell asProduct asReactant isContainedIn is
hasPart isVersionOf isVersionOf EC-Code: 3.1.3.16 isVersion Person
Annotation Uniprot:P04551 Dec 4, 2013 Uniprot:P04551 Interpro:
IPR006670 GO:0005623 SEMS | Martin Scharm, Ron Henkel, Dagmar
Waltemath, Olaf Wolkenhauer 13
- 33. retrieval & ranking Example Show me models by Tyson
describing the cell cycle and have cdc2! Document isDescribedBy
Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg
Pathway sce04111 is pM Cell asProduct asReactant isContainedIn is
hasPart isVersionOf isVersionOf EC-Code: 3.1.3.16 isVersion Person
Annotation Uniprot:P04551 Dec 4, 2013 Uniprot:P04551 Interpro:
IPR006670 GO:0005623 SEMS | Martin Scharm, Ron Henkel, Dagmar
Waltemath, Olaf Wolkenhauer 13
- 34. retrieval & ranking Example Show me models by Tyson
describing the cell cycle and have cdc2! Document isDescribedBy
Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg
Pathway sce04111 is pM Cell asProduct asReactant isContainedIn is
hasPart isVersionOf isVersionOf EC-Code: 3.1.3.16 isVersion Person
Annotation Uniprot:P04551 Dec 4, 2013 Uniprot:P04551 Interpro:
IPR006670 GO:0005623 SEMS | Martin Scharm, Ron Henkel, Dagmar
Waltemath, Olaf Wolkenhauer 13
- 35. retrieval & ranking Example Document Thank you!
isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed:
1831270 Kegg Pathway sce04111 is pM Cell asProduct asReactant
Person is hasPart isVersion 1. (0.859) Tyson1991 - Cell Cycle 6 var
2. (0.854) Tyson2001_Cell_Cycle_Regulation 3. (0.477) Chen2004 -
Cell Cycle Regulation isVersionOf isVersionOf EC-Code: 3.1.3.16
isContainedIn Annotation Uniprot:P04551 Uniprot:P04551 Interpro:
IPR006670 GO:0005623 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 track versions version x-1 version x
version x+1 what happened ? Dec 4, 2013 SEMS | Martin Scharm, Ron
Henkel, Dagmar Waltemath, Olaf Wolkenhauer 14
- 37. Version Control track versions version x-1 version x
version x+1 what happened ? Dec 4, 2013 SEMS | Martin Scharm, Ron
Henkel, Dagmar Waltemath, Olaf Wolkenhauer 14
- 38. Model Evolution Example: Cell Cycle Modeling the cell
division... Cyclin Cdc2 P Cyclin Cdc2 P John J Tyson, 1991 Dec 4,
2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf
Wolkenhauer 15
- 39. Model Evolution Example: Cell Cycle Modeling the cell
division... Cyclin Cdc2 P Numerical analysis of a comprehensive
model of M-phase control in Xenopus oocyte Cyclin Cyclin Cdc2 Cdc2
P P John J Tyson, 1991 Cdc25 Wee1 Cdc25 Wee1 Cyclin Cdc2 P Bela
Novak and John J Tyson, 1993 Dec 4, 2013 SEMS | Martin Scharm, Ron
Henkel, Dagmar Waltemath, Olaf Wolkenhauer 15
- 40. Model Evolution Example: Cell Cycle Modeling the cell
division... Quantitative analysis of a molecular model of mitotic
control in Fission yeast Cyclin Cdc2 Cyclin P Cdc2 P Mik1 Cdc25
Wee1 Cyclin Cdc2 Cdc2 P John J Tyson, 1991 Cdc25 Wee1 Cdc25
Numerical analysis of a comprehensive model of M-phase control in
Xenopus oocyte Cyclin Mik1 Cyclin P Cdc2 P Bela Novak and John J
Tyson, 1995 Wee1 Cdc25 Wee1 Cyclin Cdc2 P Bela Novak and John J
Tyson, 1993 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar
Waltemath, Olaf Wolkenhauer 15
- 41. Model Evolution Example: Cell Cycle Modeling the cell
division... Quantitative analysis of a molecular model of mitotic
control in Fission yeast Cyclin Cdc2 Cyclin Modeling the control of
DNA replication in ssion yeast P Cdc2 P Mik1 Cyclin Mik1 Cdc25 Cdc2
Cdc25 Numerical analysis of a comprehensive model of M-phase
control in Xenopus oocyte Cyclin Cdc2 Cdc25 Cyclin Cdc2 P John J
Tyson, 1991 Cdc25 Wee1 Cdc2 Mik1 Wee1 Cyclin Cdc2 Wee1 Cyclin Cdc2
Wee1 Wee1 P Bela Novak and John J Tyson, 1995 Wee1 Mik1 Cdc25
Cyclin P Cdc25 P P Cyclin P Cdc2 P Rum1 Bela Novak and John J
Tyson, 1993 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 RB/E2F free E2F RB/E2F r A C
RB-Phos r E s C B cycE/cdk2 D new insights RB-Hypo D cycE/cdk2 free
E2F B RB-Hypo 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 free E2F RB/E2F r A C RB/E2F
RB-Phos r A E s C B cycE/cdk2 D D RB-Hypo free E2F cycE/cdk2 B
RB-Hypo Biochemical Model Version Control System mapping A compares
models encoded in standadized formats (currently: and ) maps
hierarchically structured content A D D r r C C E B s B Dec 4, 2013
SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf
Wolkenhauer 17
- 44. BiVeS Difference Detection free E2F RB/E2F r A C RB/E2F
Biochemical Model Version Control System RB-Phos r A E s compares
models encoded in standadized and ) formats (currently: maps
hierarchically structured content C B cycE/cdk2 D D RB-Hypo free
E2F cycE/cdk2 RB-Hypo mapping A B constructs a diff (in XML format)
is able to interprete this diff A D D r r diff construction C C E B
s B Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath,
Olaf Wolkenhauer Di moves product of r: C deletes product of r: B
inserts species: E product of r: E reaction s 18
- 45. BudHat Diff Visualization r A RB/E2F free E2F RB/E2F A C
RB-Phos r E s C B cycE/cdk2 D D RB-Hypo A free E2F B cycE/cdk2 D r
r C C 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 D RB-Hypo E B s E B s Di
moves product of r: C deletes product of r: B inserts species: E
product of r: E reaction s A Dec 4, 2013 SEMS | Martin Scharm, Ron
Henkel, Dagmar Waltemath, Olaf Wolkenhauer r B C D 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 < --> 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?
- 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: 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: Caffeine - 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 le 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 simplies exchange
Proposal by Nicolas Le Novre, 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 A input: 2 XML documents map unambiguos
nodes/subtrees propagate mapping up/down exploit further knowledge
of biological systems B A C D C E D A SEMS | Martin Scharm, Ron
Henkel, Dagmar Waltemath, Olaf Wolkenhauer E B C D Dec 4, 2013 B E
32
- 68. Applications Investigating BiomodelsDB / PMR2 unix
Biomodels Database bives qqqqqq qqqq qqqqqqqq qqq qq qqq qqq qq qq
qq qq q q q q q qq qqqqqqqqqqqqqqqqqqqqqqqqq qqq qq qq q q qqqq qqq
qqq q q qq q qq qq qq qq q q qqqqqqqqqqqqqqqqqqqq qqqqq q q qq qq
qq qqq q qqq qq q q q q q qq qqqq qqqqqqqqqqqqqq qq qq q qq q q q
qq q q q q qq qqq q q qqqqqqqqqqq qq qq qqq qq q q qq q qq q q qq q
qqqq q q qq q 0 500 1000 q q qq qq qq q q qq q q qq q qq q q q q
1500 unix CellML Model Repository bives qq q qqqq qqqqqq qq q q q
qq qq qq qq q q q q q q qq q q qqq qqq qqqq q q q qqq qq qq qq q q
q q qq q q q q qq q qq qqqq q qqqqq q qq qqqq q q q q q q qq qq qqq
q qq qqq q q qq q qqqq q q qqqq q qq q q qqq q q qq q q q qqq q q q
q q qq qq q q q q qq q qq q 0 Dec 4, 2013 500 SEMS | Martin Scharm,
Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 1000 1500 33
- 69. Applications Investigating BiomodelsDB / PMR2 unix
Biomodels Database bives qqqq qq qqqqqq q q qq q q q q qqq q qq q q
q qq qqqqqq qq qqq qq qqqqqqq q q q q qq qq qqqqqqqqqqq qq q q qqq
qqqq q q qq q q q qqq qqq qq qq q qqq q q q q q q qq q q q q q q q
q qq q q q q q 0 500 1000 1500 q qqq qq qq q q qq q qqq q q q q qq
q q q qq q q q q q q 2000 qq 2500 q qq q q qq 3000 q q q 3500 unix
CellML Model Repository bives qq q qqq qq q qq q qq q q q qq q q q
qqq qqq q q q qq q q q qq q q q q q q q q q qq qqqqqqq q qq qqqqqqq
qqq q q q q q q q q qqqqqq q q q qq qq q q q q q q q q q qq q 0 Dec
4, 2013 500 1000 1500 2000 SEMS | Martin Scharm, Ron Henkel, Dagmar
Waltemath, Olaf Wolkenhauer q qq q qq qq q q q 2500 qq q q q 3000
qq q q q qq q q qq q q qq q qq q qq q q q q q 3500 34