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Standardized visualisation of differences between model versions
- 1. 1 Standardized visualization of differences between model versions Tom Gebhardt, Martin Scharm, Vasundra Touré, Dagmar Waltemath, Olaf Wolkenhauer Department of Systems Biology and Bioinformatics, University of Rostock COMBINE 2016 Newcastle upon Tyne 23rd of September 2016 m n the computational modeling in biology network
- 2. 2 Motivation: models are evolving Biological models are constantly evolving implying that several versions of a model can exist. Scharm et al. (2015) An algorithm to detect and communicate the differences in computational models describing biological systems - Bioinformatics. Figure courtesy: Tom Gebhart
- 3. 3 Motivation: models are evolving Biological models are constantly evolving implying that several versions of a model can exist. Statistics based on two repositories of computational models: Physiome and Biomodels. Number of models: 3237 Number of model versions: 14439 Number of deltas: 10662 Scharm et al. (2015) An algorithm to detect and communicate the differences in computational models describing biological systems - Bioinformatics. http://most.sems.uni-rostock.de/ 1 3 7 20 55 148 403 1097 2981 8103 22026 59874 162755 Changes Figure courtesy: Tom Gebhart
- 4. 4 Motivation: visualizing models Plus, it is common to have a visual representation of biological networks… Systems Biology Tools for Integrated Omics Analysis - M. Hugues H. Kim (2015), Nature Chemical Biology Brown et al. (1999), Trends in Microbiology
- 5. 5 Motivation: visualizing models Plus, it is common to have a visual representation of biological networks… … but understanding them depends on the reader’s knowledge … Ras recruits Raf Ras translocates Raf Ras activates Raf Systems Biology Tools for Integrated Omics Analysis - M. Hugues H. Kim (2015), Nature Chemical Biology Brown et al. (1999), Trends in Microbiology Ras Raf
- 6. 6 The Systems Biology Graphical Notation … unless the Systems Biology Graphical Notation is used. SBGN webpage: http://sbgn.github.io/sbgn/ standardized glyphs and arcs and semantics specific to each. sinksource SBGN webpage: http://sbgn.github.io/sbgn/
- 7. 7 The Systems Biology Graphical Notation … unless the Systems Biology Graphical Notation is used. SBGN webpage: http://sbgn.github.io/sbgn/ standardized glyphs and arcs and semantics specific to each. sinksource Process Description Biochemistry Activity Flow Molecular biology Entity Relationship Physiology, Genetics Three languages are defined. SBGN webpage: http://sbgn.github.io/sbgn/
- 8. 8 The Systems Biology Graphical Notation … unless the Systems Biology Graphical Notation is used. SBGN webpage: http://sbgn.github.io/sbgn/ standardized glyphs and arcs and semantics specific to each. sinksource Process Description Biochemistry Activity Flow Molecular biology Entity Relationship Physiology, Genetics Three languages are defined. SBGN webpage: http://sbgn.github.io/sbgn/
- 9. 9 Objective: standardize diffs visualization Highlighting of the differences between two model versions using SBGN. RAF ERK MEK MEK 2P ERK MEK P ERK P RAF P ERK 2P ADPATP ATP ADP ATP ATP ADP ADP Version 1 MEK 2P RAF P ERK P RAS active ERKERK 2P ERK RAS MEK P RAF ADP ADP ATP ATP ATP ADPATP ADP Version 2
- 10. 10 Objective: standardize diffs visualization Highlighting of the differences between two model versions using SBGN. MEK 2P RAS ERK RAF P RAF RAS active ERK 2P ERK MEK P ERK P MEK ATP ATP ATP ADP ADP ADP ADP ATPADP ATP RAF ERK MEK MEK 2P ERK MEK P ERK P RAF P ERK 2P ADPATP ATP ADP ATP ATP ADP ADP Version 1 MEK 2P RAF P ERK P RAS active ERKERK 2P ERK RAS MEK P RAF ADP ADP ATP ATP ATP ADPATP ADP Version 2 Transition version
- 11. 11 What are the steps? Scharm et al. (2015) An algorithm to detect and communicate the differences in computational models describing biological systems - Bioinformatics. 1) Generate a tool to compare differences between two versions The description of a model’s evolution is performed by the BiVeS library. Biochemical Model Version Control System http://bives.sems.uni-rostock.de C D H E communicationpb A B C D E F G A B D H E F G evaluationpb A B C D E F G A B D H E F G propagationpb A B C D E F G A B D H E F G id=“species1” id=“species1” initialmappingpb 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 pre-processingpbpre-processingcommunicationevaluationpropagationinitialmapping
- 12. 12 What are the steps? Scharm et al. (2015) An algorithm to detect and communicate the differences in computational models describing biological systems - Bioinformatics. 1) Generate a tool to compare differences between two versions 2) Generate a visual of the differences Differences are colour coded: http://budhat.sems.uni-rostock.de U. Liebal - “Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis” (Mol. BioSyst) Model Versions: laczsynth-2012-11-10 and laczsynth-2012-11-11
- 13. 13 What are the steps? 1) Generate a tool to compare differences between two versions 2) Generate a visual of the differences 3) Make the visual SBGN-compliant Differences VisuaLization https://github.com/Gebbi8/DiVil U. Liebal - “Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis” (Mol. BioSyst) Model Versions: laczsynth-2012-11-10 and laczsynth-2012-11-11
- 14. 14 Preliminary workflow BiVeS BioModels CellML highlighted network SBGN-ML PNG JPEG SVG m odels v ersions v ersion transition d ifferences visualization library compute d ifferences s pecies B s pecies A 1 2 3 4 5 89 10 11 12 highlighted reaction network 6 report of changes diff encoded in XML SBGN PD compliant JSON DOT language Graph-ML JSON 7
- 15. 15 Preliminary workflow BiVeS BioModels CellML highlighted network SBGN-ML PNG JPEG SVG m odels v ersions v ersion transition d ifferences visualization library compute d ifferences s pecies B s pecies A 1 2 3 4 5 89 10 11 12 highlighted reaction network 6 report of changes diff encoded in XML SBGN PD compliant JSON DOT language Graph-ML JSON 7
- 16. 16 Preliminary workflow BiVeS BioModels CellML highlighted network SBGN-ML PNG JPEG SVG m odels v ersions v ersion transition d ifferences visualization library compute d ifferences s pecies B s pecies A 1 2 3 4 5 89 10 11 12 highlighted reaction network 6 report of changes diff encoded in XML SBGN PD compliant JSON DOT language Graph-ML JSON 7
- 17. 17 Preliminary workflow BiVeS BioModels CellML highlighted network SBGN-ML PNG JPEG SVG m odels v ersions v ersion transition d ifferences visualization library compute d ifferences s pecies B s pecies A 1 2 3 4 5 89 10 11 12 highlighted reaction network 6 report of changes diff encoded in XML SBGN PD compliant JSON DOT language Graph-ML JSON 7
- 18. 18 Preliminary workflow BiVeS BioModels CellML highlighted network SBGN-ML PNG JPEG SVG m odels v ersions v ersion transition d ifferences visualization library compute d ifferences s pecies B s pecies A 1 2 3 4 5 89 10 11 12 highlighted reaction network 6 report of changes diff encoded in XML SBGN PD compliant JSON DOT language Graph-ML JSON 7
- 19. 19 Preliminary workflow BiVeS BioModels CellML highlighted network SBGN-ML PNG JPEG SVG m odels v ersions v ersion transition d ifferences visualization library compute d ifferences s pecies B s pecies A 1 2 3 4 5 89 10 11 12 highlighted reaction network 6 report of changes diff encoded in XML SBGN PD compliant JSON DOT language Graph-ML JSON 7
- 20. 20 Importance of SBO terms without SBO terms with SBO terms cell u z cell u EmptySet z
- 21. 21 Importance of SBO terms without SBO terms with SBO terms cell u z cell u EmptySet z Annotate your models !
- 22. 22 Importance of SBO terms without SBO terms with SBO terms cell u z cell u EmptySet z SBGN workshop: still time to join us! Annotate your models !
- 23. 23 Conclusion Necessary improvements: ● The SBGN output ● Colour information ● User interface Opportunity for a student internship in Rostock (2-4 months project) More information: www.sems.uni-rostock.de Prototype: SBGN map showing differences between model versions ● Extension of BiVeS library → information for generating SBGN map ● Automatic force-based layout ● Generation of an SBGN-ML file and graphical exports
- 24. 24 Thank you for your attention! Contact: vasundra.toure@uni-rostock.de Martin Scharm BiVeS and Budhat Tom Gebhardt DiViL The SEMS team Funded by