Conversion of mEPN Pathway Diagrams to SBGN in BioLayout Express3D (COMBINE 2013)
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Presentation given at COMBINE 2013, Institut Curie, Paris on 20th September 2013. Details the development of the mEPN pathway notation, Petri Net simulations, mapping mEPN to the SBGN community standard and a new function in BioLayout Express3D which exports mEPN to SBGN-ML. http://www.biolayout.org http://macrophages.com http://www.mepn-pathway.org
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Conversion of mEPN Pathway Diagrams to SBGN in BioLayout Express3D (COMBINE 2013)
- 1. Conversion of mEPN pathway diagrams to SBGN in BioLayout Express3D Derek Wright, Tim Angus, Athanasios Theocharidis, Tom C. Freeman The Roslin Institute, R(D)SVS, University of Edinburgh, UK
- 2. Process Modelling of Biological Pathways Aim To construct models of the current consensus view of pathways of interest, useful to biologists for data interpretation and hypothesis generation Progress to date • Initial and on-going interest in modelling macrophage activation pathways • Interest in mapping other pathways/systems • Work has involved the training and use of successive cohorts of BSc/MSc students for literature mining and pathway depiction • When this work started no standard notation system available, so we developed our own (mEPN) which has evolved through meeting challenges met during the modelling process • Pathway mapping project now in its 8th year
- 3. Freeman et al., BMC Systems Biology 4:65, 2010 http://www.mepn-pathway.org/
- 5. mEPN
- 6. Analysis and visualisation of rule-based stochastic flow through models of biological pathways 1. Pathway models drawn in yEd graph editor as bipartate graphs, parameterized and saved as .graphml files. (Also possible to convert SBML to GraphML with Cytoscape/BiNoM/SPNConverter.) 2. Models imported into BioLayout and SPN algorithm used to calculate time-dependent flow through network. 3. The results of flow simulations can be visualised as graphs (mouse-over function) or viewed as real- time animations where the size and colour of nodes is used to represent their activity/amount.
- 7. Signalling Petri Net Simulation
- 8. Conversion of mEPN diagrams to SBGN Why? • To provide a bridge to the current standard How? • Map mEPN – SBGN types • Creates glyphs from nodes • Create arcs from edges • Preserve geometry + apply scaling • Create compartments • Serialize to SBGN-ML using LibSBGN Java library Exactly How? • Source code available at www.biolayout.org
- 10. SBGN mEPN
- 11. TCA cycle in yEd (mEPN)TCA cycle in BioLayout Express3D (mEPN3D) TCA cycle In VANTED (SBGN)
- 13. BioLayout Express3D Team Roslin Institute Tom Freeman Thanasis Theocharidis Ben Boyer Tim Angus Derek Wright EMBL-EBI Anton Enright Stijn van Dongen www.biolayout.org support@biolayout.org
Notas do Editor
- I’m Derek Wright, a Software Engineer in Tom Freeman’s group at The Roslin Institute. I’m going to talk about our pathway modeling work and an exporter that we have developed in our network visualization software BioLayout Express3D that converts our pathway diagrams to the SBGN community standard.
- We provide views of the network in both 2D and 3D in BioLayout. We already had developed 3D rendering in BioLayout for large network graphs such as co-expression networks and we wanted to leverage this.We created 3D equivalents of the mEPN glyphs.Although we started with a 2D graph in yED the 3D view provides the user with the choice of a different type of interaction e.g. zooming, tilting, rotating.This example shows a large signaling network in yEd in 2D and imported into BioLayout and displayed in 3D with a view over the plane of the network.
- “And here’s one that I prepared earlier.”This is the large macrophage activation pathway from one of the previous slides. We export the network from BioLayout to SBGN-ML and then visualize it using VANTED.As you can see from the result, the conversion process scales up well and the layout is preserved, even with with large networks.
- Here I would like to show you diagrams of the TCA cycle, in order to illustrate the conversion process and to allow you to compare the models in detail.Firstly the mEPN model is constructed in yEd then exported as GraphML.This is imported into BioLayout where it may be used to run a Petri Net simulation, then exported as SBGN-ML.And finally, imported into VANTED, where the system may be visualized as SBGN.As you can see, we have succeeded in preserving a high degree of consistency in layout and details between the different views.