Practices for drawing biological networks using the SBGN standard
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1 Research seminar Practices for drawing biological networks using the SBGN standard Vasundra Touré 25 th July 2016, Rostock Contact: [email protected]
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Transcript of Practices for drawing biological networks using the SBGN standard
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Research seminar
Practices for drawing biological networks using
the SBGN standard
Vasundra Touré25th July 2016, Rostock
Contact: [email protected]
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Systems Biology: understand dynamics and interactions between components in a biological system.
Networks
Motivation
DataAnalysis
3Calzone et. al. (2007) Dynamical modeling of syncytial mitotic cycles in Drosophila embryos, Mol Syst Biol.
How would you interpret this?
Scharm et Touré (2016), model in github
Combine Archive Show Case,example model
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Inform and advise you.
Objectives
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● set of symbols
Community effort to standardize graphical notation for biological maps.
● layout syntax● semantics
Symbol of the monthrelaunched!
Templates
source
sink
Le Novère et al (2009) The Systems Biology Graphical Notation, Nat Biotechnol.
The Systems Biology Graphical Notation
SBGN covers:
6Source: http://en.wikipedia.org/wiki/Systems_Biology_Graphical_Notation
Process DescriptionBiochemistry
Activity FlowMolecular biology
Entity RelationshipPhysiology, Genetics
Example maps
SBGN languages
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SBGN-MLSBGN
Human readable and machine readable format
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SBGN-ED is a VANTED add-on with a variety of features:
Translation SBML → SBGN
TutorialsDownload/Installation
Czauderna et al. (2010) Editing, validating and translating of SBGN maps. Bioinformatics
Import/export SBGN and SBGN-ML
Creation - edition - validation of SBGN maps
Exploration of maps
Tool support: SBGN-ED
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Creation of an SBGN map with SBGN-ED.
Demo
10Calzone et. al. Dynamical modeling of syncytial mitotic cycles in Drosophila embryos, Mol Syst Biol. 2007; 3: 131.
Let’s go back to the previous model example...
11Calzone et. al. Dynamical modeling of syncytial mitotic cycles in Drosophila embryos, Mol Syst Biol. 2007; 3: 131.
… in an SBGN-compliant format
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Use the SBGN standard to visualize your networks
A good map is a lot of work:● Design, ● Layout,● Etc.
If help needed:● Check the web-pages and tutorials● Or… Come to see me!
Conclusion
Some useful links:● SBGN web-pages old - new● SBGN-ED software - SBGN-ED+ project
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Questions?
Thank you for your attention!
