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Research seminar

Practices for drawing biological networks using

the SBGN standard

Vasundra Touré25th July 2016, Rostock

Contact: vasundra.toure@uni-rostock.de

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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!