SBGN Workshop/Hackathon 2016

Summary

The Systems Biology Graphical Notation, SBGN, is a standard format to represent biological networks visually. SBGN diagrams contain agreed-upon glyphs. Once you know these glyphs, it is easy to read and exchange meaningful diagrams encoding biological information. The SBGN workshop aims to introduce scientists to the SBGN. The first part features introductory talks to the SBGN family of standards, and to software tools that offer SBGN support. The second part is dedicated to hands-on sessions that allow you to try out SBGN software. You will learn how to create SBGN-compliant diagrams. We will also have a competition for the best SBGN map!

Tutors

Björn Sommer, University of Konstanz, Germany
Falk Schreiber, University of Konstanz, Germany
Vasundra Touré, University of Rostock, Germany
Dagmar Waltemath, University of Rostock, Germany

Target audience

Experimentalists and modellers with basic experience in modelling and simulation. No previous knowledge about the used standards and tools is required.

Schedule

time slot	Topic
08:30 - 09:00	Welcome & coffee
09:00 - 09:20	Introductory talk: Visualisation (B. Sommer)
09:20 - 10:00	Introduction to SBOL Visual (R. Sidney Cox)
10:00 - 10:40	Introduction to SBGN PD (V.Touré)
10:40 - 11:10	break
11:10 - 11:50	Introduction to SBGN-ED (V. Touré)
11:50 - 12:30	Introduction to hands-on (D. Waltemath)
12:30 - 14:00	lunch
14:00 - 17:00	Hacking/Hands-on (all tutors)
17:00 - 18:00	Summary & voting for best SBGN map

Hands-on

In the afternoon we will work on SBGN-related tasks and using the SBGN-ED software tool. You will learn to:

• install and use SBGN-ED
• translate SBML models from BioModels into SBGN
• layout automatically created SBGN maps
• understand the importance of SBO terms
• use colors to improve the readability of SBGN maps
• create an SBGN map in SBGN-ED, e.g., from literature

Software requirements & registration

Attendees must bring laptops for hands-on sessions in the afternoon. They should install the VANTED software with SBGN-ED plugin before the workshop.

Please register for this tutorial online: http://bit.do/SBGN2016Reg.

Should you have further questions, suggestions, or requirements for the tutorial, please do not hesitate to contact us.

Resources for download

• Workshop flyer (PDF)
• BIOMD0000000012-noSBO.xml
  BIOM12 without SBO terms (SBML file)
• SBGN-PD-Toure.pdf
  Introduction to SBGN-PD (Vasundra Toure).
• Hands on
  Material for the hands-on, including the competition.
• Introduction to SBOLVis
  Introduction to SBOL Vis (Robert Cox).
• Visualisation of biological networks
  Introduction to Visualisation of biological networks (Bjorn Sommer)