Project duration: June 2015 – January 2017
The Systems Biology Graphical Notation (SBGN) is a standard to visually represent networks and dynamical models in biology. A format to exchange these representations is SBGN-ML.
SBGN maps can be created and modified with a variety of software tools. In this project, we focus on SBGN-ED, which is a plugin to VANTED, a tool to visualise and analyse computational models in the context of experimental data.
The major goals of this BMBF e:Bio project SBGN-ED+ are:
- to contribute to further SBGN developments, including libSBGN
- to contribute to the development of SBGN-ED
- to enhance the usability of SBGN-ML in related projects, e.g., to express differences in model versions through SBGN using BiVeS.
This project initially ran at the IPK Gatersleben, in the group of Prof. Falk Schreiber, from 2012 to 2014. SBGN-ED+ is continued at the Department of Systems Biology and Bioinformatics from September 2015 to January 2017. The SBGN-ED software is available at sbgn-ed.org.
Our most favorite publications…
- Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Fellow, IEEE, Pinar Pir, Begum Alaybeyoglu, Naveen K Aranganathan, Kambiz Baghalian, Vasundra Touré et al.Toward community standards and software for whole-cell modeling. IEEE Transactions on Biomedical Engineering (2016). doi: 10.1109/TBME.2016.2560762 (open access)
Tools
- MOST – Statistics on model changes
- STON – Storing SBGN-ML files in a graph database (github project)