About

PD2AF converter is an open-source application designed to enable communication between the Process Description and the Activity Flow languages of the SBGN standard. The converter uses the concept of the SBGN Bricks and additionally detects advanced network patterns such as, for example, “hidden” inhibition, when the mechanism of inhibition is shown in details and no inhibition arcs are used.

Acknowledgements

The PD2AF tool is built on and further develops the logic of the previously published template-based translation from PD to AF (Vogt et al., 2013, doi:10.1186/1752-0509-7-115) which is accessible as a functionality of the SBGN-ED add-on of the VANTED editor.

Availability

The tools is in development. The code is available at https://github.com/pd2af.

Contact

To contribute and discuss the project please use this email address: pd2af@googlegroups.com
Lead developer: Denis Shirshov denis.shirshov@gmail.com
PD2AF project coordinator: Alexander Mazein a.mazein@gmail.com

Project Team

Denis Shirshov

European Institute for Systems Biology and Medicine, Lyon, France

Alexander Mazein

Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg

Adrien Rougny

National Institute of Advanced Industrial Science and Technology, Tokyo, Japan

Anatoly Sorokin

Institute of Cell Biophysics, Russian Academy of Science, Pushchino, Russia





Vasundra Toure

Norwegian University of Science and Technology, Trondheim, Norway

Irina Balaur

European Institute for Systems Biology and Medicine, Lyon, France

Johann Pellet

European Institute for Systems Biology and Medicine, Lyon, France

Charles Auffray

European Institute for Systems Biology and Medicine, Lyon, France