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.
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 |
Funding
This work was supported in part by the Innovative Medicines Initiative Joint Undertaking under grant agreement no. IMI 115446 (eTRIKS), resources of which are composed of financial contribution from the European Union’s Seventh Framework Programme (FP7/2007-2013) and EFPIA companies.
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.