About

The 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 development was initiated within the eTRIKS project as a collaboration between the European Institute for Systems Biology and Medicine in France and the Institute of Cell Biophysics in Russia. The code was developed by Denis Shirshov, a volunteer software developer at the EISBM. The converter and web services are hosted and supported by the Bioinformatics Core of the Luxembourg Centre for Systems Biomedicine within the ELIXIR-LU framework.

Related friendly efforts include CaSQ (Aghamiri et al., 2020, PMID: 32403123), the Newt Editor and the SBGN-ED editor (Vogt et al., 2013, PMID: 24176088).

Availability

The converter is available at https://pd2af.lcsb.uni.lu. The code is available at https://git-r3lab.uni.lu/elixir/pd2af.

Contact

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

Project Team

Denis Shirshov, Alexander Mazein, Adrien Rougny, Anatoly Sorokin, Ilya Mazein, Vasundra Toure, Irina Balaur, Johann Pellet, Charles Auffray, Ugur Dogrusoz, Marek Ostaszewski, Yohan Jarosz, Christophe Trefois, Reinhard Schneider, Sylvain Soliman, Anna Niarakis

	Denis Shirshov Volunteer Software Developer European Institute for Systems Biology and Medicine, Lyon, France		Alexander Mazein Researcher Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
	Adrien Rougny Researcher National Institute of Advanced Industrial Science and Technology, Tokyo, Japan		Anatoly Sorokin Head of Laboratory Institute of Cell Biophysics, Russian Academy of Science, Pushchino, Russia
	Ilya Mazein MSc Student, Applied Mathematics Saint Petersburg State University, Petergof, Saint Petersburg, Russia		Vasundra Toure PhD Student Norwegian University of Science and Technology, Trondheim, Norway
	Ugur Dogrusoz PI of the Newt Editor project Professor in Computer Engineering Department of Computer Engineering, Bilkent University, Ankara, Turkey		Irina Balaur Researcher European Institute for Systems Biology and Medicine, Lyon, France
	Johann Pellet Researcher European Institute for Systems Biology and Medicine, Lyon, France		Charles Auffray Research Director at CNRS Founding Director of the EISBM European Institute for Systems Biology and Medicine, Lyon, France
	Anna Niarakis Associate Professor University of Evry, University of Paris-Saclay, Evry, France		Sylvain Soliman Computer Science Researcher Lifeware Group, Inria Saclay-Île de France, Palaiseau, France
	Marek Ostaszewski Research Scientist Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg		Yohan Jarosz Research and Development Specialist Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
	Christophe Trefois Team Leader, Responsible and Reproducible Research Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg		Reinhard Schneider Full professor / Chief Scientist 1 in Bioinformatics Head of Bioinformatics Core Facility Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg

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.

The converter and web services are hosted and supported by ELIXIR Luxembourg, the Luxembourgish node of ELIXIR.

License

The PD2AF tool is available under the GNU General Public License version 3.0 (GPLv3) License.