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.