Browsing by Author "Roy, L."

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    cd2sbgnml: Bidirectional conversion between CellDesigner and SBGN formats
    (Oxford University Press, 2020-01) Balaur, I.; Roy, L.; Mazein, A.; Karaca, S. Gökberk; Doğrusöz, Uğur; Barillot, E.; Zinovyev, A.
    Motivation: CellDesigner is a well-established biological map editor used in many large-scale scientific efforts. However, the interoperability between the Systems Biology Graphical Notation (SBGN) Markup Language (SBGNML) and the CellDesigner’s proprietary Systems Biology Markup Language (SBML) extension formats remains a challenge due to the proprietary extensions used in CellDesigner files. Results: We introduce a library named cd2sbgnml and an associated web service for bidirectional conversion between CellDesigner’s proprietary SBML extension and SBGN-ML formats. We discuss the functionality of the cd2sbgnml converter, which was successfully used for the translation of comprehensive large-scale diagrams such as the RECON Human Metabolic network and the complete Atlas of Cancer Signalling Network, from the CellDesigner file format into SBGN-ML. Availability and implementation: The cd2sbgnml conversion library and the web service were developed in Java, and distributed under the GNU Lesser General Public License v3.0. The sources along with a set of examples are available on GitHub (https://github.com/sbgn/cd2sbgnml and https://github.com/sbgn/cd2sbgnml-webservice, respectively). Supplementary information: Supplementary data are available at Bioinformatics online.
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    Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps
    (Oxford University Press, 2021-05-15) Balcı, Hasan; Siper, Metin Can; Saleh, Nasim; Safarli, İlkin; Roy, L.; Kılıçarslan, Merve; Özaydın, Rümeysa; Mazein, A.; Auffray, C.; Babur, Ö.; Demir, E.; Doğrusöz, Uğur
    Motivation Visualization of cellular processes and pathways is a key recurring requirement for effective biological data analysis. There is a considerable need for sophisticated web-based pathway viewers and editors operating with widely accepted standard formats, using the latest visualization techniques and libraries. Results We developed a web-based tool named Newt for viewing, constructing and analyzing biological maps in standard formats such as SBGN, SBML and SIF. Availability and implementation Newt’s source code is publicly available on GitHub and freely distributed under the GNU LGPL. Ample documentation on Newt can be found on http://newteditor.org and on YouTube.