Animals; Internet; Salamandridae; Signal Transduction; Software; Systems Biology; Statistics and Probability; Biochemistry; Molecular Biology; Computer Science Applications; Computational Theory and Mathematics; Computational Mathematics
Abstract :
[en] [en] 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.
Disciplines :
Biotechnology
Author, co-author :
Balci, Hasan; i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
Siper, Metin Can; i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara 06800, Turkey ; Molecular & Medical Genetics Department, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
Saleh, Nasim; i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
Safarli, Ilkin; i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara 06800, Turkey ; Visualization Design Lab, School of Computing, University of Utah, Salt Lake City, UT 84112, USA
Roy, Ludovic; European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 69007 Lyon, France
Kilicarslan, Merve; i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
Ozaydin, Rumeysa; i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
MAZEIN, Alexander ; University of Luxembourg ; European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 69007 Lyon, France
Auffray, Charles; European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 69007 Lyon, France
Babur, Özgün; Molecular & Medical Genetics Department, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA ; Computer Science Department, University of Massachusetts Boston, Boston, MA 02125, USA
Demir, Emek; Molecular & Medical Genetics Department, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
Dogrusoz, Ugur ; i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
External co-authors :
yes
Language :
English
Title :
Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps.
Scientific and Technological Research Council of Turkey Defense Advanced Research Projects Agency Communicating with Computers Program Innovative Medicines Initiative Joint Undertaking European Union’s Seventh Framework Programme
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