Hasan Balci1, Metin Can Siper1,2, Nasim Saleh1, Ilkin Safarli1,3, Ludovic Roy4, Merve Kilicarslan1, Rumeysa Ozaydin1, Alexander Mazein4,5, Charles Auffray4, Özgün Babur2,6, Emek Demir2, Ugur Dogrusoz1. 1. i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara 06800, Turkey. 2. Molecular & Medical Genetics Department, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA. 3. Visualization Design Lab, School of Computing, University of Utah, Salt Lake City, UT 84112, USA. 4. European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 69007 Lyon, France. 5. Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg. 6. Computer Science Department, University of Massachusetts Boston, Boston, MA 02125, USA.
Abstract
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.
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.
Authors: Marvin Martens; Ammar Ammar; Anders Riutta; Andra Waagmeester; Denise N Slenter; Kristina Hanspers; Ryan A Miller; Daniela Digles; Elisson N Lopes; Friederike Ehrhart; Lauren J Dupuis; Laurent A Winckers; Susan L Coort; Egon L Willighagen; Chris T Evelo; Alexander R Pico; Martina Kutmon Journal: Nucleic Acids Res Date: 2021-01-08 Impact factor: 16.971
Authors: Augustin Luna; Metin Can Siper; Anil Korkut; Funda Durupinar; Ugur Dogrusoz; Joseph E Aslan; Chris Sander; Emek Demir; Ozgun Babur Journal: STAR Protoc Date: 2021-11-23