Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps

Hasan Balci; Metin Can Siper; Nasim Saleh; Ilkin Safarli; Ludovic Roy; Merve Kilicarslan; Rumeysa Ozaydin; Alexander Mazein; Charles Auffray; Özgün Babur; Emek Demir; Ugur Dogrusoz

doi:10.1093/bioinformatics/btaa850

Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps

Bioinformatics. 2021 Jun 16;37(10):1475-1477. doi: 10.1093/bioinformatics/btaa850.

Authors

Hasan Balci¹, Metin Can Siper^{1

2}, Nasim Saleh¹, Ilkin Safarli^{1

3}, Ludovic Roy⁴, Merve Kilicarslan¹, Rumeysa Ozaydin¹, Alexander Mazein^{4

5}, Charles Auffray⁴, Özgün Babur^{2

6}, Emek Demir², Ugur Dogrusoz¹

Affiliations

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.

PMID: 33010165
DOI: 10.1093/bioinformatics/btaa850

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.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Internet
Salamandridae
Signal Transduction
Software*
Systems Biology*