Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps-Reference-Cited by-同舟云学术

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

Published:2020-11-25 Issue:10 Volume:37 Page:1475-1477
ISSN:1367-4803
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Balci Hasan¹,Siper Metin Can¹²,Saleh Nasim¹,Safarli Ilkin¹³,Roy Ludovic⁴,Kilicarslan Merve¹,Ozaydin Rumeysa¹,Mazein Alexander⁴⁵^ORCID,Auffray Charles⁴,Babur Özgün²⁶,Demir Emek²,Dogrusoz Ugur¹^ORCID

Affiliation:

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

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.

Funder

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

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

http://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaa850/34542339/btaa850.pdf

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