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

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 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.

[1]  Lincoln Stein,et al.  Reactome: a database of reactions, pathways and biological processes , 2010, Nucleic Acids Res..

[2]  Emek Demir,et al.  Algorithms for effective querying of compound graph-based pathway databases , 2009, BMC Bioinformatics.

[3]  Astrid Junker,et al.  Wiring diagrams in biology: towards the standardized representation of biological information. , 2012, Trends in biotechnology.

[4]  Yukiko Matsuoka,et al.  Software support for SBGN maps: SBGN-ML and LibSBGN , 2012, Bioinform..

[5]  Emek Demir,et al.  A layout algorithm for undirected compound graphs , 2009, Inf. Sci..

[6]  Bernhard O. Palsson,et al.  Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways , 2015, PLoS Comput. Biol..

[7]  Ugur Dogrusoz,et al.  Efficient methods and readily customizable libraries for managing complexity of large networks , 2018, PloS one.

[8]  Wilmot Li,et al.  Design principles for visual communication , 2011, Commun. ACM.

[9]  Ugur Dogrusoz,et al.  SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps , 2015, PloS one.

[10]  Falk Schreiber,et al.  Editing, validating and translating of SBGN maps , 2010, Bioinform..

[11]  Sarala M. Wimalaratne,et al.  The Systems Biology Graphical Notation , 2009, Nature Biotechnology.

[12]  Kei-Hoi Cheung,et al.  BioPAX – A community standard for pathway data sharing , 2010, Nature Biotechnology.

[13]  Piotr Gawron,et al.  MINERVA API and plugins: opening molecular network analysis and visualization to the community , 2019, Bioinform..

[14]  Chris Sander,et al.  Integrating biological pathways and genomic profiles with ChiBE 2 , 2014, BMC Genomics.

[15]  Hiroaki Kitano,et al.  CellDesigner: a process diagram editor for gene-regulatory and biochemical networks , 2003 .

[16]  Guoan Zhang,et al.  γCaMKII Shuttles Ca2+/CaM to the Nucleus to Trigger CREB Phosphorylation and Gene Expression , 2014, Cell.

[17]  Ryan Miller,et al.  WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research , 2017, Nucleic Acids Res..

[18]  Andrei Zinovyev,et al.  cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats , 2020, Bioinform..

[19]  Chris Sander,et al.  Pathway Commons 2019 Update: integration, analysis and exploration of pathway data , 2019, Nucleic Acids Res..

[20]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..