Ruth Dannenfelser1, Alexander Lachmann, Mariola Szenk, Avi Ma'ayan. 1. Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA.
Abstract
MOTIVATION: Network diagrams are commonly used to visualize biochemical pathways by displaying the relationships between genes, proteins, mRNAs, microRNAs, metabolites, regulatory DNA elements, diseases, viruses and drugs. While there are several currently available web-based pathway viewers, there is still room for improvement. To this end, we have developed a flash-based network viewer (FNV) for the visualization of small to moderately sized biological networks and pathways. SUMMARY: Written in Adobe ActionScript 3.0, the viewer accepts simple Extensible Markup Language (XML) formatted input files to display pathways in vector graphics on any web-page providing flexible layout options, interactivity with the user through tool tips, hyperlinks and the ability to rearrange nodes on the screen. FNV was utilized as a component in several web-based systems, namely Genes2Networks, Lists2Networks, KEA, ChEA and PathwayGenerator. In addition, FVN can be used to embed pathways inside pdf files for the communication of pathways in soft publication materials. AVAILABILITY: FNV is available for use and download along with the supporting documentation and sample networks at http://www.maayanlab.net/FNV. CONTACT: avi.maayan@mssm.edu.
MOTIVATION: Network diagrams are commonly used to visualize biochemical pathways by displaying the relationships between genes, proteins, mRNAs, microRNAs, metabolites, regulatory DNA elements, diseases, viruses and drugs. While there are several currently available web-based pathway viewers, there is still room for improvement. To this end, we have developed a flash-based network viewer (FNV) for the visualization of small to moderately sized biological networks and pathways. SUMMARY: Written in Adobe ActionScript 3.0, the viewer accepts simple Extensible Markup Language (XML) formatted input files to display pathways in vector graphics on any web-page providing flexible layout options, interactivity with the user through tool tips, hyperlinks and the ability to rearrange nodes on the screen. FNV was utilized as a component in several web-based systems, namely Genes2Networks, Lists2Networks, KEA, ChEA and PathwayGenerator. In addition, FVN can be used to embed pathways inside pdf files for the communication of pathways in soft publication materials. AVAILABILITY: FNV is available for use and download along with the supporting documentation and sample networks at http://www.maayanlab.net/FNV. CONTACT: avi.maayan@mssm.edu.
Authors: Brian Saunders; Stephen Lyon; Matthew Day; Brenda Riley; Emily Chenette; Shankar Subramaniam; Ilango Vadivelu Journal: Nucleic Acids Res Date: 2007-10-26 Impact factor: 16.971
Authors: Nathan Salomonis; Kristina Hanspers; Alexander C Zambon; Karen Vranizan; Steven C Lawlor; Kam D Dahlquist; Scott W Doniger; Josh Stuart; Bruce R Conklin; Alexander R Pico Journal: BMC Bioinformatics Date: 2007-06-24 Impact factor: 3.169
Authors: Johannes Tuikkala; Heidi Vähämaa; Pekka Salmela; Olli S Nevalainen; Tero Aittokallio Journal: BioData Min Date: 2012-03-26 Impact factor: 2.522