FNV: Light-weight Flash-based network

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 PathwayGene- rator. 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 sup- porting documentation and sample networks at http://www.maayanlab.net/FNV. Contact: avi.maayan@mssm.edu 1 INTRODUCTION Pathway databases such KEGG (Ogata et al., 1999), BioCarta (http://www.biocarta.com), WikiPathways (Pico et al., 2008) Science Signaling Connection Maps (Gough, 2002), and UCSD- Nature Signaling Gateway (Saunders et al., 2008) communicate over the web: cell signaling, transcriptional, and metabolic path- ways, as diagrams made of nodes and links. Such diagrams are visualized using different layout algorithms embedded in network viewers implemented with a variety of technologies. The majority of web-based network viewers make use of the Java web technolo- gies. For example, PATIKAweb (Dogrusoz et al., 2006) uses Java Server Pages (JSP) to retrieve information stored in the manually curated PATIKA database, or passed through a file to generate pathway diagrams using a force-directed algorithm to arrange stat- ic images of nodes and edges. Tools such as WebInterViewer (Han et al. 2004) and VisANT (Hu et al., 2008) are useful for large pro- * To whom correspondence should be addressed. tein-protein interaction networks utilizing JavaWebStart. However, JavaWebStart runs in a sandbox and does not easily communicate with the browser. Other tools such as jSquid, (Klammer et al., 2007) are powerful but since they utilize Java Applets they are slow to start and are inconsistent across browsers. Several web- based pathway viewers have been implemented without the use of Java. For example, CellDesigner (Funahashi et al., 2003) used by KEGG, creates static network images with hyperlinks. It was used, for example, by BioPP (Viswanathan, 2007) with Perl and CGI displaying static images with annotations mapped to the nodes as hyperlinks. AVIS (Berger et al., 2007), a network drawing tool that we developed, uses Asynchronous JavaScript and XML (AJAX) and underlying Perl libraries to draw static networks that are ren- dered using GraphViz. GraphViz (Gansner and North, 1999) is one of the most commonly used graph drawing tool for displaying...

Website: bioinformatics.oxfordjournals.org | Filesize: -
No of Page(s): 2
Download FNV: Light-weight Flash-based network and ... - Bioinformatics.pdf