BIOINFORMATICS APPLICATIONS NOTE
Vol. 27 no. 8 2011, pages 1181–1182
FNV: light-weight flash-based network and pathway viewer
Ruth Dannenfelser, Alexander Lachmann, Mariola Szenk and Avi Ma’ayan∗
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
Associate Editor: Trey Ideker
Advance Access publication February 23, 2011
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
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
FNV is available for use and download along
with the supporting documentation and sample networks at
Received and revised on December 22, 2010; accepted on February
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-
the web: cell signaling, transcriptional and metabolic pathways, 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 technologies.
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 static images
of nodes and edges. Tools such as WebInterViewer (Han et al.,
2004) and VisANT (Hu et al., 2008) are useful for large protein–
protein interaction networks utilizing JavaWebStart. However,
JavaWebStart runs in a sandbox and does not easily communicate
∗To whom correspondence should be addressed.
with the browser. Other tools, such as jSquid (Klammer et al.,
2008), 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., 2007a), a network drawing
(AJAX) and underlying Perl libraries to draw static networks
that are rendered using GraphViz. GraphViz (Gansner and North,
1999) is one of the most commonly used graph drawing tools for
displaying pathways. Written in C, GraphViz takes text files as
input to render nodes and links for generating a static network
image that can be saved in different formats, i.e. scalable vector
graphics (SVG), JPEG/PNG/GIF or as a postscript file. While
network images can be mapped to hyperlinks, such mapping lacks
interactivity such as panning and zooming, or movement of nodes
and links with the mouse by the user. SVG can be made interactive
but is not universally supported across browsers and is a fading
technology.Although somewhat limited, GraphViz has been widely
used by leading pathway databases to display their pathways online.
For example, Science Signaling Connection Maps and UCSD-
Nature Signaling-Gateway databases use SVG diagrams created
with GraphViz. WikiPathways and BioCarta, on the other hand, use
static images drawn by hand.The static images inWikiPathways are
created manually with PathVisio, a tool that is a part of GenMAPP
(Salomonis et al., 2007). Recently, a light-weight flash network
viewer (FNV) for web applications called Cytoscape Web (Lopes
et al., 2010) was launched. This viewer provides a variety of
dynamic features. The use of vector graphics, provided through
Flash, makes the implementation much more responsive and sharp
looking. With Cytoscape, Web uploaded pathways can be altered
Here we present FNV. Implemented first 2 years ago, the viewer
attempts to take the positives of all the existing viewers and provide
users with a light-weight tool for incorporating biological pathways
into their web applications.Written inAdobeActionScript 3.0, FNV
is a flash-based pathway viewer that is cross-platform and cross-
browser compatible with little to no extra overhead. It contains
several features that are not currently included in most existing
pathway viewers, such as a content box for displaying descriptive
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R.Dannenfelser et al. Download full-text
Fig. 1. Bradykinin to CREB pathway automatically created using
PathwayGenerator (http://amp.pharm.mssm.edu/maayan-lab/pg) visualized
information about nodes and edges, which includes support for
hyperlinks and images, and the ability to use images as nodes.
In an effort to maintain simplicity and readability, FNV uses a
we provide users with the ability to easily embed the viewer within
pdf files for the communication of pathways within publications.
FNV is delivered as a small web format file. This allows for the
complete abstraction of the ActionScript code requiring that the
user only have knowledge of extensible markup language (XML).
The XML file is the only input to FNV and therefore controls all
of the layout and viewing options as well as all node and edge
information. If the viewer is embedded in HTML, flash vars can be
used to pass in parameters to FNV. Users can choose from five graph
layout algorithms: force, spectral, hierarchy, spectral-hierarchy and
radial. The force layout algorithm treats the nodes as objects
that repel each other and the edges as springs with the objective
of making edges relatively equal in length with few intersecting
edges. Spectral layouts use eigenvalues of the adjacency matrix
to generate coordinates for node placement. The hierarchy layout
nodes to sink nodes. The spectral-hierarchy layout option combines
both hierarchical layout and spectral layout by first computing a
hierarchy and then arranging nodes in each layer of the hierarchy
using the spectral algorithm. Lastly, the radial algorithm positions
nodes around the center of a circle depending on an inputted
level. Descriptive text can include links to relevant databases and
images. Interactions between nodes can be represented using three
edge types: ortholine, arrow or bidirectional. Edge thicknesses,
edge colors as well as node type, shape, size and color can be
adjusted. Additionally, images can be used to represent nodes with
or without text labels. Once rendered, the network can be rearranged
dynamically by dragging nodes. In addition, zooming and panning
support is implemented. The network can be saved as a pdf file or
directly printed. A pathway created with FNV can be embedded
inside pdf files as dynamic interactive figures in publications.
FNV was used for several web-based systems: Genes2Networks
(Berger et al., 2007b), a tool for finding relationships among an
input list of genes; KEA (Lachmann and Ma’ayan, 2007), a tool
for kinase enrichment analysis; ChEA (Lachmann et al., 2010),
a tool to compute transcription factor binding enrichment; and
and receptors to downstream effectors (Fig. 1).
Funding: National Institute of Health (grants 5P50GM071558-
Conflict of Interest: none declared.
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