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AMEBA Interactive visualization of metabolic networks Ren e Rex - - PowerPoint PPT Presentation
AMEBA Interactive visualization of metabolic networks Ren e Rex - - PowerPoint PPT Presentation
AMEBA Interactive visualization of metabolic networks Ren e Rex Include even more information: reaction fluxes Ren e Rex | AMEBA Interactive visualization of metabolic networks | 3 Visualization of metabolic networks Ren e Rex |
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Include even more information: reaction fluxes
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Visualization of metabolic networks
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Visualization of metabolic networks
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Metabolic context
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Graph handling
NetworkX http://networkx.github.com graph.degree(node) graph.edge[newNode][successor]["disconnected"] = True
- utput: various graph formats (e.g. GML, GraphML, dot)
However, interactive usage would be handy. . .
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xdot – exactly what I needed
http://code.google.com/p/jrfonseca/wiki/XDot an interactive viewer for graphs written in Graphviz’s dot language can be used either as a standalone application from command line, or as a library embedded in your python application
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xdot – exactly what I needed
http://code.google.com/p/jrfonseca/wiki/XDot an interactive viewer for graphs written in Graphviz’s dot language can be used either as a standalone application from command line, or as a library embedded in your python application Features Since it doesn’t use bitmaps it is fast and has a small memory footprint Arbitrary zoom, Keyboard/mouse navigation Supports events on the nodes with URLs Animated jumping between nodes Highlights node/edge under mouse
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Sample code and clickable nodes
def __init__(self): xdot.DotWindow.__init__(self) self.widget.connect(’clicked’, self.on_url_clicked) def on_url_clicked(self, widget, url, event): dialog = gtk.MessageDialog( parent = self, buttons = gtk.BUTTONS_OK, message_format="%s clicked" % url) dialog.connect(’response’, lambda dialog, response: dialog.destroy()) dialog.run() return True
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Clickable nodes
xdot: self.emit("clicked", unicode(url.url), event)
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Clickable nodes
xdot: self.emit("clicked", unicode(url.url), event) AMEBA: self.splitRatioGraph.node[node]["URL"] = node [...] self.widget.connect("clicked", self._node_clicked)
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AMEBA: Advanced MEtabolic Branchpoint Analysis
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AMEBA: Advanced MEtabolic Branchpoint Analysis
Interactively visualizes metabolic networks and display flux distributions Easily configurable to produce high-quality figures Available online, GPLv3, http://metano.tu-bs.de/ameba
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AMEBA: Advanced MEtabolic Branchpoint Analysis
Interactively visualizes metabolic networks and display flux distributions Easily configurable to produce high-quality figures Available online, GPLv3, http://metano.tu-bs.de/ameba Thank your for your attention! r.rex@tu-bs.de
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