FluxViz Cytoscape Plugin Matthias Knig Group seminar Berlin - PowerPoint PPT Presentation

Mar 08, 2023 •123 likes •259 views

FluxViz Cytoscape Plugin Matthias Knig Group seminar Berlin 01|02|10 Outline Cytoscape FluxViz Further Plugins SBMLReader2 PositionReuse HepatoBase Connection Cytoscape open source software for visualizing

FluxViz – Cytoscape Plugin Matthias König Group seminar Berlin 01|02|10
Outline  Cytoscape  FluxViz  Further Plugins  SBMLReader2  PositionReuse  HepatoBase Connection
Cytoscape  open source software for visualizing molecular interaction networks  integrating gene expression profiles and other state data  general platform for complex network analysis and visualization  Additional features as plugins http://www.cytoscape.org/
FluxViz  Plugin for visualization of flux distributions  FBA in biochemical reaction networks  frontend for FASIMU  Features  full Cytoscape functionality (filters, additional visual mappings, …)  cycle through flux distributions  visualize flux containing subgraph  export vector and scalar images
FluxViz installation I  2 Click solution  Download fluxviz.jar  Move in PluginFolder  Control over version
FluxViz Installation II  1 Click solution  Cytoscape Plugin Manager  Automatic Updates
Usage example  Installation  Loading example data  Standard example  Erythrocyte network  Hepatocyte Core network  Export of images
Examples
Flux subnetwork
Further plugins  SBMLReader2 [finished]  New SBML parser for Cytoscape with support of all SBML versions and all node and edge attributes  http://sourceforge.net/projects/sbmlreader2/  PositionalData [starting]  Reuse of layouts  Compartments  HepatoBase integration [usage case]  SQL queries
References  FluxViz http://sourceforge.net/projects/fluxvizplugin/ http://www.charite.de/sysbio/people/koenig/  SBMLReader2 http://sourceforge.net/projects/sbmlreader2/  Cytoscape http://www.cytoscape.org/  Cytoscape plugins http://chianti.ucsd.edu/cyto_web/plugins/index.php  FASIMU http://www.bioinformatics.org/fasimu/

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