Systems biology visualizations

• BioGPS plugin for plotting gene expression levels, demo.
• EINVis for analyzing and exploring genetic interactions in large-scale association studies.
• WholeCellViz to interactively analyze many aspects of cell physiology including:
  • Cell mass, volume, and shape
  • Metabolite, RNA, and protein copy numbers
  • Metabolic reaction fluxes
  • Molecular machine statuses – DNA polymerase, RNA polymerase, ribosome, FtsZ ring
  • Chromosome copy number, superhelicity, integrity, and DNA binding status
• Omix, a commercial modeling & visualization tool for metabolic pathways.
• NaviCell, a web-based environment for navigation, curation and maintenance of large molecular interaction maps. doi:10.1186/1752-0509-7-100
• Biographer is a biological network layout and visualization tool.
  • Demo: http://semanticsbml.org/biographer
• Visbi conference, an annual conference highlighting visualizations for biological data.
• MetDraw, a tool for automated layout of metabolic reaction maps.
• EcoCyc maps
• Human Transcription Factor Regulatory Networks browser, force-directed visualizations of regulatory networks using d3.js.
• Pathway Pioneer, a metabolic model reconstruction and visualization toolbox with a web interface.
• BioJS, reusable components for presenting Biological data at EMBL.
• Partek
• MapMan
• MetaboAnalyst
• InCroMAP Integrated analysis of Cross-platform MicroArray and Pathway data
• Mimoza, a web-based metabolic model visualization and navigation system