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If you use these install instructions, please cite: Graham G.M. Alvare, Natalie K. Björklund, John Schellenberg, Richard Sparling, Brian Fristensky; Koala: Overlaying Local Gene Expression Data on BioCyc Pathway Diagrams

Starting Pathway Tools Web Server

  1. Start the pathway tools web server




  2. Open firefox


  3. If you get the following screen, then you need to patch Pathway tools. Click here for instructions on how to patch pathway tools. Apply the patch, then proceed to the next step.


  4. Verify that Koala is installed in firefox by opening up a pathway in pathway tools (32-bit Windows, by default, does not appear to display Koala on the main pathway tools page; therefore, you must navigate to an actual pathway or other page, such as glycolysis or cellular overview)