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Network Map Section

Introduction

The network map provides a computer-generated visual summary of author-entered states of this molecule and the transitions between them. The graph is made up of a collection of ovals, which represent states, and arrows, which represent transitions between the states. The author-defined state name is displayed in each oval (it may be truncated if the state name is too long) and the full computed state name appears in a pop-up text box when you scroll the mouse over an oval. You may find the Network Map useful as a summary and also as a navigational tool. Clicking on the ovals or asterisks in the Network Map will take you to the details for that particular state and transition, respectively.

screenshot of the network map section of a molecule page

Technical Information

The transition network is generated automatically using WebDot, which is part of AT&T's GraphViz package. Graph layout is thus not determined by the author, and is not peer reviewed. The network is available in two formats: GIF (Graphics Interchange Format) and SVG (Scalable Vector Graphics). GIF is a bitmap format that can be viewed in all Web browsers, but which will be physically large for large networks. SVG is, as the name implies, scalable, so a large network can be scaled down and presented in a small area and the user can then zoom and navigate around the network as desired. The SVG provided on the website is designed to be viewed with the Adobe SVG plug-in.

Using the Adobe plug-in

When Adobe's SVG plug-in is installed correctly, a network similar to the GIF version will be displayed after clicking on the "See SVG Version" link in the Network Map section of a Molecule Page. The area of display is limited to 500 pixels however, and the network will be scaled so that it fits within that area. Scrolling the mouse over the ovals and arrows in the network will display detailed information about the item in a pop-up text box.

Users can zoom the network in and out by either right-clicking on the network (Mac users control+click) and choosing the zoom in or zoom out options, or by control+clicking (Mac users command+click) directly on the network to zoom in, or shift+control+clicking (Mac users shift+command+click) to zoom out. You can pan around the network can be done by holding down the alt key (also labeled the option key on Macs) and dragging the network around. The cursor should change to an appropriate icon when the correct keys are pressed.

For Firefox users

Recent versions of the Firefox browser (since 1.5) have a built-in SVG renderer enabled by default. Unfortunately several of the features that make the SVG version of the transition network useful have not been implemented. These include the ability to zoom and pan, and the functions needed to generate dynamic tooltips. Hopefully these features will be implemented in future upgrades to Firefox. It is possible to use the Adobe plugin instead of Firefox's built-in renderer on Windows but this is not for the faint-hearted. Follow these instructions at your own risk! The built-in renderer can be deactivated by setting the "svg.enabled" configuration to "false". Type "about:config" in Firefox's location bar, filter on "svg" to find the option, and then double-click to set it to "false". Then download and install version 6.0 of the Adobe SVG plug-in. As of May 2006, this was only available as a beta version. The plug-in is now installed for Internet Explorer, but not for Firefox. To get the plug-in working for Firefox, you need to copy the two plug-in files (NPSVG6.DLL and NPSVG6.ZIP) from their installation directory to Firefox's "plugins" directory. The most reliable way to find the installation directory is just to run "Search For Files or Folders" for one of the above filenames (on our test system it was in "C:\Program Files\Common Files\Adobe\SVG Viewer 6.0\Plugins"). Firefox's "plugins" directory will normally be "C:\Program Files\Mozilla Firefox\plugins" but may be in a different location if you customized your installation. You will have to restart Firefox for the plug-in to be found.