This document serves as a brief introduction to Prometheus' graphical user interface. The interface makes use of tabs to facilitate working with multiple models at one time. Unless otherwise noted, any references to the model refer to the model displayed in the currently visible tab. Menus ========== File Open Open a process model in a new tab. If there are syntax errors in the model, a message will be displayed in a dialog and also in the status bar at the bottom of the application window. Once the dialog is dismissed, the source of the model will be displayed to you with the line containing the error highlighted. At this time, the model can be corrected and saved. Once corrected, open the model again. See the notes on saving a model under 'File->Save' Close Close the model. Reload Close the model and reopen it in a new tab using the original process model file. Save Save the model to its original file note that saving the model will remove any comments from a source file and reorder the variable declarations and processes. If you wish to maintain the text layout of your model, you are advised to change it with a standard text editor. The current layout of the model will also be saved in a file called ..layout, where 'model_name' and 'extension' are identical to the model name and extension of the original file. Adding processes or variables can result in a stale layout, so if the model has an odd configuration when loaded, delete the corresponding layout file. Save as Same as 'save' except a file selection dialog is presented so that you can choose a new file name and/or location for your model. There is no warning if you attempt to overwrite a file that already exists. Save layout Save the layout of the model. This does not save the model itself. Exit Close all tabs and exit the program. Edit Add process Create a new process and add it to the model. If a generic process library has been loaded, you can select a generic process to serve as a template for process creation. Otherwise a standard template is presented. Add observable variable Add a new variable to the model. You should provide a name and select a type for the variable. The types are contained in the program's type file. The most general type is 'number'. Settings Set process library Select a library of generic processes and open it. A generic process library is mandatory for model revision, and can also help with graphical editing of the model (see 'Add process'). Syntax errors in the library will be reported, but currently you must fix the file with a standard text editor. Tools Simulate Simulate the behavior of the model. Revise Automatically revise the model using constraints that you provide. Set addable processes for revision State which generic processes, or which instantiations of those generic processes, can be considered for addition to the model by the automatic revision system. View Causal The default view of the model displays the processes and variables in a left to right ordering based roughly on causal influence. A line from a process to a variable indicates that the process influences the variable (i.e., the variable is on the left hand side of an equation within that process). A line drawn from a variable to a process indicates that the variable provides input to that process (i.e., the variable occurs only on the right hand side of equations within the process). A thin, blue line indicates that the variable is only involved in algebraic equations within the process . A thick orange line indicates that the variable is involved in at least on differential equation within the process. Componential This view places all the variables on the left and all the processes on the right. The lines have the same meaning as those in the causal view. Source code View the text of the process model. You can edit this text, but note that choosing to apply the changes will save the model. View equations View the differential and algebraic equations contained within the model. View observed trajectories Plot the observed data with the simulated results. If the initialization file for the simulation of the process model contains data for the variables (beyond the initial conditions), this data will be displayed on the plot along with the simulated trajectories. View revision history Color code the processes within the model when viewing an automatically revised model. The meanings of the colors can be seen in the legend. Revision history tree Currently undocumented. View legend Show the legend for Prometheus' graphical display. Currently only the colors for automatically revised models are shown. Toggle color display Switch the model display between color and black & white. The black and white display is useful when capturing screen shots for publication purposes. Help About Display copyright and contact information related to Prometheus. ---------- Other features ========== Processes Double-Click Clicking twice on a process opens a window displaying that process's definition. This definition can be altered, allowing you to update the model. Unlike with the 'View source' option, the model itself is not saved when you alter a single process definition. Right-Click If you right click on a process, the revision permissions dialog appears. Here you can see the process definition, select the generic process related to this process, and tell Prometheus whether it should consider changing the parameters of the process or completely deleting the process during automated revision. Note that a generic process must be selected if you wish the system to change the parameters. Variables Double-Click After simulating the model, the results are associated with the variable nodes. By double-clicking on these nodes, you can view the resulting trajectories. Right-Click Experimental: You can trace the influence of a variable one step forward or one step back. Selecting 'forward' will show the processes for which the variable is input. Selecting 'backward' shows which processes affect the value of the variable. ---------- Simulation and Revision ========== Simulation The dialog shown when you choose to simulate the model allows the specification of four options. First, you must specify an initialization file. The format of this file is described in README.txt. Second, you must select an output file. The default output file is called 'simulation.out' and is stored in the Prometheus directory. The third and fourth options specify how long the simulation should run. Timestep size indicates the granularity of the simulation, and the number of timesteps specifies how many steps of the specified size should be simulated. Revision The revision dialog shows which processes you have selected for addition, deletion, and alteration during automated revision. You must specify a data file containing observed trajectories. The format of this file is discussed in README.txt. Optionally, you can specify a type file. The part of the program that performs revisions is currently disconnected from the rest of Prometheus and therefore requires its own file that defines type hierarchies (unfortunately in a different format than Prometheus expects). Without a type file, all variable types are assumed to inherit directly from 'number.' This dialog also allows you to place limits on the size of the model, the number of instantiations of a generic process, and the number of models returned for examination. The relevant information for performing a revision is contained in README.txt.