The screenshot below is the first window shown after starting the modeler application. Besides the welcome message in the main body of the window, there are two main functional areas at the top: menu bar and tool bar.
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Menu bar
Includes "
Model" , "View", "Tools" and "Help" menus.
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Model: for model file management. -
View: for application navigation. -
Tools: for application tools. -
Help: for application information and documentations.
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Tool Bar
Includes the tool buttons corresponding to some menus in the "
menu bar" above and some convenient buttons. Detailed explanations of the functionalities are provided in the following sections.
Click "Model" in the menu bar (or Alt+M) to activate a
dropdown menu displaying menu options for model file management.
There are three ways to create a new model.
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From the menu bar dropdown menu,click the "
New..."
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On the keyboard, press "
Ctrl+N" -
From the tool bar,click the "
new model" icon
A file dialog prompts the user for the name of the new model file.
After a new model is created, the model summary page is shown with the model
file name listed on the top. Whether the full file path or just the model name
is displayed can be configured in the preferences window.
There are 3 ways to open an existing model file.
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From the menu bar dropdown menu, click "
Open..."
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On the keyboard, press "
Ctrl+O" -
From the tool bar, click the "
open model" icon
A message window prompts the user to select a model file.
The user can select an existing model file and click the "Open"
button.
The user can also open a recently opened file from the menu bar dropdown menu.
And the user can clear the history of recent files by choosing "Clear
Menu"
The following screenshot shows an example model file loaded into the modeler application.
Note
From version 2.1.0, the user may run multiple modeler applications at the same time. However, a model file can only be opened by one modeler application. A warning message displays when the second modeler is trying to open a model file.
The user should first check if the file to open is used by another modeler application. In case the modeler is just recovered from a crash or the user can make sure there is no other modeler using the model file, the user may click "Remove Lock" button to continue.
When a model file is created/opened as the current working model, the user can save the content in the current editing window to the model.
There are three ways to save from the main window.
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From the menu bar dropdown menu, select "
Save".
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On the keyboard, press "
Ctrl+S". -
From the tool bar, click the "
save" icon.
Note
The "Save" buttons in the individual windows have the same function.
The user can save data to a different file.
Note
The original model file will not be deleted ( the modeler application performs "save + copy").
After the "Save As" operation the working model will be saved
to the model file with the new name.
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From the menu bar dropdown menu, select "
Save As..."
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On the keyboard, press "
Ctrl+A"
A message window appears and prompts the user to select a directory and define/select a file name. If the new model file name is valid, the modeler application will use a model file with the new name to save any future changes to the model. The original model file still exists and the user can delete it through standard file manipulations of the operating system.
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From the menu bar dropdown menu, select "
Close Current Model".
The modeler will save the current open page first and then disconnect the current model file.
The user can use both, the menu bar and the tool bar, to navigate the modeler application.
At anytime, user can go back to the "home" page.
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From the menu bar dropdown menu, select "
Home"
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From the tool bar, click the "
home" icon.
The user can return to previously visited screens (or pages) of the modeler application.
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From the menu bar dropdown menu, select "
Prev" or "Next".
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From the tool bar,click the "Prev" or "Next" icon.
Note
The "Prev" and "Next" actions will not change data. The current window before the action will be tempory hidden and can be brought to front by the "Prev" or "Next" action.
The user can clear the navigation history by selecting "Clear
History" from the "View" dropdown menu.
Note
Please be careful using this functionality! Some unsaved data contained in the hidden windows may not be recovered.
There are two tools available in the current version of the modeler application:
"Test Simulator API", and "Preferences".
These tools can help the users to costomize the modeler configuration and the Simmune development team to handle some special cases or for debugging.
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Test Simulator APIPrint special debug message to a clipboard window. The user can send the printout message to the Simmune development team. This tool is for the purpose of trouble-shooting and software debugging.
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Preferences
Note
The preferences parameters will be stored in the operating system cache and shared by the all instances of the modeler application.
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Start Options"Parameters used by the modeler application when it starts or restarts.
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Screen Size"three options, "
Most Recent", "1440X900(Default)" or "Full Screen". -
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Start Page"two options, "
Last Model" (preload with model of the last saved), or "Home Page (Default)".
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Application Title"Set up how to display the current model file name in the application title.
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No display
Check off the "
Display Model File Location" checkbox. -
Display only the file name (default).
Check the "
Display Model File Location" checkbox and select "Model File Name Only" . -
Display the absolute path of the current model file
Check the "
Display Model File Location" checkbox and select "Model File Path and Name".
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"
Icon Size and Line Space"Set up the icon size for molecules, complex species and complexes and line space for icon-related tables and trees.
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Small (20X15)" -
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Medium (40X30)" -
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Large (80X60)" -
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Customize"The user can select from
1-200for width and height. -
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Line Space For Icon-related Tables and Trees"Default line space is 10.
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"
Tooltips Configuration for Molecule Components and Binding Sites"-
"
Display Tooltips" checkbox.If checked, tooltips display at mouseover on the items.
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"
Molecule Component or Binding Site Only" -
"
With Related Name(s) (Default)"Includes names of parent(s). For example,
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Checkbox: "
Single Molecule Complex Species"When checked, "
Automatically Create Single Molecule Complex Species When Saving New Molecule". -
Checkbox: "Display 'Center' buttons for graphical windows"
When checked, the "Center" buttons appears for the graphical windows with enabled editing functions such as molecule, molecule interaction, complex species and association windows. Otherwise, the buttons are hidden. The "Center" buttons provide convenient function to move the graphical items to the view center.
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Checkbox: "Display Fullname Fields"
The user may choose to use a single name (same as "
Short Name") for an entity by unchecking this box. Otherwise both "Short Name" and "Full Name" display in the window.
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Buttons.
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"
Apply"Apply the parameter by saving them to the system cache.
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"
Reset To Default"Clear the system cache and use the default values.
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OK"Apply the parameters and close the
Preferenceswindow. -
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Close"Close the "
Preferences" window.
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The user can export the current model to SBML and ODEs. Select "Export
Simmune Model ..." from the model dropdown menu.
And a window will ask the user to specify how to export the model.
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Specifying seed complexes and assigning initial concentrations
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Specifying seed complexes and assigning initial concentrations
Note
Simmune creates reaction networks based on the seed complexes specified by the user, which are also referred to "
Completely Specified Complexes" in the window. The seed complexes do not contain any "Don't Care" or negation molecule component tag state. All binding sites other than those involved in in-complex binding must have "Unbound" status.If, for instance, a model contains complexes A, B and C and A and B can associate to form AB and B and C can form BC but the user specifies as seed complexes only A and B the reaction network will contain A, B and AB but not C and BC.
Check the checkbox at the first column of the table to select the corresponding complex as a "seed" and enter the concentration. Repeat this process to specify those complexes you want to be used for the creation of the reaction network. A status bar at the bottom of the window will display warning message(s) if necessary and suggest modifications.
When the current initial assignment is valid, the "Export SBML" and "Export ODEs" buttons are enabled.
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Save current initial assignment
The user can save the current initial assignment. A default name will be assigned if no name is entered and the current initial assignment is saved by clicking "
Save Current Initial Assignment".
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Loading/deleting saved assignment(s)
The user can browse the saved intial assignment(s) by clicking "
List of Saved Initial Assignment(s)".Check the the checkbox(es) to select initial assignment(s).
If only one initial assignment is checked, the "Load" button is enabled.
If one or more initial assignment(s) is/are checked, the "Delete" button is enabled.
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Export SBML
Click the "Export SBML" button to export the current model with the current initial assignment to SBML in a clipboard window.
The user can choose one of the three SBML versions: "
SBML 2.1", "SBML 2.4" and "SBML 3.1".The user can copy the SBML text to the system clipboard or save it to a file.
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Export ODEs
Note
When creating reaction networks from complex interaction definitions, Simmune step by step creates all complexes (up to a user-defined maximal number of molecular components) resulting from the specified interactions. Typically, most of these result complexes will not be complexes that have explicitly been defined by the modeler (user). They can, however, uniquely be identified by their structure and the states of their molecular components. Strings encoding this information will be used in the SBML and ODE export functionality as identifiers, in addition to any user-defined names. The structure of these 'structure and state codes' is as follows: molecule name, list of state values, binding codes for the binding sites of the molecule: /_/_/_/ means unbound site, /x/y/z/ means bound to site x of component y of molecule z in the complex.
Click the "Export ODEs" button to export the current model to ODEs in a clipboard window.
Similarly, the user can copy the ODEs to the system clipboard, or save to a file.
