Workflow

Here, a short step-by-step manual is provided showing how to work with the CELLmicrocosmos CellExplorer. Of course, not all functionalities will be discussed. The focuse here will be laid on the navigation and the generation of tours.


1) How to load a Cell Model?

Below the menu bar there is a button bar. There, a number of preconfigured models are available which can be directly loaded into the CellExplorer. Of course, it is also possible to load any other .Cm3 or .Cm4 file into the CellExplorer by using the menu entry: "File" ⇒ "Load Cm3/Cm4 File". But which file formats are these?

  • .Cm3 is the CellEditor format, describing a cell with its cell components. These files can be saved with the CellExplorer (Cm1 project) as well as the CellEditor (Cm3 project).
  • .Cm4 is the PathwayIntegration format, containing the previously mentioned cell model as well as pathway, protein, and localization information. These files are saved with the PathwayIntegration (Cm4 project).
  • For proceeding now with this tutorial, please load a cell model. In the following text we will expect you to have loaded an animal cell model.

    2) How to navigate inside a Cell?

    The standard navigation in Floating Mode is done with the W/A/S/D keys (forward/left/backward/right movement). By holding shift, the view changes temporarily to Flight Mode and the user can turn the camera by using the arrow keys. Moreover, he can use the mouse for navigation: left mouse button - forward, right mouse button - backward, and mouse movement rotates the camera. With caps lock pressed, the Flight Mode can be permanently activated. For zooming the view, the mouse wheel can be used. To move around objects, double click an object during Floating Mode, switching to Object-bound Mode. Again, the WASD keys can be used for movement, but now around the object, as well as the mouse by pressing the left mouse button. To rotate the camera, use the right mouse button. To change the distance towards the object, use the center mouse button (or the right mouse button by pressing the ALT key. To leave the Object-bound mode, double-click onto a free place with the mouse cursor (or use the context menu by pressing the right mouse button or the Page-down key).


    3) How to get Information regarding the Cell Components (CE3 only)

    The educational edition - CE3 - provides information for every cell component, describing biochemical basics of a selected cell component.

    To get this information, please right-click on a cell component in the CellUniverse or by selecting the corresponding entry in the CellEditor (right click onto a cell component term) "Show Information". The window InformationBrowser will be shown. In case, more information are required and you have an active Internet connection, just click on the link "Further Information" which will lead you to the corresponding Wikipedia web page.

     Several studies show that the Quality of Wikipedia can nowadays often compete with the one of established lexica. Please be aware that you should be always critical towards the content of Wikipedia because it can be changed on a daily basis by different users with different backgrounds and opinions.


    4) How to create a Tour?

    To create a tour Um jetzt eine kleine Tour zu erstellen, wird, wie bei der Informationsanzeige, ein Rechtsklick auf die gewünschten Komponenten ausgeführt, aber der Menüpunkt "Add Component to Tour". Repeat this process e.g. for Nucleus, Mitochondrion and Peroxisome. You just created you first tour. But we will give you now a few other information how to edit this tour.


    5) Additional Information for Tour Editing

  • The TourEditor provides a number of functionalities to work with tours, but it is not always visible. First, make sure the 2DViewer is visible. In case, you do not see this window, select in the menu GUI ⇒ Restore 2DViewer. Then, make the Tour Mode of the 2DViewer is activated and right click on the right tour list, selecting "Show Tour Details".
  • There are two options to change the sequence of tour entries. The first one is to "Drag & Drop" the entries in the right tour list in the 2DViewer. The second one to is to "Drag & Drop" the entries in the previously-mentioned TourEditor.
  • The time the actual view will maintain at specific tour entry is defined by the "Delay".
  • The "Distance" defines were the camera will be located relative to the actual tour entry.
  • CE3 only: If during a tour a cell component is shown, the corresponding information will be shown in the InformationBrowser. Alternative HTML files can be defined in the TourEditor. Moreover, it is also possible to complete deactivate an information for a tour entry.


    6) How to save a Tour?

    To save a tour with its settings, a .Cm4 file has to be saved. For this purpose, select in the menu bar "File" ⇒ "Save as Cm4 File".


    7) And how to start the Tour?

    The tour can be started by selecting "Start Tour" after right-clicking 1) in the CellUniverse, 2) onto the tour list in the 2DViewer, or 3) pressing the corresponding button in the bottom bar of the 2DViewer.