Romain BOURQUI
Contact
bourqui[at]labri.fr
LaBRI, Université de Bordeaux
UMR CNRS 5800
351, cours de la Libération
F-33405 Talence cedex
France
Tel.: +33 5 4000 3530






















































































































































































































MetaViz Tutorial

Installing MetaViz
  1. Download MetaViz at http://www.labri.fr/perso/bourqui/software.html
  2. Download sample files at the same address (for instance
    primCpdsSmmReactionsCompoundsYeast.xml).
  3. Install and start MetaViz.
Looking for the TCA cycle without constraining the drawing algorithm
  1. Click the Open button.


  2. Open the yeast metabolic network: primCpdsMetabSmmReactionsCompoundsYeast.xml. You should obtain this kind of representation. This representaion means that the network is loaded but not drawn (see next step to draw it).

  3. Click the draw button (1). You will get the drawing paramater interface, click the "ok" button (2).

  4. After a few seconds, you will get the drawing of the yeast metabolic network. To highlight in purple a chosen pathway select it from the list on the left. For instance, select "TCA cycle, aerobic respiration".

  5. Using mouse wheel, you can zoom-in and see that the TCA cycle is split by the drawing algorithm. In the next section we are going to present a way to draw this pathway carefully.

Looking for the TCA cycle by constraining the drawing algorithm
  1. Select again the draw button. Answer "yes" at the question "Do you wish to visualize particular pathways ?". In the list, select "TCA cycle, aerobic respiration". Then click "ok" to start the drawing.

  2. You will get this view. Select again the "TCA cycle, aerobic respiration" in the list.

  3. If you zoom-in, you will see that the TCA cycle is entirely drawn.

Interaction and Navigation Buttons
Each time, one clicks on an interaction button, effects of left/right button and wheel of mouse change.
Navigation
After clicking on this button, the mouse allows to navigate in the drawing : left button to "move" and wheel to zoom in or out.
This button allows to go down in the hierarchy. Click on a metanode to focus on nodes it contain.
This button allows to go up in hierarchy. Click on it to go up of one level.
This button allows to go up in hierarchy. Click on it to go to the upper level of the hierarchy.
Selection
This button allows to select a node or a metanode, when cliking on a node (using left button), it is highlightened in pink. Properties of the node are described on the top (if it is a metabolic pathway) and on the bottom.
This button allows to visualize the neighborhood of a node. When clicking on a node (using left button), it is highlightened and so are its neighbors. If the clicked node is a metanode, all nodes (and all their neighbors) in it are highlightened.
This functionality allows to visualize each metabolic pathway a node (compound) belongs to. First click on a node, then scroll the wheel to see pathways it belongs to (name of these pathways are written on the top and composition of these pathways are shown on the bottom).
This button allows to unselect all nodes.
Interaction
This functionality allows to change the layout of nodes. To move a node, you first have to "select" it using the cross button described below, then left-click on the selected node, drag it and release at its new position .
After selecting a metanode (using the selection interactor), click on this button to open a metanode.
This button allows to "re-group" the lastest opened metanodes.