MBL User Manual

MBL (Module‐Based Layout algorithm) is a new layout algorithm that is aimed to clarify the 

network complexity according to its inherent modular structure or the modules predefined by 

user. MBL has been implemented as a VisANT plugin and is developed using Java language.   

The plugin provides additional menus to allow users to run the three main steps (see the 

manuscript) of MBL separately and it also allows user to configure key parameters of the layout  1 Visualize network through additional menus of three  main  steps  with  default  algorithm 

parameters. 1.1 Import a new network

 Start VisANT  and  open  local  visANT  network  file  (  format  of VisML  or  other  supported formats) in your computer to import a new network. In this tutorial, we import a network named Y2H‐CCSB which can be found in supporting materials 

1.2 Network clustering (Step 1 of MBL) Click  menu  item  "Layout",  open  submenu  "Module  Based  Layout"  and  navigate  to 

"Clustering to Modularize" 

Click "Clustering to Modularize" to show the result of network clustering  

1.3 Global optimization of module’s layout (Step 2 of MBL)

Select "Global Optimization of Module  Layout"  in  "Module Based  Layout" menu  and click it to view the global layout. 

1.4 Local optimization of the layout for the nodes embedded in modules (Step 3 of

MBL) Select "Local Optimization of Module Layout" in "Module Based Layout"

menu and click it to view the layout for the nodes embedded in modules.  

Note:   1) If click "Start MBL" in "Module Based Layout" menu, the MBL algorithm

can be run as a whole (including all three main steps).

2) The operation of mouse scrolling can zoom in/out the network to help user

discerning the detail topological connections, as shown below.               

 

2 Visualization of networks having predefined modules

It is the important feature of MBL to visualize the networks having predefined modules. Users can create predefined metanodes in any step of MBL and view the result layout. The process is shown as following.

2.1 Create predefined metanodes with "Grouping" menu. When in the selection mode, dragging the mouse will draw a rectangular and all

nodes within the rectangular will be selected, then click menu item "MetaGraph", open submenu "Grouping " and navigate to "Group Selected Nodes" 

Click "Group Selected Nodes" to create a new metanode, as shown below

2.2 Visualize the new network

In "Module Based Layout" menu, click submenu "Start MBL" to view the result layout or click submenu "Clustering to Modularize" to view the clustering layout as described above.

3 Configure key parameters of the layout MBL plugin allows user to configure key parameters of the layout.  3.1 Click "Configure MBL" in "Module Based Layout" menu to open configure panel

The MBL "configure panel" is shown as below, user can set parameter "Number of iteration ", " Random color and shape ", and " Advance settings (weight matrix settings)" .

3.2 The value "Number of iteration " is corresponded to parameter "niter " in grid

optimization for local layout (nodes embedded in metanodes). Smaller "niter " is obviously preferred for computation speed but usually results in relatively low quality of layouts ,but too large "niter " is usually not necessary because as the optimization proceeds, better layouts are harder and harder to obtain. To generate satisfied layouts, in practice, the values of "niter " can be set from 8-20.

3.3 Selection of check box "Random color and shape" will mark metanodes with random different colors and shape after running MBL, as shown below.

3.4 "Advance settings (weight matrix settings)" is corresponded to weight matrix in

grid optimization for local layout (nodes embedded in metanodes). The default values are set based on the comprehensive testing, they may not need to be changed. If user need to change them, please make sure the value of "Weight for path of 1" > "Weight for path of 2" > "Weight for path of 3+" and "Weight for path of 3+" be negative.

4 Other feature——Visualize the network having orphan island structure. In biological networks, there are often isolated components or orphan nodes which have no any connections with others and the layout of these components or nodes should be considered carefully. MBL algorithm ranged these nodes automatically in descending order according to nodes number from left to right at the bottom of main graph.