Medical Systems Biology

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AutoScreenBN

Changing internal and external conditions can influence the long-term behavior of the Boolean network model. The perturbation of a Boolean network by stripping a component of the system or simulating a surplus of another component can lead to different attractors. Obviously, the number of possible perturbations and combinations of perturbations increases with the size of the network. Manual screening a set of possible components for combinations, that have a desired effect on the long-term behavior, can be time consuming. We developed a method to automatically screen for perturbations that lead to a user-specified change in the networks behavior.
Simulation of the network under perturbation conditions allows to get a deeper understanding of the dynamics in the Boolean network model. 

 

Downloads : 

  runnable jar-file

  source code

 

Getting Started : 

The downloaded jar file is runnable and can be started by double-clicking. To run the application a java version (JRE) 8.71 or later is required (https://java.com/download/).

After launching the application an example can be loaded by clicking "load example network" in the middle of the window. 
A network model of the mammalian cellcycle and an exemplary simulation setup are loaded.
 
You can also download the example file cellcycle.visibool (Right click and save link as...). In some browsers the file extension might be changed. The file then has to be renamed to cellcycle.visibool again. 

 

For automatic screening for perturbations switch to the exhaustive simulation panel via the simulation menubar. On the right side the attractors of the network are displayed. The button "Perturbation Screening" starts the automatic screening routine. This routine is sperated into three major steps :

  1. Select the desired changes in the long-term behavior of the system. Attractors can be either selected to delete, to be kept or unselected if this attractors is not relevant.
  2. After pressing "Next", choose the maximum number of components to be in the set of perturbations. Below the components that are possible targets for the perturbation can be selected.
    - Grey means normal behavior
    - Red means permanent knock-out
    - Green means permanent over-expression
    - Blue mean knock-out and over-expression is tested in the set (default for perturbation)
  3. After pressing "Next", the components of interest can be selected. The selected components are used for comparison of the long-term behavior.
    Pressing "Simulate" starts the screening process.

Finally, the perturbation sets which show the previously selected effects on the long-term behavior of the network are shown.
By double-clicking a perturbation set of interest the resulting attractors are displayed.
The "Save"-Button stores a log-file with the settings of the perturbation screening and its results.

 

Latest News

Our paper "Inflammatory response of mesenchymal stromal cells after in vivo exposure with selected trauma-related factors and polytrauma serum" has been published in PLoS One.

Our paper "3D Network exploration and visualisation for lifespan data" has been published in BMC Bioinformatics.