What's New for Version 2.2

Simulation of Stochastic Flow through Biological Pathways and other Network Systems

BioLayout Express3D now possesses an advanced interface for running Petri net-based stochastic flow simulations through biological pathway models or other networks drawn as bipartite graphs comprised of places, transitions and edges.  The algorithm used is based on the Signalling Petri Net (SPN) algorithm reported by Ruths et al. PLoS Comp Biol. 4:76 (2008) but has been heavily refactored and modified during its incorporation and implementation within BioLayout Express3D.
Input files need to be prepared in the network editing program yEd, and nodes (places), transitions and edges defined graphically using preset standards (see mEPN v2.0 notation scheme).  yEd files saved in the .graphml format are then loaded into BioLayout Express3D.   The following sections outline the next series of windows:
 

Running Simulations using the SPN Dialog

SPN simulation dialog

  1. Define number of time-blocks over which to run the flow simulation
  2. Number of runs on which results will be based (the higher the number the less stochastic the token flow
  3. Options for controlling the degree of inherent stochasticity in the token flow
  4. Type of transition: Consumptive Transitions loose tokens in situations where flow is prevented (prevents build up in situations of constant input); Original Transitions will accumulate tokens at the node prior to transitions where flow is blocked or reduced
  5. Run SPN algorithm
 
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SPN Results Dialog

Results dialog appears following simulation run:

  1. Reports time taken to run simulation
  2. Results can be saved to a text file
  3. Run another simulation
  4. Open animation control (see below)
 
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Animation of Results

Following a simulation run results can be visualised in one of a number of ways.  Firstly, if results have been saved as a text file these may be opened in a tool such as Excel and the results for a given node(s) plotted.  Secondly, following a SPN run the cursor may be placed on top of a node of interest and the results for that node will be displayed as a graph of the number of tokens accumulated over time.  Finally, the accumulation of tokens across the entire network may be viewed as an animation where nodes become larger and change colour as the number of tokens increases (see below).

SPN simulation dialog

  1. Animation of mEPN component nodes only
  2. If specific nodes are selected on the graph the flow through these nodes only will appear animated
  3. Shows node label and token value as text
  4. Flow animation viewed as either discrete steps between runs (as reported in the results file) or as linear or polynomial interpolations of the values between these points
  5. Number of time blocks per second to be animated/starting from
  6. The maximum size of a node when fully loaded with tokens
  7. The token value at which node size is at its maximum (tokens often accumulate on nodes where flow is blocked, hence lowering this value may be necessary to view components of interest
  8. Change colour/spectrum of node animation
  9. Start, pause, step, stop animation.  (note when animation in progress some functions are disabled).
 
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In order to try the new shape editors, open file, select node(s) and click on the ‘Nodes’ tab

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Select 1 for the Model Shape Editor: Lathe3D Shape

Model Shape Editor: Lathe3D Shape [1]

Here shapes can be called upon or created by creating a shape profile that will then be rotated 360 degrees. 
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  1. A range of pre-drawn shapes can be selected from the top pull down menu and further changed depending on the choice in the Lathe3D Type menu directly below
  2. Shape profiles can be drawn (click on window) and the corresponding shape generated from its 360 degree rotation will appear in the main node view window (right)
  3. Stretch the shape on its X, Y or Z axis
  4. Rotate its orientation in the main window on its X, Y or Z axis
  5. View as wireframe, autorotate, view with texture
  6. Save shape as .obj file (can be loaded later using OBL model loader) or in a 3D CAD system
  7. Manipulate the view in the main node view window

 

Model Shape Editor: SuperQuadric Shape [2][3]

Here shapes can be modified using the SuperQuadric topology geometry algorithm. Taking an existing shape the E or N exponents of the SuperQuadric algorithm can be modified to change the shapes appearance.

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  1. A range of pre-drawn shapes can be selected from the top pull down menu and further changed depending on the choice in the Lathe3D Type menu
  2. Shape profiles can be dramatically altered by changing the SuperQuadric E and N exponent values
  3. The V revolution factor and alpha radius (toroid-type only) values will further alter the shape
  4. Stretch the shape on its X, Y or Z axis
  5. Rotate its orientation in the main window on its X, Y or Z axis
  6. View as wireframe, autorotate, view with texture
  7. Save shape as .obj file (can be loaded later using OBL model loader) or in a 3D CAD system
  8. Manipulate the view in the main node view window

 

Model Shape Editor: OBJ Model Loader Shape [4]

Almost any object, person, animal, plant, shape or entity can now be modelled in 3D using 3D Computer Aided Design (CAD) software packages and saved as a file.  These files can now be loaded into BioLayout Express3D and used to define the appearance of nodes.
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  1. A range of 3D models are preloaded that can be selected from the top pull-down menu and the loading size of the model altered below.
  2. Models (.obj files only) can be loaded from an external file.
  3. Stretch the shape on its X, Y or Z axis
  4. Rotate its orientation in the main window on its X, Y or Z axis
  5. View as wireframe, autorotate, view with texture
  6. Manipulate the view in the main node view window
 

References

1. Davison Andrew. (2005). Killer Game Programming in Java. O'Reilly.
2. Metzgar Jonathan. (2000). SuperQuadric Ellipsoids and Toroids. (http://www.gamedev.net/page/resources/_/technical/opengl/superquadric-ellipsoids-and-toroids-opengl-lig-r1172 accessed on August 2011)
3. Barr H. Alan. (1981). Superquadrics and Angle-Preserving Transformations. IEEE CG&A.
4. Davison Andrew. (2007). Pro Java 6 3D Game Development - Java 3D™, JOGL, JInput, and JOAL APIs. Apress.