[[public.kgi.edu/~fbergman]]

3D Simulation Viewer

2007-01-23 Update: Ok ... good news, the Qt Viewer now makes the modification of parameters possible. This lead me to modify the SBML a little bit though, all local parameters will be promoted to global parameters. This obviously will not be to the liking of everyone, as now you see a whole bunch of parameters appearing all the time. So I will quickly add some mechanism to filter the view for parameters that are of interest.

2007-01-18 Update: Finally the current version is able to modify the species concentrations. Also worked a little bit better on preserving settings from previous settings. A new version will have to wait for a little while, until i figure out how to best change the parameters. Here some screenshots though, that demonstrate how the dock dialogs changed today, hope to get some feedback soon (As far as I'm concerned the new version works out much better):

• Old Version : Screenshot 1, Screenshot 2
• New Version : Screenshot

2007-01-17 Update: Work on the Qt Version is progressing nicely. Just thought to put some more videos up, that show that I finally solved the reaction rate scaling issue. Finally the reaction rates are displayed so that, the faster reactions appear faster, and slower reactions slower. Here have a look at the JanaWolf model illustrating that (DIVX codec required):

Video of the JanaWolf Model #1 and Video of the JanaWolf Model #2

On Second thought, here a youtube version:

2006-12-21 Update: Good news, with an update to the layout generation tool, it now is much more appealing, to watch the flow for autogenerated graphs. If you compare today's video of Biomodel #12 to yesterdays, you will see, that now finally the flow observes the right direction. Unfortunately I noticed the same problem for the importer of models from JD1, so this is what will be fixed next.

2006-12-20 Update: It has been some time since the last update of this site. By now all dependency modules of hte 3D Tool are heavily used by many other SBW enabled applications. Thus the installer has changed to not install them by default. Future versions of the installer will no longer distribute these modules, as they have become part of the main SBW installation. New too, is a Qt frontend to the 3D Tool, that is still in development. More information about that is to come soon. The actual 3D tool is also again in development. This time around I look for interesting ways to display flows. Here my first attempts (DIVX codec), the singleGene network seems to work fine (have a look at the singleGene-video) on the other hand the BioModels #12 video shows that there are still issues to work on.

2006-06-25 Update: There have been continuous updates to all the tools. So let me just mention the most recent ones: The 3D Viewer can now run in two modes. The first mode, as before takes an SBML file and simulates it continuously using roadRunner. The second one allows to replay time-series data (in CSV or BioSPICE timeseries format.).

This new structure made it necessary to redesign the 3D Launcher. It now looks like this:

This modified version allows to obtain the simulation data either by continuous time course simulation as before or by specifying the time course data to be used. It should be noted that the time course data can also be generated by one of the installed SBW Simulators.

As the 3D Launcher is currently not yet portable (but i keep my faith in the mono-team) it is possible to export the settings to a set of configuration files (using the export button). These config files are then sufficient to run the linux or mac osx version of the 3D Viewer. Although it should be noted, that the files have to be modified using dos2unix, and the paths in the .config3D file have to be modified. But i hope to revise the process soon. For the time being just invoke the Simulate3D program with the command line switch:

		./Simulate3D --config <config3Dfile>

and everything should be running fine. As I don't have a fast linux box here I use VMWare to test my linux code. Which is suboptimal for 3D graphics. Anyway ... here a couple of screenshots how the 3D tool works on Fedora Core 5 and Ubuntu 6.06.

I also recorded two very short movies demonstrating it running on FC5:

• Simulating Feedback.xml
• Simulating p53 and Glycolysis

Again the videos are of poor quality as the tool is running on a virtual machine. As can be seen in the screenshot and videos I finally added some playback buttons. These allow to control the playback of the timeseries data. If you care to try the tool on your machine you first have to install OpenSceneGraph on your linux box. Fedora and Ubuntu make it easy with their package tools. After that is done you just need these files to have it running:

• Instructions on how to use the tool.
• The binaries (compiled for FC5 (tar.gz))

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2006-02-26 Update: This version contains again updates for all modules: the simulator is more stable, the layout algorithm adheres to compartments, and the 3D Viewer runs on slower systems.

2006-02-02 Update: The new version removes threading issues of previous versions along with a different auto-layout tool.

2006-01-27 Update: A new version is online containing a more stable simulator, also the SBMLLayout viewer has been updated so as to only render when necessary ... thus the overall speed has improved.

2005-12-01 Update: I just uploaded a new version of the 3D Simulation viewer. Now even with an optional Screen Saver mode. On the more serious side Configuration parameters have been added. Most important the texture size parameter that allows you to determine how large a texture your model should get.
NOTE: I allow to specify any parameter ... although reasonable choices are << 4k. The default is 1536 pixel and most graphics cards seem fine with that. If you don't see a texture please reduce this value.

I finally got around to work with 3D graphics again. This tool uses several SBW Modules in the following scenario:

• Ana's Network tool:
  This tool creates a layout for networks that don't contain a Layout in form of the SBML Layout Extension or JDesigner Layout specification.
  
• SBML Layout Viewer:
  This tool displays SBML Models with SBML Layout Extension / JDesigner Annotations. This tool provides on the SBW side of things methods to interrogate the SBML Layout, or to create a SBML layout for a SBML model.
  
• RoadRunner:
  This is a beta version of a new Simulator developed by Herbert Sauro. This Simulator compiles the information contained in the SBML and is so able to simulate very fast. RoadRunner uses KinSolve and CVODE.
  
• 3D Simulator:
  The application depicted below allows to load a SBML model, preview it's current layout and to generate a new layout. After a click on 'run' this model will be rendered and simulated:
  
  
  • initial time step: 0.05 (change using the 'HOME' or 'END' key)
    the step size will integrate how large a timestep the integrator will take
  • initial scale factor: 1 (change using the 'PGUP' or 'PGDN' key)
    the scale factor allows to make species concentration visible by scaling the concentrations.
  • initial sleep factor: 50ms (change using the '.' or ',' key)
    the sleep factor determines the sleep time between two time steps.
  • The 'Esc' will end the 3D visualization mode.

  Installation:

  • Install the .NET Framework 2.0
  • Install SBW
  • Install Simulate3D

  Availability: Currently this test version is only avalable for Win32. The programming languages used where C/C++ and C#. At least the C++ side will be available soon for OS X (10.4) and Linux within the year. The C# code should soon run fine on Linux using Mono. The Mac version of Mono might actually take a bit longer until graphic issues are resolved.