Oscill8 = Bifurcation²

Official SourceForge project page

Documentation for v1.12

User Features:

• Time course/integration (using CVODE)
• Multiple time course generation (incrementing parameters, etc)
• One parameter bifurcation diagrams (batch mode, several parameters)
• Two parameter bifurcation diagrams (batch mode, several parameters)**
• Bifurcation searches (subsequent restart available)
• Organization of output, including:
  • notes for each run
  • analysis on subsets of parameters
  • graphical output is stored with model and state

Developer Features:

• C++ library version of AUTO2000 (which can be used separate from Oscill8)
• C++ library version of Oscill8: API interface, easy XML file run control
• Rapid prototyping/testing interface (very easy to add features and test)
• Can be run on a server and accessed from anywhere
• Runs on Windows, Linux, Mac OS X**

Why, you ask, is it "Bifurcation²?" Well, the goal of this tool is to allow a user to concentrate less on the details of bifurcation analysis, and more on the results obtained from that analysis. When dealing with models containing a large number of parameters, you need access to large amounts of graphical data revealing the bifurcation behavior of the model, and you need to be able to get this data rapidly. For most applications, the analysis is routine and shouldn't require user interaction with the software. Naturally, there are interesting systems that can't be analyzed without understanding a great deal about the mathematics involved and how to set and run the tool correctly, but this is not the typical case for biological models for much of the process.

Of course, any useful bifurcation tool should also expose the lower level, numerical control parameters to the expert user, and this is something that is include as well. There is a "raw" AUTO interface to satisfy the zealot!

The first official release will be made in Q1 2005. The old web interface has been replaced by a brand new .NET (and hopefully Mono or DotGNU very soon) interface written in C#. Click here to download from Source Forge.