Software Tools for Cell and Cognitive Modeling Research


My long term research plans are to build autonomous agents with emotional attributes that move autonomously through a 3D virtual world.
  • My ongoing research into the development of mutable software architectures to implement ideas abstracted from neurobiology are taking form. My progress in these neural code arena can be viewed by clicking here.

    This version is dated 2/15/2001.
  • The first step towards realizing this is to develop a general software architecture for linking together arbitrary computational modules. I have chosen to use typeless graphs for this purpose. The html documentation is now in five parts: tutorial information on writing C and Fortran programs (Volume -1); tutorial information on writing X Window/ Motif applications (Volume 0), how to write classes in C++ and dynamic binding (Volume 1), how to write other classes for abstract data types such as lists (Volume 2), full descriptions of the typeless graph classes (Volume 3) and finally, the use of typeless graphs in constructing dynamic programming objects (Volume 4).

  • If you wish to browse the html tutorial on C/ Fortran programming please click here. This version is fairly old and dates from 1997.

  • If you wish to browse the html tutorial on X Windows/ Motif programming please click here.

    This version is dated 4/13/99.

  • If you wish to browse the html tutorial on class design and dynamic binding please click here.

    This version is dated 4/22/99 and includes some new material on designing matrix applications like simple linear equation solvers using row reduction.

  • If you wish to browse the html tutorial on the class design of other abstract data types such as lists, polynomials using lists and applications such as the Fast Fourier Transform, please click here.

    This version is dated 4/22/99. This version is now closer to completion. I have added exercises for most of the chapters (although they are still very sketchy) and completely redone the documentation on the complex class, the complex polynomials and the Fast Fourier Transform code.

  • If you wish to browse the html document on the design and building of graph classes and the extension of the class to typeless data (void *) please click here.

    This version also includes new material on typeless list objects occuring as an early chapter. Eventually, there will be full coverage of the typeless list classes which will force a rewrite of how some of the typeless graph material is covered.

    I have completely rewritten both the code and the documentation of the graph class for the class methods removeNode() and removeEdge(). These functions use the PtrEdgeBagManip and PtrNodeBagManip classes and some of the class methods in these classes were implemented incorrectly. They have now been rewritten, debugged and run-time examples of their use are included. This version is dated 5/16/99.

  • If you wish to browse the html document on the design and building of the dynamic programming objects using the typeless graph classes please click here.

    This version is dated 3/3/99.

  • The tutorial documents on CORBA programming are currently pretty raw, but they are getting better.
  • If you wish to browse the html document we have written on CORBA programming using ILU, a non standard version of CORBA from Xerox PARC please click here.

  • If you wish to browse the html document we have written on CORBA programming using ORBit, the CORBA C language orb underneath the gnome window manager please click here.

  • If you wish to browse the html document we have written on CORBA programming using Orbacus, a nice CORBA C++ orb please here.

  • If you wish to browse the first html document we have written on our ideas on how to implement plastic software objects that are based on ideas from biological information processing please click here. Now in this document, we pushed the object oriented programming environment of C++ as far as it would go. We learned a great deal from this exercise and we are using our experiences in our new work with CORBA. The new CORBA ideas are quite raw still, but eventually, they will be accessible on the web also.

  • The typeless graph architecture tool will be used to develop agents with emotional attributes. This is ongoing work.
  • The typeless graph architectures coupled with instantiated agents will then be coupled to 3D sprites in a 3D virtual world. This is ongoing work.
    • Author: Dr. Peterson, Mathematical Sciences, Clemson University
    Last Updated: April 30, 2002
    petersj@clemson.edu