LinMap - A visualisation tool for exploring complex spaces

Nic Geard (nic@itee.uq.edu.au)
School of Information Technology and Electrical Engineering
The University of Queensland

Introduction:

LinMap was developed to enable visualisation and exploration of high-dimensional ontogenetic landscapes.

To run LinMap:
- unzip linmap.zip
- cd LinMap
- java -jar LinMap.jar 

-OR- you may be able to double click on the LinMap.jar file on Windows (?)

IMPORTANT: You must have the Java 5.0 Runtime Environment installed to be able to run LinMap!
(available from http://java.sun.com/javase/downloads/)

Please note that LinMap is primarily research code.  It remains under
continual (sporadic) development.  The file TODO.txt describes several
possible extensions that could be implemented to improve the speed,
functionality and usability of the software.

If you are interested in using or extending LinMap and would like further
information on any design or implementation issues, please feel free to
contact me.


Background:

In several species, the sequence of cell division and differentiation events that occur during embryogenesis are highly stereotyped and have been precisely measured. The ontogeny of these organisms can be represented by a cell lineage diagram: a binary tree in which the root node represents the initial fertilised egg cell, terminal nodes represent the fully differentiated cells that constitute the final phenotype, and non-terminal nodes represent intermediate cellular states.

While contextual information from the environment plays an important role in ontogeny, the key locus of control is the gene regulatory network. We have previously developed a dynamic gene network model of this system as well as a means by which it may be used to generate a cell lineage (Geard & Wiles, 2005a).

One problem with complex genotype-phenotype mappings is that the combinatorial explosion of parameters and variables results in a high-dimensional ontogenetic space that is difficult to visualise and explore. LinMap was developed to assist in understanding the mapping between dynamic network genotypes and cell lineage phenotypes.


Further information:

http://www.itee.uq.edu.au/~nic/_linmap/

Geard, N., (2006). Artificial Ontogenies: A Computational Model of the Control and Evolution of Development. PhD Thesis, School of Information Technology and Electrical Engineering, The University of Queensland. 

Geard, N. and Wiles, J., (2006). Investigating ontogenetic space with developmental cell lineages. In Rocha, L. M., Yaeger, L. S., Bedau, M. A., Floreano, D., Goldstone, R. L., and Vespignani, A., editors, Artificial Life X: Proceedings of the Tenth International Confereonce on the Synthesis and Simulation of Living Systems, pp. 56-62, Cambridge, MA. The MIT Press.

Geard, N. (2006). Visualising complexity: two design patterns. Draft ACCS
Technical Report.

Geard, N. & Wiles, J., (2005). A Gene Network Model for Developing Cell Lineages. Artificial Life 11(3):249-268. 


Acknowledgements:

LinMap makes use of several 3rd party libraries and classes:

* the JGoodies looks and forms libraries.  For convenience, the appropriate JAR files have been included here (along with original licenses).  Full source and documentation can be obtained from the JGoodies website http://www.jgoodies.com/

* the VTextIcon class provided by Lee Ann Rucker; available at http://www.macdevcenter.com/pub/a/mac/2002/03/22/vertical_text.html

* the Gradient class from the Generation5 JDK by James Matthews; available at http://www.generation5.org/jdk/

The design and development of LinMap has benefitted from input from Janet
Wiles, Kai Willadsen, James Watson and Mark Wakabayashi.
