transsys is a formal language for modelling regulatory network
systems conssisting of transcription factors and genes encoding them.
It is developed by Jan
T. Kim, initially at the Institute for
Neuro- and Bioinformatics, and now at the
School of Computing Sciences
of the University of East Anglia.
This site is under constant development. As with biological systems,
development may sometimes take place at some underlying levels of organisation
((the transsys software) without such changes
being reflected by the phenotype (this website). However, major steps
in development will be reflected here, too.
In other words: Please check this site regularly, and also have a
look at the software repository, because, in
a further biological analogy, development is influenced by interaction
with others and the environment, i.e. with you. Therefore, your
comments, suggestions and contributions are highly appreciated.
transsys and its applications is described in these papers:
- Kim, Jan T.: transsys: A Generic Formalism for Modelling
Regulatory Networks in Morphogenesis. In Kelemen, Jozef and Petr
Sosík (editors): Advances in Artificial Life , volume 2159
of Lecture Notes in Artificial Intelligence, pages 242-251, Berlin
Heidelberg, 2001. Springer Verlag.
- Repsilber, Dirk and Jan T. Kim: Developing and Testing Methods
for Microarray Data Analysis Using an Artificial Life Framework. In
Banzhaf, Wolfgang, Thomas Christaller, Peter Dittrich, Jan T. Kim and
Jens Ziegler (editors): Advances in Artificial Life, volume
2801 of Lecture Notes in Artificial Intelligence, pages 686-695,
Berlin Heidelberg, 2003. Springer Verlag.
- Kim, Jan T.: Effects of Spatial Growth on Gene Expression
Dynamics and on Regulatory Network Reconstruction. In Mathieu S.
Capcarrere, Alex A. Freitas, Peter J. Bentley, Coling G. Johnson and
Jon Timmis (editors): Advances in Artificial Life, volume
3630 of Lecture Notes in Artificial Intelligence, pages 825-834,
Berlin Heidelberg, 2005. Springer Verlag.
- Kim, Jan T.: A Rule-Based Approach to Selecting Developmental
Processes. In Stefan Artmann and Peter Dittrich (editors):
Proceedings of the German Workshop on Artificial Life
infix Verlag, 2006, in press.
Some additional technical information is found in the software archive.
The transsys software archive is
Here are some pictures from L-transsys, a
Lindenmayer system enhanced with transsys:
|wild type flower|
|loss of A
||gain of A|
|loss of B
||gain of B|
|loss of C
||gain of C|