The following archive contains Khoros/VisiQuest workspaces for image segmentation as described in:
Janssens et al.. A high-throughput method for quantifying gene expression data from early Drosophila embryos. Submitted to Development, Genes and Evolution.
Image Segmentation Workspaces, last updated: Jan 17, 2005.
The following archives contain source code for numerically integrating gene circuit models, for evaluating the least-squares score of a gene circuit compared to data, and for gene circuit optimization by Serial and Parallel Lam Simulated Annealing. The archives also contain Perl and Bourne shell scripts for gene circuit analysis.
This code is written in C according to the POSIX standard. It shold compile and run on any Unix platform, including MacOS X. The code was written and tested using gcc 2.9 - 3.2 under Red Hat Linux.
Documentation can be found within the doc folder of each archive. Documentation is still somewhat, ahem, preliminary. Better documentation should be available shortly. Meanwhile, see comments in the source code for more detailed information.
This code is experimental and under constant development. The authors cannot provide any support of any kind for this code. Use it at your own risk.
Fly Code v9.4 (serial-only version), last updated: Jul 19, 2004.
Fly Code v9.4 (parallel version), last updated: Feb 2, 2004.
The parallel version of the code uses the message passing interface (MPI).
Users of MacOS X will need to have the Apple Developer Tools installed to be able to compile the code.
A web-based simulator (written in Java) is available here.
The following archive contains model & data files for all gap gene circuits published in
Jaeger et al. (2004). Dynamic control of positional information in the early Drosophila blastoderm. Nature 430: 368-371.
Jaeger et al. (2004). Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster. Genetics, in press.
Gap gene circuits, last updated: Feb 2, 2004.
Please send questions, comments and/or bug reports to:
yoginho__odd.bio.sunysb.edu (replace "__" by "@")
Although your feedback is appreciated, we cannot guarantee that inquiries will be answered.