In constructing the Endomesoderm Network, the Davidson Lab, together with the Bolouri Biocomputation Group and the Wold Lab, has adapted or developed several software packages. Please investigate the links below for details on these software packages.

The Davidson Lab & our collaborators are continuing to work on these packages. If you would like to be informed as new tools become available and as old tools improve, please subscribe to the TOOLS mailing list. This is used only for announcements.

The following software is described in Brown et al., New Computational Approaches for Analysis of cis-Regulatory Networks. (Dev Biol. 2002, in press.)

BioArray is a Windows program for analyzing macroarray spots.

SUGAR, the Sea Urchin Genome Annotation Resource, is a locally adapted version of Genotator, a large BAC annotation tool. It runs on UNIX systems and requires Perl and Tk.

SeqComp and FamilyRelations are a pair of programs for comparative sequence analysis. SeqComp is a batch analysis program that runs on UNIX systems, while FamilyRelations is a graphical user interface program written in Java and is cross-platform.

NetBuilder is a Windows package for constructing mixed, qualitative and quantitative logical models of Genetic Regulatory Networks.

We are also working on several software systems that have not been released yet.

Cartwheel is a bioinformatics applications infrastructure and developers toolkit that connects (among other programs) SeqComp and FamilyRelations. While it is not yet released, it is in active use at Caltech by several labs, and can be made accessible upon request (contact Titus Brown).

SUGARv2, a new version of SUGAR that is based on FamilyRelations and Cartwheel, is also under development.

GeD, an experimental platform for generic model organism genome databases, is being developed for the Sea Urchin Genome Project.

SUGAR and BioArray were developed in collaboration with the Bolouri Biocomputation Group at the University of Hertfordshire, under the supervision of Dr. Hamid Bolouri.

SeqComp and FamilyRelations were developed in collaboration with the Wold Lab at Caltech, under the supervision of Dr. Barbara J. Wold. The Wold Lab is also contributing to the development of Cartwheel.

People:

• C. Titus Brown (Davidson Lab) wrote FamilyRelations and Cartwheel;
• Peter Clarke (Bolouri Biocomputation Group) extended and maintained SUGAR;
• Tristan De Buysscher (Wold Lab) wrote SeqComp;
• Zhengjun Pan (Bolouri Biocomputation Group) wrote BioArray;
• Alistair Rust (Bolouri Biocomputation Group) adapted Genotator for our use (SUGAR);

  and

• Maria Schilstra (Bolouri Biocomputation Group) wrote NetBuilder.