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The CYRENE Project

Our first unpublicized release of the Cyrene cis-Regulatory Browser including the Endo16 gene can be downloaded here.

We are currently preparing to release the full cis-GRN Browser with a lexicon describing the cis-regulatory regions of over 550 genes.

For support in using the cis-GRN Browser, please contact Sorin Istrail.

The guides below walkthrough the annotation of the Snail gene in Strongylocentrotus purpuratus (purple sea urchin).

Annotator's Instructions.pdf
Annotator's FAQ.pdf

CYRENE Publications and Presentations

CYRENE offers robust annotation capabilities.

The cis-Browser and cis-Lexicon are the two core components of the CYRENE project. The cis-Lexicon is a database for all types of cis-regulatory information, with an emphasis on site and module function and logic. The browser is partly a view of the cis-Lexicon, but more fully it is designed as a laboratory for the researcher to use throughout his experiments.

The figures and graphs used in published papers display volumes of information in a small space, and help to communicate many of the researcher's insights into the problem he is studying. As he is performing his experiments, however, this type of view is unavailable. A powerful, visual environment for integrating known genomic information and experimental data would allow him to better formulate new hypotheses for testing in the lab. The cis-Browser is built upon the the Celera Genome Browser, an application developed by a team of programmers over several years with constant input from biologists and ultimately released as Open Source software. The cis-Browser itself is released under the LGPL license, permitting non-commercial modification and use of its source code.

This material is based upon work supported by the National Science Foundation under Grant Number 0645955. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.