What is the Clinical and Expression Database?
The Clinical and Expression Database (CED) is a database being developed by Andy Smothers for the labs of Dr. Bento Soares and Dr. Tom Casavant and for the Center for BioInformatics and Computation Biology (CBCB) at the University of Iowa. This database is initially being developed to store and retrieve clinical data and gene expression data in a study of chondrosarcoma; however, the database is being developed to accomodate diverse projects incorporating human disease and gene expression techniques. For more information, contact Andy Smothers.

CED is under development to initially support analysis of clinical and gene expression data relating to chondrosarcoma; however, the project is being developed to support studies relating to diseases as diverse as other cancers and cystic fibrosis. The database currently holds data from human, rat, and mouse and allows analysis of Expressed Sequence Tags (EST) and Serial Analysis of Gene Expression (SAGE) tags. Support for microarray data is forthcoming. Data for the National Institutes of Health (NIH) generated by the Soares and Casavant labs in the CGAP and BMAP projects are also available.

Eventually, complex searches will be available on clinical and expression data allowing users to do complex queries of both of these data sets as well as searches based on results of statistical tests of gene expression data, clinical data, and synergistic data.

Various queries can currently be performed on EST and SAGE data allowing parallel viewing of various data sets.

How do I connect to the database?
The database is available by secure connection at: https://boo.ped-gen.uiowa.edu/chondev/CED. Currently, login is required to access information in the database; however, sample screen shots are available through the images to the left.

Presentations based on CED (all in PDF format):

• Expanded Casavant Lab Presentation November 14, 2003
• Casavant Lab Presentation November 10, 2003
• NCI caBIG pre-Presentation August 25, 2003
• Casavant/Soares Lab Presentations May 12, 2003
• Joint BioInformatics Workshop 2003
• Casavant Lab Presentation October 21, 2002
• Joint BioInformatics Workshop 2002

What tools general tools are used by the database?

• Apache
• PostgreSQL
• PHP
• JPGraph
  

What system currently hosts the database?
The system uses standard libraries that should function well on any Unix or Linux platform. The database currently runs on a dual processor (1.0 GHz) PowerMac G4 with 1.5 GB of memory running Mac OS X 10.3 (Panther).

Contact Information for CED:

Andrew Smothers
Genetics PhD Candidate
University of Iowa
4156 MERF
Iowa City, IA 52242
319-353-5753
andrew-smothers@uiowa.edu