|
|
 |
|
| |||||
|
|||||
Alliance Information Management System
(AIMS)
San Diego Supercomputer Center
University of California at San Diego
San Diego, California
The primary mission of the Alliance for Cellular Signaling (AfCS) Data Management, Analysis, and Bioinformatics Laboratory is to define, design and implement the Alliance Information Management System (AIMS). This system will allow the acquisition, analysis, and storage of data from AfCS laboratories. The Bioinformatics Laboratory has created a relational database management system (Oracle-based) for the experimental data that the AfCS will generate. Bar coding is an important component of data management, and we have established a system that will provide a history and profile for experimental data and will facilitate sample handling, material transfer, quality control, and data validation for all samples. The lab is also working to display primary and processed information on the AfCS Web site. For this effort, the lab will develop ontologies for the creation and storage of various types of data, including protein sequence and functional annotation, cell preparation, gene array, proteomics, cell based and molecular assays, and microscopy. The Bioinformatics Laboratory will continue to analyze yeast-two hybrid data generated through collaboration between the AfCS and Myriad Genetics iin order to reconstruct intracellular signaling networks. Researchers will be able to query and analyze all of the data from the AfCS/AIMS Web site (http://www.signaling-gateway.org).
The Bioinformatics Laboratory is also creating a management system for a literature-derived signaling database. The AfCS Web site currently contains a list of more than 3600 proteins of interest to the signaling community. The list has been incorporated into an Oracle database with a query interface accessible via the Web. Each protein on the list is linked to a Mini-Molecule Page (where available) and will ultimately be linked to a full-length Molecule Page. Molecule Pages will be written by the AfCS Membership and will be peer reviewed. They will contain an exhaustive set of data about all aspects of the subject molecule. Proteins on the list will also be linked to pathway maps, the Biology Workbench, the Riken mouse sequence, and Blast results from sequence blasts stored in the database.
The Bioinformatics Laboratory anticipates that the combined use of the AfCS experimental and literature-derived databases will lead to the identification of signaling modules. It will ultimately be possible to model signaling pathways in terms of the component modules. This will enable us to achieve the overall goal of the AfCS—to understand fully how cells interpret signals in a context-dependent manner.
Alliance for Cellular Signaling
Data Management, Analysis, and Bioinformatics Laboratory
San Diego Supercomputer Center
9500 Gilman Dr.
La Jolla, California 92093
Phone: 858-822-0986
Fax: 858-822-3752
| Director | Shankar Subramaniam, Ph.D. |
| Project Coordinator | Bob Sinkovits, Ph.D. |
| Software Engineer | Brian Saunders, Ph.D. |
| Systems Administrator | Brad Kroeger |
| Webmaster | Stephen Lyon |
| Database Administrator | Ray Bean |
| Database Programmer | Joshua Li, Ph.D. |
| Database Programmer | Yuhong Ning, Ph.D. |
| Research Programmer | Madhusudan, Ph.D. |
| Research Programmer | Warren Hedley |
| Research Programmer | Ilango Vadivelu |
| Research Programmer | Stuart Johnson, Ph.D. |
| Research Programmer | Jingwei Meng, Ph.D. |
| Research Programmer | Sylvain Pradervand, Ph.D. |
| Research Programmer | Andreia Maer, Ph.D. |
| Research Programmer | Yi-Xiong Zhou, Ph.D. |
| Principal Statistician | Dennis Mock |
| Administrative Assistant | Jan Lenington |
| Consultant | Timo Hannay, Ph.D. |
| Consultant | Nicole Tindill |
|
|
|
|
HOME |
SIGNALING UPDATE |
MOLECULE PAGES |
DATA CENTER |
ABOUT US |
STAFF
|
|
