A Robust User Interface to the Stanford Microarray Database (SDM) M.S. Pilot Adviser: M. W. Berry

1. A Robust User Interface to the Stanford Microarray Database (SDM) M.S. Pilot Adviser: M. W. Berry John Clayton England, III 04/10/2003

2. SMD@UTK File Manger • The Stanford Microarray Database (SMD) • Problems with user file transfer to the SMD • First file transfer solution at UTK • How the SMD retrieves data from the client filesystem • Designing a web based interface • Using the web based interface • Future work

3. The SMD is database that holds genomic data. This data is accessed through a web-based interface. From this interface you can view, analyze, and share data. You cannot upload data from a local machine to the database from this interface. The graphic on the right shows an example of a slide that has been scanned and loaded into the database. The grid on the graphic is over laid on the spots by the user before the graphic is uploaded. Though SMD can also preform this action, it is not as the user defined grid.

4. To get files into the database a user must transfer these files to a filesystem that the Oracle database, the back-end of the SMD, can access. Stanford suggests using a UNIX account to allow these transfers. Problems with using a UNIX account for this transfer: • Users may not be familiar with UNIX file transfers • Ftp, sftp, rcp, scp • Creating and maintaining full UNIX accounts adds over head for the system administrators • User education • Security concerns that arise from local accounts

5. The UNIX account solution has worked for Stanford but they have found the large number of accounts they have to support has become a problem. They have over 500 accounts and maintaining them is beginning to stress the system administrators.

6. Here at UTK we have not given UNIX accounts to the users who use the database. The solution implemented was Zip disk transfers. Meaning the users copy their experiments to a Zip disk and physically hand the disk to the SMD system administrators. User copies file to Zip disk User gives disk to admins Admins load data to client filesystem Data is loaded into the database 1 2 3 4

7. This system works without requiring local UNIX accounts for the users. This was interesting and lead to the discovery that it does not matter what UNIX user owns the files on the filesystem. The database is only concerned with the directory structure in which the files are stored. /<basepath>/<username>/incoming The username above is the only is the only key for the database to know the files owner. With this knowledge a system that did not require a UNIX account could be implemented.

8. Designing a web based interface • A web based interface would require file transfers and filesystem access • PHP does both of these well • Authentication must be addressed • PHP can handle authentication • A simple user interface must be possible • PHP again can fill this need

9. Parts of the web based file manager • Login Page / Authentication • Main Menu • File Uploads • File Lists • File Deletions • File Renaming

10. Authentication A username and password are need to enter the file manager. A perl script is provided to create a password file.

11. Main Menu The main menu is base of the file manager. It leads the user to the other functions of the interface.

12. Uploads From this page users can access local files on their machines and move those files to the database client.

13. File Lists A user can from this page see the files that have been uploaded to the database client.

14. File Deletion From this page uploaded files can be removed.

15. File Renaming Uploaded files can be renamed from this page.

16. SMD@UTK File Manager adding a user demo SMD@UTK File Manager demo

17. Future Work • Adding encryption via SSL • Tying authentication to the SMD authentication • Multiple file uploads

18. Acknowledgments • Comity • Dr. Berry • Dr. Moore • Dr. Becker • Web Services • Colton Smith • John Rose • Bob Hillhouse • Bhanu Prasad Rekapalli • SMD Developers