a robust user interface to the stanford microarray database (sdm) m.s. pilot adviser: m. w. berry

SMD@UTK File Manager

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

John Clayton England, III04/10/2003


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


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 graphicis uploaded. Though SMD can also preform this action, it is not as the userdefined grid.


To get files into the database a user must transfer these files to a filesystemthat 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


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


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 theSMD system administrators.

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1.User copies file to Zip disk2.User gives disk to admins3.Admins load data to client filesystem4.Data is loaded into the database


This system works without requiring local UNIX accounts for the users. Thiswas 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 knowthe files owner.

With this knowledge a system that did not require a UNIX account couldbe implemented.


●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

Designing a web based interface


Parts of the web based file manager

●Login Page / Authentication

●Main Menu

●File Uploads

●File Lists

●File Deletions

●File Renaming


Authentication

A username and password are need to enter the file manager.

A perl script is provided to create a password file.


Main Menu

The main menu is base of the file manager. It leads the user to the otherfunctions of the interface.


Uploads

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


File Lists

A user can from this page see the files that have been uploaded to thedatabase client.


File Deletion

From this page uploaded files can be removed.


File Renaming

Uploaded files can be renamed from this page.


SMD@UTK File Manager demo

SMD@UTK File Manager adding a user demo


Future Work

●Adding encryption via SSL●Tying authentication to the SMD authentication●Multiple file uploads


Acknowledgments

●Comity

●Dr. Berry

●Dr. Moore

●Dr. Becker

●Web Services

●Colton Smith

●John Rose

●Bob Hillhouse

●Bhanu Prasad Rekapalli

●SMD Developers

a robust user interface to the stanford microarray database (sdm) m.s. pilot adviser: m. w. berry

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