A Web-based Microarray Experiment Management System

1. A Web-based Microarray Experiment Management System Yan Xiong Advisor: Prof. Meiliu Lu Department of Computer Science California State University Spring 2002

2. Agenda • Background • PHP • Project • General Design • Detailed Design • Conclusion • Future work • Reference

3. Background -- PHP • What is PHP? • A server-side scripting language designed specifically for the web to generate dynamic web pages. • History of PHP • Conceived in 1994, by Rasmus Lerdorf. • V1 & V2: 1995; V3: 1997; V4: 2000 • PHP Present • Growth rate 15% /month, in use in 7 million domains.

4. Background -- PHP • Some of PHP’s strengths: • Broad functionality for databases, strings, network connectivity, file system support, Java, COM, XML, CORBA, WDDX, and Macromedia Flash. • Native connections to many databases: • MySQL, Oracle, SQL server, Sybase, PostgreSQL, mSQL, dbm, FilePro, Informix, InterBase, Hyperwave, etc • By using ODBC, it connects to more DBMS such as MS Access. • Learning • Simple Syntax, based on C and Perl.

5. Background -- PHP • Some of PHP’s strengths: • Portability: Platform independent • Available for many operating systems: • Different versions of Microsoft Windows; Many version of Unix; QNX, MacOS(WebTen), OSX, OS/2 and BeOS. • Work with any fully-functional Web Server: • Apache, IIS (Microsoft Internet Information Server),etc. • Source code • Open source. Do not need to wait for manufacturer to release patches. • Cost • Free. Download the latest version at any time.

6. Background -- PHP • PHP’s main competitors: • Microsoft active server pages (ASP) • Allaire cold fusion • Perl • Java server pages (JSP)

7. Background -- PHP • Comparison of PHP with other scripting languages: • PHP vs. ASP • ASP generally slower (COM based architecture). • ASP is mostly run on IIS. Versions for Unix-cost high. • PHP vs. Cold Fusion • Cold Fusion only available on Win32, Solaris, Linux, HP/UX. • PHP initially requires more programming knowledge in contrast with Cold Fusion. PHP is less resource intensive. • PHP vs. Perl • PHP is designed specifically for web and it is easier to integrated into existing HTML. • PHP vs. Java • PHP is simpler to use than java. • PHP does not have some nice features such as object pooling or database mapping as in Java. Expected in new engine design.

8. Background -- Project • Goal of the project: • To build a dynamic web-based microarray experiment management system. • What is microarray? • A technique that provides powerful insights in to gene expression. • www.google.com search “gene chips”.

9. Background -- Project • Current practice of Microarray service: • Expensive. Usually a centralized service. • Involve hundreds of CD making, traditional postal distribution, many phone inquiring and paper work to keep track of each experiment. • A web-based microarray experiment management system: • Improves the accessibility of microarray facility • Speed up functional genomics research • Easy to keep track, with use of Database driven web system

10. General Design -- System • Involves four open source components: • an Apache Web server • PHP for interfacing to the database • MySQL database • Linux operating system. • This system is compatible with all major web browsers.

11. Affymetrix Server General Design Work Station Work Station User Menu Admin Menu Web Server Gene Chip Management User Management Request Management Result Management MySQL Database

12. Detailed Design -- Work Flow Analysis

13. Detailed Design – Database ER Diagram

14. System Functions • Two groups of functions: • Administrator URL: • manage users • monitor all experiment requests • edit experiment status • upload experiment results from Affymetrix GeneChip array machine • summery generating • User URL: • sign up • experiment-request submission and validation • experiment status checking • experiment result download

15. New Group Approve/ Disapprove 1.Process Pending Request New User New Exp 2. Group Management Add/Edit 3. User Management Add/Edit Login 4. Experiment Management Add/Edit/Delete Upload/Download /Delete 5. File Management 6. Chip Management Add/Edit 7. Summary Reports Detailed Design – Admin(1)

16. 1.1 New Group Approve/ Disapprove 1. Process Pending Request 1.2 New User 1.3 New Exp Detailed Design – Admin(2) Approve: *Move Request from Queue to Permanent Tables. * Create a directory in server for this Group/User * Send Information Email to P.I./P.I.& user, along with password. Disapprove: * delete Request from Queue. * Send Email to P.I./P.I.& user

17. Upload/Download /Delete 5. File Management Detailed Design – Admin(3) Upload: * Upload result files of a specific request from Affymetrix server to web server. * Insert a new record in database about the file name and path. * Send informing emails to PI and user . Download: download the result file from the web server to local machine. Delete: * delete file name and path from database * delete file from web server

18. 6. Chip Inventory Management Add/Edit Detailed Design – Admin(4) * Display a table showing gene chip type, total number of purchased, used, pending, available. * A small page for Admin to update total chip when there is a new purchase. * Other information calculate from database table about samples.

19. 7. Summary Report Detailed Design – Admin(5) * Generate tables showing: How many chips are used in a certain period? Average turn around time per experiment. Total number of sample analysis requested. Total number of users, groups and experiments

20. S1.Modify Group Information S2. Modify User Account Login S3. Exp Request 1. New Group Register S4.View Exp and Down Load Result 2. New User Register Detailed Design – User(1)

21. Detailed Design – User(2) 1. New Group Register 2. New User Register * Group Register: Provide a series of information about the research group. Request needs to be approved by system Admin. * User Register: Must belongs to a group. Request needs to be approved by PI and system Admin.

22. S1.Modify Group Information S2. Modify User Account Login Detailed Design – User(3) S1: Modify Group Information: Only Group PI can do it. S2: Modify User Account: Modify User’s name, email, password, etc.

23. Detailed Design – User(4) S3. Exp Request Login S3:Exp Request Enter general exp information Enter sample information Enter sample analysis information Request will be in pending state until both PI and Admin approved it.

24. Detailed Design – User(5) S4. View Exp and Download results Login S4:View Experiment status, information, and download results A table show all exp that the login user has submitted. A table show downloadable result files. If Login person is PI, he can see all exp and result files in his group.

25. Detailed Design -- Admin URL View

26. Detailed Design -- User URL View

27. Conclusion • Combination of PHP, MySQL database server, Apache web server and Linux makes an efficient and cost effective application server. • Gain valuable experience working with biologists. • Good experience of learning through real world projects and solving a practical problem at the same time

28. Future Work • Expend current project to provide more functions such as : • development of tissue database, clinic trails database to keep track of cancer survivors, and data integration to assist doctors in profiling hospital patients • More solid web management capability

29. REFERENCES • Linux, http://www.linux.org • Apache, http://www.apache.org • MySQL, http://www.mysql.com • PHP, http://www.php.net • PHP tips and tutorials www.phpbuilder.com

30. Acknowledgement • Many thanks to Prof. Lu and Prof. Smith • and other students and friends.

31. Submit Experiment Request – Step 1

32. Submit Experiment Request – Step 2

33. Submit Experiment Request – Step 3

34. Submit Experiment Request – Step 4

35. Submit Experiment Request – Step 5

36. View Request/Download Result

37. Admin--Pending Request

38. Admin—Sample Status

39. Admin—File Management

40. Admin—Chip Inventory