Dr. Yang: Data Mining at SFSU, Dr. Puder: Writing AJAX Applications in Java or C#, Dr. Runquist: Web application for Q-Anal, an algorithm for comparative quantitative PCR analysis

Date: 
Wednesday, March 5, 2008 - 17:30
Location: 
TH 331
Presenter: 
5:30 Hui Yang, San Francisco State University, 5:50 Arno Puder, San Francisco State University, 6:10 Elizabeth Runquist, San Francisco State University
Abstract: 
Dr. Yang: Data mining is a relatively new interdisciplinary field in Computer Science. One of its primary objectives is to discover hidden knowledge patterns in datasets drawn from a wide range of domains, such as Web-based information retrieval, retail marketing, drug design, and many scientific disciplines (e.g., physics and biology). Many Data Mining techniques have been developed and successfully applied to a variety of real-world problems. In this short talk, we will first give a brief introduction to Data Mining by identifying key techniques and applications. We will then go over several ongoing Data Mining projects at SFSU. Finally, we summarize this talk by suggesting different ways through which you can be part of the Data Mining team at SFSU. Dr. Puder: AJAX (Asynchronous JavaScript and XML) has become very popular for building web applications. AJAX basically proposes to move part of the application to the browser without requiring a JRE-plugin. In order to do so, the application needs to be written in JavaScript since JavaScript is the lowest common denominator across different web browsers in terms of technical prerequisites. Writing portable JavaScript is a daunting and tedious task. In this presentation I will demonstrate how AJAX can be written in Java or C# which is then cross-compiled to portable JavaScript. Just like a C++-compiler shields the programmer from the assembly language, the framework introduced in this presentation shields the web-developer from the intrinsic complexities of writing cross-browser portable JavaScript code. Our approach is based on a byte-code level cross-compiler that also supports use cases outside the domain of AJAX. Dr. Runquist: We have developed a program, Q-Anal which if a web application is developed will allow researchers in the scientific, medical and diagnostic communities to analyze their comparative quantitative polymerase chain reaction (qPCR) data. The program requires the input of two comma separated values (csv) files; the raw delta Rn csv files exported from the ABI instrument and a user defined csv description file. The proposed web application will allow users to import their raw delta Rn csv files and will provide a ?template? description csv file which the user must complete and then submit with each delta Rn csv file. Once both files are submitted, the application will be required to specify to the program how many points should be used for analysis. After analysis; the application will provide users with results; Q-Anal generates a csv file. This application will allow users to quickly test the program under a number of different experimental conditions so that strengths and weaknesses of the program can establish with the goal of developing an extremely powerful method to quickly analyze q-PCR data by minimizing error.
Bio: 

Hui Yang is an Assistant Professor in the Computer Science Department at SFSU since Fall 2006. She received her Ph.D. Degree in Computer Science from The Ohio State University in the same year. Her main research interests are in data mining and its applications in life sciences, especially, Bioinformatics and Nutritional Genomics.

Arno Puder, currently an assistant professor at San Francisco State University, received his Ph.D. in Computer Science from the University of Frankfurt, Germany. Before joining the faculty at SFSU, he also worked with AT&T Labs and Deutsche Telekom. The founder and maintainer of the Open Source CORBA implementation MICO has special interests including distributed systems, middleware architectures, and ubiquitous computing environments.

Elizabeth Runquist is an adjunct professor and lecturer in the Chemistry and Biochemistry department.