Computational
Genomics 2003
Kansas
State University
- REU Announcement (March 2003)
- REU Orientation Workshop Agenda (May 2003)
- REU Tutorials (May - June 2003)
- Introduction to Database Systems by W. H. Hsu - 29 May 2003
- Bioinformatics Data Warehouses and Portals by W. H. Hsu - 04 Jun 2003
- Other Tutorials (May - July 2003)
- McGill University Relational Database Tutorial by W. R. J. Funnell - 29 May 2003
- King's College London DBMS Tutorial by M. Jessop - 29 May 2003
- SUROP Final Presentations (24 July 2003)
- Veronica Blackman
- Molecular Cloning of Oxalate Oxidase and Thaumatin Genes in Oryza sativa - Florence Loo
- REU Presentations (29 July 2003)
- Molecular Sequencing Techniques and An Online Database for Specific Rice Defense Response Genes - John Gu and Brandon Robben
- Cloning and Sequencing Defense Response Genes from Rice and Online Genome Database Design - Veronica Blackman and Alexander Garrett
- Sequencing of Oxalate Oxidase and Thaumatin Genes in Oryza sativa for Bioinformatic Purposes - Florence Loo and Ryan Williams
- Reports (July, 2003)
Host Labs
- Leach Lab
- Laboratory for Knowledge Discovery in Databases (KDD)
- International Rice Research Institute (IRRI)
Sister Program: K-State Summer Undergraduate Research Opportunity Program (SUROP)
Affiliate Sites
- International Crop Information System (ICIS)
- International Rice Information System (IRIS)
- myGrid UK eScience Programme
Online Resources
- Bioinformatics
- Polymerase Chain Reaction (PCR) and Multiplex PCR Guide - Yale University
- Primer3 - Whitehead Institute / MIT Center for Genome Research
- Untranslated Region (UTR) home page - Italian National Research Council, Biomedical Technology Institute
- BLASTn - National Center for Biotechnology Information (NCBI)
- ClustalW - European Bioinformatics Institute (EBI)
- Ensembl Genome Browser - Wellcome Trust Sanger Institute
- Relational Databases (RDBs)
- mySQL
- PHPmyAdmin
Database management system (DBMS) configuration software with graphical user interface (GUI)- Bayesian Network tools in Java (BNJ) - Kansas State University
Graphical models software package with DBMS GUI for uploading/downloading data to and from mySQL
Web Sites Produced and Updated
- KSU Defense Gene Collection (DGC) Portal [new]
- Java Server Page (JSP) edition [under construction]
- DGC data (Excel format)
- Old KSU DGC Web Site [to be updated]
Funding
This REU was supported by a grant from the U.S. National Science Foundation (NSF):
NSF-PGRP-0110154: Research Experience for Undergraduates (REU) supplement to: Inducible Ac elements for activation-tagging and PCR-based detection of deleted genes in rice (J. E. Leach, P. Ronald), Plant Genome Research Program, 15 May 2003 - 31 Jul 2003
Coordinators
- Dr. Jan E. Leach (coodinator) - KSU Department of Plant Pathology
- Dr. William H. Hsu (co-coordinator) - KSU Department of Computing and Information Sciences
- Dr. Richard M. Bruskiewich (off-site collaborator) - International Rice Research Institute (IRRI)
- Roby Joehanes - KSU Department of Computing and Information Sciences
- Patricia M. Manosalva - KSU Department of Plant Pathology
- Marietta Ryba-White - KSU Department of Plant Pathology
Student Participants
- Veronica Blackman - Tuskegee University, Department of Biology
- Alexander Garrett - Kansas State University, Department of Management Information Systems
- John Gu - University of Texas at Austin, Department of Mathematics
- Florence L. Loo - Duke University, Department of Biology
- Brandon Robben - Kansas State University, Division of Biology
- Ryan A. Williams - Kansas State University, Department of Computing and Information Sciences
Photographs
- Group photograph - Thu 24 Jul 2003, SUROP finale and luncheon, K-State Union (Bluemont Room)
[ Full Size (2053x1501, 250Kb) | Medium Size (1027x751, 139Kb) | Small Size (514x376, 46Kb) ]
People pictured (left to right): John Gu, Patty Manosalva, Florence Loo, Veronica Blackman, Marietta Ryba-White, Ryan Williams, William Hsu
Page created: Tue 29 Jul 2003
Last updated: Fri 01 Aug 2003
William H. Hsu
