This is a short 6.5 week summer course that will be very intense. There are two full lectures a week. You will be required to do three individual assignments requiring a 5-10 page report (single-spaced). You will be required to write an individual term paper about 20 pages (single-spaced). This will require a lot of reading, research on the web, and looking at actual implementations of systems. Plan to spend at least 30 hours per week on this course for every week from July 7 to August 30.
The principal objectives of the course are to survey the needs of bioinformatics for data management, knowledge management, and computational support; to provide in-depth description of an example of each kind of database and system; and to introduce advanced database technology and software technology relevant to the needs of bioinformatics.
Bioinformatics is a relatively new discipline dealing with the computational needs of genomics. Biology has become a data-intensive activity. Genomics databases must deal with this variety and scale, as well they must integrate disparate databases that are their information sources; must provide flexible, friendly user interfaces for querying and data mining; and cope with incomplete and uncertain data.
Information technology must also address the workflow within the laboratory, including the automated analysis of data. Some analysis techniques require significant computational resources, and the management of large-scale distributed computation is an issue.
Bioinformatics: Databases and Systems, editted by Stan Letovsky. Kluwer Academic Press, Boston, 1999. This book is available in Webster Library Reserve.
IBM Systems Journal, volume 40, no. 2, 2001.
Selected journal and conference articles. Selected web sites. Selected software systems, databases systems, their documentation, and implementations.
These are available at an internal web site.
Students are required to complete three individual assignments (60%) and a term paper (40%).
The assignments will be written reviews that critique a particular database or system in the context of other available systems for the task at hand. Each report should be 5-10 pages, single-spaced. They will require detailed knowledge of the systems.
The term paper will concern the design of a specific bioinformatics system. A task will be given to you that will require one or more databases to be designed, together with the application software. You will need to review the available systems for the task. In the term paper, you should select a set of features that are important for the task, write the requirements, and document the design. Use of UML is recommended. The term paper should be 20 pages, single-spaced.
You will have about 2 weeks to do each assignment, and at least 6 weeks to do the term paper. The term paper will be due 1 week after the last lecture of the course.