Introduction to Bioinformatics

• Text(s):
  • Beginning Perl for Bioinformatics by James Tisdall. O'Reilly & Associates. [ISBN: 0-596-00080-4]. Code examples from your book are also available on-line. (Please note: Text can sometimes be found for as low as $16 on amazon.com.)
  • Course material from other textbooks will be provided in class.
• Course Website: The on-line course WWW site supplements the text, with relevant links to labs, hands-on assignments and other laboratories conducting research in bioinformatics. Keeping current on the Web material throughout the semester is an important part of the course.
• Global Websites: Leading university/government bioinformatics centers, such as:
  • National Center for Biotechnology Information
    
• UWF Library: Additional supplemental readings will be provided on reserve at the UWF library.

Your term project will encompass the implementation of a practical application in the emerging field of bioinformatics, utilizing your research/experimental design and numerical analysis/modeling skills. Although lab examples will be in the area of genetics, the course sequence PCB 3063/PCB 3063L: Genetics is not a required prerequisite for this course unless you wish to develop a project in this area. Alternately, students in previous semesters have applied the skills developed in this class to create successful projects encompassing the subfields of ecological, medical, or public health informatics.

Computer phobic? Think again ...

No prior knowledge of programming is required as a prerequisite. Students will be taught programming basics in the course and will also have the opportunity to attend tutorial sessions for additional skill development in order to complete programming assignments in the area of bioinformatics for this course.

The course has been designed with the following major course modules:

• Lectures

  Traditional lecture-style instruction will account for approximately 2.0-2.5 contact hours/week. We will also have 1-2 invited scholars or graduate students discussing their research projects in the field of bioinformatics.

• Tutorials:

  Several tutorials will be scheduled during the first few weeks of class for those students with limited computer backgrounds. These tutorials will cover how to log in and use your computer account and how to post assignments on the WWW.
  
  

• Programming Labs/Discussion

  Laboratory exercises and discussion group meetings will account for an additional 0.5-1.0 contact hours/week. These assignments provide the hands-on component to the course and will be completed utilizing UWF's computer labs. You may find it convenient to use other facilities for project development, however, you must ensure that your assignments run successfully under the UWF environment, as that is what will be graded. In some of these assignments, you will be investigating case studies related to modern biomedical applications. Furthermore, projects involving globally accessible databases or source code will (hopefully) help you to develop a better understanding of "good" design and algorithmic development which can impact the larger industrial and research communities.

• Term Project

  Part of your course grade will be based on the development, implementation, and presentation of your term project. A list of possible topics in bioinformatics will be provided, and project brainstorming and milestone discussions will be scheduled throughout the semester. All final projects will be presented as Websites, and you will be taught basics of Website design in a course lab. Part of your grade for this component will include providing professional feedback to your classmates.

• Tests

  Tests will be based on lecture material, supplemental handouts, laboratory exercises, and the provided on-line resources. The test materials will include multiple choice, fill-in-the-blank, short answer, and essay questions that take into account the varied background and knowledge of the enrolled undergraduate and graduate students.