COURSE SYLLABUS Introduction to Bioinformatics, ONLINE! school of allied health and life sciences WELCOME ! COURSE NUMBER: BSC4434/5459 COURSE TITLE: Introduction to Bioinformatics COURSE OVERVIEW: In order to keep pace with recent developments in genomics and proteomics, biology must develop and teach new tools so our students will have the skills to enter this burgeoning job market. As one example, to find out who is hiring, how much you are worth, and online hiring trends, see biohealthmatics.com. Central to these new technologies is bioinformatics, a field that did not exist a decade ago. No one predicted the collision of two fundamental technologies: molecular biology and small fast computers. Biology is now publishing more than 50,000 pages of literature per day. Over 125,000 different genomic sequences have been submitted to the North American GenBank (the world wide repository of genetic sequence information database) IN A SINGLE DAY. 10 years ago there were only two bacteria fully sequenced. Now there are 820 fully sequenced life forms, including 152 eukaryotes (one of which is Homo sapiens), 109 bacteria and more than 550 viruses. We now have full sequences for the mouse, the fruit fly and brewers yeast. Biologists are literally in danger of drowning in their own success. This absolutely necessitates the creation of new tools that allow us to move through all this information and make some sense of it. This requires very fast computers, very clever programming and well educated operators. The field is now known as bioinformatics, and some universities now have whole Bioinformatics Departments offering Ph.D. programs in this area. It has become one of the most sought after degrees by the pharmaceutical industry where all molecular research groups now include one bioinformaticist. Most NIH and NSF grants to universities dealing with sequence information have a similar bias. At UWF, this course is based on a hands-on approach that I hope will develop your interests in scientific discovery.The course is also structured to involve you in meaningful ways with practical (and exciting) aspects of real research in bioinformatics, by showcasing UWF faculty in various modules using computer-based tools to enhance their research. What do former students say about this class? Here is one example: "I listed you as one of my contacts for reference and there is a professor at LSU's Coastal Fisheries Institute and Department of Oceanography and Coastal Sciences that [is] interested in me...his work involves [sic] population modeling. He has told me that his students do a lot of programming and that he is aware of the work that I did in Bioinformatics. I really am glad that I took your class because as it turns out my experiences in that class may help me get an assistantship..." COURSE COORDINATOR: Melanie A. Sutton, Ph.D. CONTACT INFORMATION: http://uwf.edu/content/enforced/61035DEVELOP.MelanieSutton.msutton/importantcourseinformation/mailto:msutton @uwf.edu or (850) 474-2650 School of Allied Helath and Life Sciences, University of West Florida PREREQUISITES OR COREQUISITES: Please see the official UWF Catalog. 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 utilize online tutorial sessions for additional skill development in order to complete programming assignments in the area of bioinformatics for this course. 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. This will be team-based assignment. Although the initial 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 (or your team) 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, public health, or pharmaceutical informatics. COURSE DESCRIPTION: Please see the official UWF Catalog. COURSE OBJECTIVES AND STUDENT LEARNING OUTCOMES: This course meets the following programmatic goals for the Department of Biology, the Interdisciplinary Information Technology-Bioinformation track program, and the MSA-Biomedical/Pharmaceutical track program. Upon completion of this course, students will be able to: o o Integrity/Values: Defend use of the IEEE-ACM Software Engineering Code of Ethics and Professional Practice as it relates to assignements in this course and development of their team-based term project. Project Management: Defend uses of bioinformatics resources, including software, database search engines, and other Internet tools. Defend uses of data mining and data visualization tools in informatics research. Implement computational procedures and algorithms to analyze structures and functions of biological systems and systems related to a term project. Program basic methods for digitizing, storing, processing and displaying information related to informatics applications. Fulfillment of these goals will be assessed through examinations, a set of laboratory exercises (with associated online discussion, quizzes, or other assessment requirements), and completion of a team-based, term project in the area of bioinformatics. For the purposes of programmatic assessment, the following mastery levels will be used: Characteristics of Submitted Student Work and Assignments SKILL MASTERY LEVEL INTEGRITY/VALUES PROJECT MANAGEMENT Exceeds Expectations (Very Good to Excellent) Student consistently demonstrates clarity of Student has a clearly defined sense of the value of thought process, ability to communicate well with biomedical/pharmaceutical research and related ethical team members, and consistently demonstrates issues. Student can articulate and defend arguments with abilities and understanding that surpass expected specificity. average. Meets Expectations (Satisfactory) Student demonstrates adequate awareness of the value of biomedical/pharmaceutical research and related ethical issues. Student can articulate and defend arguments, but lacks some specificity. Below Expectations (Unsatisfactory) Student demonstrates poor communication skills Student does not demonstrate adequate awareness of the with team members or demonstrates a critical value of biomedical/pharmaceutical research and related inability to grasp central concepts, execute ethical issues, or student is unable to articulate and technologies, or think logically to synthesize defend arguments with any specificity. appropriate conclusions. TOPICS COVERED: Student has adequate communication skills and demonstrates basic level of understanding of project management, however, these abilities rarely surpass expectations. Topic Approximate coverage (all 1. Designing and maintaining a course website; Clickable image images 4 hours 2. Beginner's guide to bioinformatics and Perl; Programming strategies 4 hours 3. Representing and reasoning about sequence data 4 hours 4. Recap of Perl constructs; Introduction to searching for motifs 4 hours 5. Practice with subroutines and regular expressions in Perl 4 hours 6. Simulating a DNA sequence by programming randomization 4 hours 7. Creating a reusable Perl module 4 hours 8. Introduction to databases 4 hours 9. Databases: Case studies in informatics-based research 4 hours 10. Database Issues with implementation in Perl 4 hours 11. Term Project Brainstorming, Milestones, and Defense 4 hours ) 12. A professional code of ethics and professional practice for you as a programmer 4 hours Total instructional hours 48 hours total (all ) indicates online course modules that may be completed from home or using UWF computer labs. REQUIRED TEXTS/MATERIALS: Beginning Perl for Bioinformatics by James Tisdall. O'Reilly & Associates. [ISBN: 0-596-00080-4]. Code examples from your book are also available online. (Please note: Text can sometimes be found for as low as $16 on amazon.com.) SPECIAL TECHNOLOGY UTILIZED BY STUDENTS: (beyond baseline requirements of e-mail and word processing) Students are encouraged to complete this course utilizing the equivalent of a cable-speed modem. Completing the course modules via a telephone dial-up connection will require significant download times for larger audio-visual content. REFERENCES/BIBLIOGRAPHY: IEEE-ACM Software Engineering Code of Ethics and Professional Practice See additional links embedded in modules in eLearning. GRADING/EVALUATION: Fulfillment of the programmatic goals described above will be assessed as follows: o o o 60% Examinations (Midterm Exam and Final Exam, weighted equally) 20% Participation (laboratory exercises and associated assessment) 20% Term Project, including Website (team-based) Examinations: There will be a midterm and final exam in the course. These exams will be based on module materials, textbook readings, supplemental readings, laboratory exercises, and the provided on-line resources. These exams will include multiple choice, fill-in-the-blank, short answer, and essay questions. Participation: Laboratory exercises and associated assessment in the form of quizzes or discussion participation provide the hands-on component to the course. In some of these exercises, you will be investigating case studies related to modern informatics applications, exploring research conducted by faculty here at UWF, or learning how to use globally accessible databases or source code. The goal is to motivate you by showing you the excitement of informatics-based projects, while also helping you to develop a better understanding of "good" design and algorithmic development which can impact the larger industrial and research communities. To emphasize the importance and significance of developing your ability to communicate scientific information effectively, participation in selected online forum discussions will be graded using a Discussion Forum Grading Rubric available in the eLearning course. Term Project: Students will be assigned to teams including approximately 45 students per team. 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 (1) defending your Website online and (2) providing professional feedback to your classmates. Information on these requirements will be made available as associated term project deadlines approach. To help you prepare for this assignment, please also review the Term Project Guidelines and Examples document when it is posted, which also contains links to tutorials developed by the UWF Library to help you prepare your abstract and include professional referencing within your paper. Optional Tutorials: Several tutorials will be posted during the first few weeks of the course for those students with limited computer backgrounds. These tutorials will cover how to use eDesktop, common programming errors, how to create a course Website, and how to link assignments on your new Website. Calculation of Final Gade: Due to the distance learning nature of this course, all requirements must be completed within the time scheduled, unless prior arrangements are made with the instructor. Your final grade will be determined by the points you accumulate within each category, divided by the total points available within that category. These scores will then be weighted based upon the percentages indicated above to determine your final grade. On-line facilities will be provided so students can monitor their own progress. The final grade will be on a 10-point scale, roughly: A range = 90100, B range = 80-89, etc., with plus/minus grades as appropriate. EXPECTATIONS FOR ACADEMIC CONDUCT/PLAGIARISM POLICY: Academic Conduct Policy [Web] Plagiarism Policy [ PDF] Student Handbook [ PDF] It is the philosophy of The University of West Florida that academic dishonesty is a completely unacceptable mode of conduct and will not be tolerated in any form. All persons involved in academic dishonesty will be disciplined in accordance with University regulations and procedures. Discipline may include suspension or expulsion from the University. Scholastic dishonesty includes but is not limited to cheating, plagiarism, collusion, the submission for credit of any work or materials that are attributable in whole or in part to another person, taking an examination for another person, any act designed to give unfair advantage to a student or the attempt to commit such acts. In addition, any behavior that interferes with the conduct of a class is classified as disruptive behavior and will not be tolerated. Although not exhaustive, examples of disruptive behavior would include: inappropriate or threatening online postings or e-mails, etc. QUALITY ASSURANCE: This course is reviewed for quality by assessment personnel within the School of Allied Health and Life Sciences (SAHLS) to meet national standards established by the Southern Association of Colleges and Schools and to address quality enhancement initiatives of SAHLS. ASSISTANCE: Students with special needs who require specific examination-related or other course-related accommodations should contact Disabled Student Services (DSS), [email protected]f.edu, (850) 474-2387. DSS will provide the student with a letter for the instructor that will specify any recommended accommodations. Every effort will be made to accommodate the special needs of disabled students. Please inform the instructor privately during the first week of class to indicate your particular needs. All such accommodations are officially arranged through the Office for Disabled Student Services and a letter from this office must accompany your request.