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Coastal Carolina University Spring 2019Phage Bioinformatics Syllabus BIOL 302L Q

Phage BioinformaticsBIOL 303 2 creditsMonday, Wednesday & Friday 11:00 - 12:25 KESH 221Instructor and Office HoursDaniel C. WilliamsKenneth E. Swain Hall (KESH) 231dwilliams@coastal.eduphone 843.349.6566OFFICE HOURS HERECourse Description (from the CCU Undergraduate Catalog)BIOL 303 Q - Phage Bioinformatics (2 credits) Prereq (BIOL 302L, or permission of instructor) Phage Bioinformatics is the second semester in a sequence of inquiry courses designed to provide entry-level science students with an extensive classroom-based research experience. Throughout the semester, students will use a number of bioinformatic tools to annotate the genome of a phage obtained during Phage Discovery. In the process students learn about phage biology, gene structure, and genome organization. Completed genome annotations will be deposited in a publicly available DNA sequence database. Spring Course Objectives and Instructional ContentThis course will familiarize students with the use of multiple bioinformatic tools involved in the annotation of phage genomes. Students will become proficient in the use of these tools and how they are applied to analysis of DNA sequence data, gene structure, and genome organization. During the semester students will complete a genome annotation of novel phages that were previously discovered by CCU students. Students will experience the rigors, challenges, and achievements that accompany scientific research, as well as the satisfaction of making a significant contributions to the broader scientific community.Student Learning OutcomesSLO 1: Students will demonstrate the knowledge and skills obtained through participation in experiential learning activities that are relevant/pertinent to their academic programs and/or career goals.SLO 2.1: Students will demonstrate a high level of comprehension and skill in connecting theory with practice which is correlated to their level of participation in experiential learning activities.1. Competently use basic bioinformatic tools (DNAMaster, Phamerator, GeneMark) to create

preliminary genome annotations. 2. Apply basic understanding of viral transcription and translation to identify open reading frames and

support predictions of start codons.3. Predict phage gene functions based on homology using BLAST and HHPred.4. Pose and investigate a valid scientific question related based on annotation predictions and

understanding of phage biology5. Present outcomes of an independent research project.

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Coastal Carolina University Spring 2019Phage Bioinformatics Syllabus BIOL 302L Q

Grading ProcedureThe above learning outcomes will be assessed using the following metics. weights. Final grades will be determined according to the following weights using a standard 90/80/70/60 = A/B/C/D scale.

Participation 30% Weekly annotation tasks 30% Peer annotation reviews 20% Poster production and presentation 20%TOTAL 100%

Participation:Students are expected to be prepared and participate in all class activities. During Phage Bioinformatics, you will be working toward annotating the genome of a novel phage. There is an expectation that we will collectively be able to submit a finished product by the end of the semester. Completing the genome annotation can only be accomplished by your work and participation in all aspects of this class. Attendance is mandatory for each and every class period!! Excused absences will be allowed with prior notification and proper documentation as discussed below.Annotation tasks and reviews:On a weekly basis, students will be tasked with a number of genes that need to be annotated, which will make up the bulk of this course. In addition, others will be reviewing your work (and you will be reviewing others) as a check to ensure we are collectively producing high quality work. You will be evaluated on completion of these annotations and reviews for completeness and documented evidence to support your gene predictions.Poster production and presentationPart of the scientific process is communication and the dissemination of newly obtained information. By the end of the semester, we will have annotated a genome and made some discoveries about a phage that was discovered at CCU. To present this to the larger community, students will be making scientific posters and then presenting them at the annual Undergraduate Research Symposium at the end of the semester. Specific guidance on making posters and presenting your will be discussed in class.

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Coastal Carolina University Spring 2019Phage Bioinformatics Syllabus BIOL 302L Q

Text and Required MaterialsStudents will need access to the SEA-PHAGES Bioinformatics Guide, which is completely online and freely available at:https://seaphagesbioinformatics.helpdocsonline.com/homeAttendance PolicyUniversity policy indicates that students are obligated to attend class regularly. Absences, excused or not, do not absolve a student from the responsibility of completing all assigned work promptly. The attendance policy of this course will adhere to University policy, https://www.coastal.edu/policies/pdf/acad-125classattendance.pdf.Institutional PoliciesCoastal Carolina University is committed to equitable access and inclusion of individuals with disabilities in accordance with the Americans with Disabilities Act and Section 504 of the Rehabilitation Act. Individuals seeking reasonable accommodations should contact Accessibil ity & Disability Services (843-349-2503 or  https://www.coastal.edu/disabilityservices/).Open CommunicationOne of the best ways of contacting your instructors (other than during office hours) is via email. I will do my best to respond to emails within 24 hours. Any electronic communication will be via your official university email account. In addition, I have an open doo policy in my office and research lab, please feel free to stop by anytime to discuss specifics of this course or anything else. Dr. Williams’s Teaching PhilosophyAt the end of an undergraduate career, students should possess the following: (1) a body of knowledge within and relevant to their major, (2) the capacity to think deeply and critically, (3) the ability to work as part of a group, and (4) intellectual curiosity about the workings of the universe. My goal as a teacher is to work with you and develop readings, assignments, activities, and assessments that facilitate development of these attributes. Your responsibilities include active participation in course activities and discussions, preparation for each class, reflection on the topics covered, and diligent work in class. Success in this class is dependent on demonstration of real learning and your progress toward the success criteria described above.Getting helpIf you have a qualified disability and require accommodations, please let your instructor know as soon as possible. Moreover, please communicate early on if you are having difficulty in this course - donʼt wait until the day before an assignment to come for help. Stop by my office, send an email message, call, or set up an appointment with me. I am here to help you learn to become a better scientist! Another great means of getting help is to ask questions in class and discuss things with your bench mates. If you are unsure about something, it is likely that your colleagues are uncertain as well. I highly encourage using the classroom time to ask and discuss questions you might have.

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Coastal Carolina University Spring 2019Phage Bioinformatics Syllabus BIOL 302L Q

Feedback, Problems, and Complaints:I welcome feedback on any aspect of this class. If you have concerns or complaints about this class, policies, or environment you are encouraged to discuss them with me first. However, if you are not comfortable discussing issues directly with me, or are not satisfied with resolutions to any issue, you should contact the Chair of the Department of Biology, Dr. John Hutchens (jjhutche@coastal.edu), x2169).Academic Honesty:Science necessarily makes use of the intellectual work of others – existing ideas form the context and basis for new hypotheses, and an open exchange of information is essential for the process to work effectively. But science also relies on honesty in the attribution of intellectual property; when you use the ideas of someone, proper credit must be given. Cheating, plagiarism, falsification of data, or any other form of academic dishonesty will be handled in accordance with the Policy of Academic Integrity**. Possible consequences of violations of this policy include: a failing grade on the assignment in question, a failing grade in the course, and dismissal from the University. Although we encourage you to work with your peers to understand the material covered this semester, unless you are specifically told otherwise, every assignment you turn in must be your own, original work. I welcome an open discussion about this policy, or any questions you have about what constitutes violations of Academic Integrity.

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Coastal Carolina University Spring 2019Phage Bioinformatics Syllabus BIOL 302L Q

Tentative Schedule of Lab Activities

Benchmarks and deadlines must be completed to ensure production of a high quality annotation and posters to be presented at the undergraduate research competition.

Week Topics Assignments & Deadlines

1 Course OverviewPhage Genomes

Bioinformatics BasicsGenome Announcement Reading

Obtain FASTA files of phage

2 DNA MasterORFs

Phamerator

Generate draft annotationObtain phamerator comparison

3 GeneMark and coding potentialStarterator comparison

BLASTHHPred

Complete Annotation of a single gene

4

Annotation, annotation, annotation, and then some more annotation.

Writing abstracts for poster

Weekly annotation and review tasks

Draft Abstract for URC

Final Abstracts DUE: TBD

5

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8

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10 Components of a Poster Production of figure 1

11 Poster Preparation Draft of poster

12 Final poster

13 Undergraduate Research Competition Present your poster

14 Genome AnnouncementsApply skills to further research

Final Annotation Submission!!!Reflection on SEA-PHAGES

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