This course will take students from raw DNA sequencing data through quality assurance, through to data interpretation, statistical analysis, and presentation of the results as a mock scientific article. A background in microbiology, microbial ecology, or genetics would be beneficial. No programming or data analysis experience is required. Students who are performing research may bring their own sequencing data to process in class. Students will become familiar with command-line programs and basic computer programming techniques; understand bioinformatics methods such as quality trimming, assembling contigs, sequence alignment, using reference databases, and statistical comparisons; gain hands-on experience in bioinformatic analysis of DNA sequences using the R platform and its packages; primarily, DADA2, phyloseq, vegan, ggplot2; and be able to apply the knowledge gained in class to other sequence types and programs. Students may bring their own data, or some can be provided. AVS 454 and 554 cannot both be taken for credit.
Student Learning Objectives:
After completion of the course, students will be able to:
- Use an understanding of bioinformatics methods, such as quality trimming, assembling contigs, sequence alignment, using reference databases, and statistical comparisons, to curate a data processing and analysis workflow. This may include bioinformatic analysis of DNA sequences, using the R platform and its packages, MEGA, NCBI genome assembly, MG-RAST, etc. (Quantitative Literacy)
- Demonstrate proficiency in taking raw DNA sequence data through quality control steps to interpretation, and summation of the workflow and results into mock scientific journal article manuscripts. (Quantitative Literacy)
- Demonstrate scientific writing skills, specific to manuscript preparation, including incorporating instructor and peer-review comments and revisions. Submit multiple drafts and progression the ideas with each draft.
- Demonstrate skills in peer-reviewing manuscripts, including reviewing, editing, and scientific critique.
Taught annually in the spring semester
** Syllabus is subject to change.
- Students are expected to attend lectures, but it is understood that life often precludes this and that students may be performing field work or are located off-campus. Students may attend class virtually, through Zoom, which will be offered for each class. Students who will miss a significant number of classes, or who require additional accommodations, may contact me to make alternate arrangements.
- Pregnancy, lactation, and parenting: I am happy to make accommodations for students based on pregnancy, lactation, and parental needs, as well as work with the Office of Equal Opportunities. Maine state and UMaine policy allows students to breastfeed in any space, including in class. If a lactation space is required, please contact E.O. for arrangements.
- Pregnant on Campus Initiative, pregnancy and parenting resources in Orono https://pregnantoncampus.studentsforlife.org/campus/umaine-orono/
- Food insecure? Need clothes? Check out the Black Bear Exchange’s Food Pantry: https://umaine.edu/volunteer/black-bear-exchange/ or Old Town Crossroads Ministry.
Class participation: Students are expected to participate in discussions in class. I strive to create inclusive discussions, but if students still find it challenging to participate please notify me and I will alter the discussion format as needed.
Late Assignments: Assignments will be accepted after deadlines, but you might not receive feedback. Assignments will not be accepted after the last day of the semester.
Note on authorship: If you are pursuing a manuscript for publication in this class, the work you generate is your intellectual property. I do not expect to be an author on your manuscript, or to have ownership over any materials you generate. I would like me/the class to be mentioned in the Acknowledgments section. I will help you facilitate authorship roles with the full research team (i.e. the people that generated these data).
Classroom policy: Supporting inclusion and community in science is an active process that involves both invitation, and support to ensure that the scientific community is and remains an equitable and inclusive place. Students are expected to conduct themselves in a professional and courteous manner, and to abide by University policies.
Campus Policies: “The University of Maine is an EEO/AA employer, and does not discriminate on the grounds of race, color, religion, sex, sexual orientation, transgender status, gender expression, national origin, citizenship status, age, disability, genetic information or veteran’s status in employment, education, and all other programs and activities.” Follow the links for more information.
** I am a “mandatory reporter”. If you disclose something to me, I am obligated to disclose to the relevant campus Title IX office. This includes information revealed in class assignments.
Note: this course was previously developed as a special topics precursor, taught Spring 2020; AVS 590: Special Topics in DNA Sequence Analysis Lab