Amie Jo McClellan
Genomics at Bennington College
Genome Jumpstart – an introduction to bioinformatic analysis
This course offers an immersive experience into the world of DNA, genes, and genomes in eukaryotic organisms. In addition to getting a grasp of the foundational biology, we will become familiar with the computational algorithms and methodologies used to analyze and mine the ever-increasing data generated from whole-genome sequencing, high-throughput proteomic analyses, and our improved understanding of evolutionary relationships between organisms based on their molecular fingerprints. For the project portion of the course, all students will utilize public genomic databases and software to contribute to a multi-institute on-going analysis and annotation of understudied regions of the Drosophila genome. This project work makes students eligible for future co-author status on emerging publications by the Genomics Education Partnership consortium.
This course has been taught twice (Fall 2015 and Fall 2016) and will be taught a third time in Fall 2017. 75% of seats in the course are reserved for incoming first-year students. In the first half of the course, one of the twice-weekly meetings is a lecture providing relevant background and in the second weekly meeting the students go through a walkthrough (the intro curriculum walkthroughs by Laakso et al.). At midterm, students are divided into groups of two and each group is assigned a contig. The bulk of the remainder of the term is in-class work time on their contigs, as well as updates by student groups. At the end of the term each group has the choice of a more extensive in-class presentation or a poster presentation in our department's end-of-term "posterpalooza".
Lessons Learned and Future Plans
Having peer instructors is critical because I can not effectively go around the computer lab to 10 different groups that have questions. This coming term I may schedule groups for in-class time with me so that I can keep better track of where they are/what their difficulties are - sometimes the groups that need the most help are the ones that do not ask for it...
I would like to have more homeworks/problem sets to gauge their understanding and progress. Currently there are two exams, one around midterm and one at the end. There were still two students that, on the final exam, were unable to successfully annotate a gene and get it to pass gene model checker within the allocated 60 minute time limit. This implies that their group partners are doing all of the work on the contig, which should not be the case.
Syllabus for Genome Jumpstart
BIO 2117.01 4 Credits Fall 2016
Genome Jumpstart – An Introduction to Bioinformatic Analysis
Class Meetings: Monday/Thursday 10:30 am – 12:20 pm, Catlab
Instructor: Amie Jo McClellan, Ph.D., Dickinson 110/111
Office Hours: Tuesdays 1-3 pm and by appointment
(sign up sheet will be posted weekly outside lab door)
Phone: X4469 Email: email@example.com
Peer Instructor(s): Mary Roth and Sarah gross
Peer Instructor Catlab hour(s): Wednesdays 6-8 pm
The goal of this course is to familiarize students with the flow of genetic information by focusing on eukaryotic genes, genomes, & gene structure and regulation. The primary means for doing so will be through the lens of bioinformatics. Specifically, we will learn how to utilize available online resources to explore and annotate DNA sequences from Drosophila species. Students that successfully annotate regions of DNA will submit their data to a consortium and are eligible as co-authors on any scientific publication that uses their data. This is an excellent and unique opportunity to jump right into scientific research early in your undergraduate trajectory! Students with projects that have progressed well will have the opportunity to present a research poster at Dickinson’s end-of-term “poster-palooza”.
Most of our learning and class work will involve being online, but there will also be some lectures for background information and context. We will start out with a few lectures, but try to move very quickly to spending more and more time familiarizing ourselves with the online genome browser and all it has to offer. In general, at least one of your two class meetings a week will be computer work time.
Week Day Date Topic
1 Th 9/1/16 Course overview; introductory assessments
1 M 9/5/16 Course overview, continued; What is a Gene?
2 Th 9/8/16 Gene structure (promoters); Start Gene walkthrough
2 M 9/12/16 Introduction to the BLAST algorithm – computational context for evolution; hands-on BLAST exercise
3 Th 9/15/16 Gene structure (introns, splicing overview); Continue Gene walkthrough
3 M 9/19/16 Transcription – DNA to RNA molecule; Start Transcription walkthrough
4 Th 9/22/16 Transcription – processing to mature mRNA; Continue Transcription walkthrough
4 M 9/26/16 Splicing – correctly identifying splice sites; Start Splicing walkthrough
5 Th 9/29/16 Finish Splicing walkthrough
5 M 10/3/16 Translation; Translation walkthrough
6 Th 10/6/16 Alternative splicing; Alternative splicing walkthrough
6 M 10/10/16 Exam 1: part written and part computer-based
7 Th 10/13/16 Gene Annotation walkthrough; assign project pairs/groups
End of 1st 7 weeks Last day to withdraw from classes is 10/13/16
M 10/17/16 Long Weekend - No Class Meeting
The majority of remaining class times will be spent on your assigned gene annotation projects. Additional lectures and activities are likely to occur, especially as questions arise and progress is made with annotation. Brief student presentations/updates to the class will also be scheduled during these class periods.
7 Th 10/20/16 Gene Annotation work time
8 M 10/24/16 Gene Annotation work time; 2 student updates
8 Th 10/27/16 NO CLASS MEETING (Plan Day)
9 M 10/31/16 Gene Annotation work time; 2 student updates
9 Th 11/3/16 Gene Annotation work time; 2 student updates
10 M 11/7/16 Gene Annotation work time; 2 student updates
10 Th 11/10/16 Gene Annotation work time; 2 student updates
11 M 11/14/16 Gene Annotation work time; 2 student updates
11 Th 11/17/16 Gene Annotation work time; 2 student updates
12 M 11/21/16 Gene Annotation Report Preparation work time; 3 student updates
12 Th 11/24/16 THANKSGIVING BREAK – No Class Meeting
13 M 11/28/16 Gene Report presentations
13 Th 12/1/16 Gene Report presentations
14 M 12/5/16 Exam 2: timed computer-based exam
14 Th 12/8/16 Online exit assessment; submission of completed Gene Annotation Reports
An introduction to the primary areas of biology relevant to this course will be critical for your understanding of the genome annotation process on the computer. Lectures will be posted on populi so you may review/download them. The majority of class time, however, will be spent exploring, learning, and utilizing online bioinformatic tools and resources. For the first half of the term there will be guided online walkthroughs to help familiarize you with the relevant web pages, tools, interfaces, software, and work flow practice(s) for genome annotation. The sooner you can independently work on annotating your assigned DNA region, the further you will progress in your research.
Textbook/Instructional Resources: There is no required textbook for this course. Most general biology, cell biology, molecular biology, or genetics textbooks can be used as resources for understanding the basic flow of genetic information; there are a number of such books in the Dickinson reading room – and I generally have a few in my office that can be borrowed. The internet will also be invaluable for this class, as long as you are using appropriate academic websites, resources, and walkthrough-based tutorials.
Attendance policy: More than 3 missed classes will result in a Marginal Pass (or a letter grade of D). More than 4 missed classes is an automatic Fail (letter grade of F).
Plagiarism policy: Any student that plagiarizes in this course (copying work, representing the work of others as their own, including copying text from websites, etc.) will AUTOMATICALLY FAIL the course and be subject to further repercussions, at the discretion of the administration, which could include dismissal from the College.