Kristi Jones

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Genomics at Huntingdon College

Course Overview

I taught this course as a research course. Class met one time each week for 2 hours. The first few classes were introduction, where I lectured some and they worked on homework assignments to get students familiar with the websites and the process. After the initial introduction there were two more lectures (one on the biology of chomatin and one on sequencing) the rest of the class meetings were run as "lab meetings" in which students presented their progress and worked with each other to peer teach on areas of the annotation they were having difficulty with. Students were assessed on their weekly presentaions and feedback to classmates, their homework assignments and the final written document with the verbal presentation. 

Implementation

This class was offered as a seminar course this semester, that was run like a lab/research course. Independent work, outside of class time was expected of each student. Class time was used to focus on areas of difficulty and practice presenting progress on the project. 

Lessons Learned and Future Plans

This itteration of the course was my first time teaching with the GEP. Overall I was happy with the progress and work of the students (they presented their annotations at a regional tri-beta meeting as a poster). Some of the hangups I had were with the homework assignments, I used the ones available on the GEP website without adapting them to my students. Next time I will modify the assignments. The students expressed frustration with the process in the begining, however following the course they all seemed to have learned and were proud of their accomplishments. They seemed to gain a real research experience! I plan to teach this again in the fall as an independent study and plan to use the same basic approach.

Syllabus for


Syllabus BIOL371 Research Seminar in Bioinformatics and Genomics using Drosophila as model organism (GEP consortium)
Fall 2013

Instructor: Dr. Kristi Jones
Phone: 833-4218
Email: kristi.jones@huntingdon.edu
Office Location: Bellingrath 303
Office Hours: M, W and F 8:00a-9:30a, Friday 11:30a-2p and by appointment
Course meeting room: Thurs 1-3:30p, Bellingrath 104

Required Text: Supplemental Reading available at print shop and handouts.

Course Description:
This is a research-based course. It will focus on understanding genomics by utilizing bioinformatics in the context of Drosophila as a model organism. Students will participate in an annotation project to determine the genome structure of various Drosophila species and how they compare to Drosophila melanogaster. This is accomplished through collaboration in the GEP program run out of Washington University, St. Louis. It is funded by HHMI (please let me know if you have any questions regarding this partnership).

As a research course the students are expected to take full responsibility for their projects therefore requiring significant out of class commitment to their project. Through the collaboration however, this research may lead to student publications. It is each student’s responsibility to maintain contact with the instructor ensuring up to date contact information as publication may occur after you have graduated.

Prerequisite: instructor’s approval

Specific Objectives:
1. Application of scientific method
a. Hypothesis formation
b. Data evaluation
c. Numerous lines of evidence to support hypothesis
d. Writing and presentation of scientific findings
2. Understanding of bioinformatics tools and application of these tools
3. Increased understanding of eukaryotic gene structure, specifically understanding isoforms, introns, exons and how these are determined.
4. Use of homology to determine gene structure and predict function.
5. Increased understanding of promoter region and reading frames for translation.
6. Experience in scientific literature reading.

BIOL371 Course Policies
Attendance Policy - As per Huntingdon College policy attendance is mandatory. Additionally this is a research-based course; therefore it is necessary for you to be present to obtain the materials/knowledge to perform the research.

Missed classes
College Sanctioned Events - If you must miss class due to a College sanctioned event, you must notify me BEFORE the missed class. Participation will be verified by travel roster. Failure to follow these steps at least one day PRIOR to the absence results in an unexcused absence.

Emergencies – If you have a personal emergency and miss class you can petition for an excused absence. Documentation and a typed statement arguing why you should be allowed to make up the exam is required for petition. You have 24 hours from the time you return to campus to initiate the petition.
What is an emergency?
1. Personal illness – you personally are sick and go to a medical doctor. You must provide a note signed by the doctor indicating you were in their office, or an emergency room. Scheduled doctors appointments are NOT medical emergencies.
2. Family illness – your child is sick and goes to a medical doctor. Again you must provide a note signed by the doctor indicating you were in the office with your child. Spouse is ill, you must provide medical documentation indicating there was no way the adult could drive themselves to the doctor and your presence there was absolutely essential from a medical standpoint.
3. Death – immediate family death (parent, sibling, child, spouse, grandparent). You will be asked to provide documentation such as an obituary that states the date of the funeral service.
4. Miscellaneous – the instructor will listen to what you feel was a legitimate reason for missing an exam and evaluate on a case-by-case basis with input from other faculty.

It is your responsibility to obtain any notes, handouts etc. that were missed due to any absence.


Academic Misconduct:
All acts of dishonesty in any work constitute academic misconduct. This includes, but is not limited to, cheating, plagiarism, fabrication of information, misrepresentation, and abetting any of the above. Academic misconduct is considered a violation of the Huntingdon Honor Code and will not be tolerated. Consult the student handbook’s section discussing the honor code. The student handbook can be found online at http://www.huntingdon.edu/student_life/handbook If you have questions in this regard, please contact me immediately.

Classroom Conduct:
This course will be conducted as a series of short informative lectures (providing pertinent background information regarding both the science and the tools necessary for the project), work sessions and student presentations.

As a research course peer teaching is important, therefore collaboration is highly encouraged. All students in the class must treat others with civility and respect and conduct themselves during class sessions in a way that does not unreasonably interfere with the opportunity of other students to learn. Failure to comply with this requirement may result in your dismissal from the class and/or disciplinary action.

Computer Use:
Computer use is essential to this course. However, any observed non-scholarly use of the computer during scheduled work time or lectures will result in being dismissed from the class. Excessive in ability to stay on task will result in failure of the class.

Grading: Your grade in this course will be calculated as follows:
Homework 20%
(HW includes formal assignments and informal lab notebook checks)
Weekly presentations/participation 40%
Final presentation 20%
Final report 20%
Final course grades will be assigned based on the following scale:
Percentile Grade
90-100% A
80-89% B
70-79% C There will be no scaling of grades
60-69% D
<59% F


Accommodation of Special Needs
Faculty at Huntingdon College make every effort to accommodate unique and special needs of students with respect to speech, hearing, vision, seating, or other possible adaptions. Please notify the Disability Services Intake Coordinator, Ms. Camilla Irvin, as soon as possible of requested accommodations. She may be reached at 833-4577 or by email at disabilityservices@huntingdon.edu.

If You Have a Problem
If you have difficulties or complaints related to this course, your first action should be to discuss them with me. If such a discussion would be uncomfortable for you or fails to resolve your difficulties, you should contact Dr. Erastus Dudley, Chair of The Department (tdudley@hutingdon.edu). Should you remain unsatisfied you may speak to Dr. Sidney Stubbs, Provost and Dean of the College (Flowers 105, Phone 833-4236).

Miscellany
It is my policy not to give grades out via email or phone. Please don’t ask. However, I am happy to discuss your grades with you during office hours or during a scheduled appointment.

No video recording is permitted.

Tips to assist in your success in this course:
1. Work on your project EVERY day
2. Keep good notes in an electronic notebook and BACKUP your data on an external device
3. Visit me often; I have additional, separate office hours specifically for this class on Friday’s. This will be fun and I want to help!
4. Communicate with your peers and me as this is a learning experience for all of us and peer teaching is important!
5. Remember this is a research class; therefore you are working with open-ended questions. As frustrations arise, walk away momentarily then come back with a clear mind and tackle the task again.

Tentative Important Dates
• Thursday, Aug 29, 2013 - classes begin; have first reading assignment completed, as we will discuss course syllabus and these readings.
• Tuesday, Sep 3, 2013 – assignment 1 due
• Thursday, Sep 5, 2013 – lecture (how BLAST works)
• Tuesday, Sep 10, 2013 – assignment 2 due
• Thursday, Sep 12, 2013 – contig assignment
• Thursday, Oct 3, 2013 – lecture (sequencing and finishing)
• Thursday, Oct 17, 2013 – lecture (model organism science)
• Thursday, Oct 31, 2013 – lecture (gene predictors)
• Thursday, Dec 5, 2013 – final written report due
• Monday, Dec 9, 2013 – final presentation of annotation

NOTES: These dates are tentative and can change at instructor’s discretion. All other class meeting times not specified will consist of short, informal discussion of progress of your research, much like a lab meeting followed by independent work time. Each student is expected to present where they are that week and offer suggestions on their peer’s projects.

If your contig is adequately annotated prior to the end of the semester you may be given another contig to annotate or paired up with another student to assist with their contig, this will be determined by the instructor.