David Dunbar

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Genomics at Cabrini College

Course Overview

Major advances in the fields of genomics have led to an explosive growth in the biological information. This deluge of genomic information has, in turn, led to an absolute requirement for computerized databases to store, organize and index the data, and for specialized tools to view and analyze the data. Bioinformatics is the field of science in which biology, computer science and information technology merges to form a single discipline.
This is a research-based class run in collaboration with the Genomics Education Partnership at Washington Univ. in St. Louis (http://gep.wustl.edu). The research that you complete during the course will be published in a peer-reviewed scientific paper, and you will be listed as a co-author. This is an excellent opportunity to work in a student-scientist partnership and gain undergraduate research experience.
We will be studying how DNA sequence affects chromosome organization by comparing the sequences of various Drosophila species. These sequences are publicly available, but they are 'draft' sequences and not highly reliable. In the first phase of the project, you will be conducting annotation, which involves identifying genes and other features in your sequences. You will do this by comparison to Drosophila melanogaster, which is much better studied so that data about gene expression is available for at least some of the genes. This is a great project to look at evolutionary questions, and to see the divergence that has occurred over a rather short time frame, between very similar species. 

This course will include genome sequence acquisition and analysis sequence analysis software, pairwise and multiple, sequence alignments, database searches, and some case studies. Students will learn from extensive hands on exercises.

Implementation

At Cabrini College, we have taught the GEP course as a three credit bioinformatics course. Because this was the first time students were exposed to bioinformatics tools, three hours of instructional time was needed for the semester to get the students "up to speed" with their individual annotation projects. We really had no time for students to conduct any finishing projects. However, several students are conducting independent finishing projects during the spring semester as undergraduate research credits.

Lessons Learned and Future Plans

Students at Cabrini College have had very little experience with Bioinformatics tools before the GEP coures. As such, it was a sharp learning curve for the Cabrini students, mostly juniors and seniors. However, students were able to master the bioinformatics tools and successfully complete their individual annotation projects by the end of the semester. Student evaluations indicated that they learned a lot during the course of the semester and were very impressed by how much they learned by the end of the semeter. The course instructors received high marks on the student course evaluations.

After taking the course, several students indicated that they are very interested in the field of bioinformatics and are considering this as a career option after graduation. Two such students are conducting GEP finishing projects during the spring semester aas a result of their favorable experience in the fall course.  

Syllabus for  
Bioinformatics
BIO 350A
Fall, 2011
Prerequisites: BIO 101-102, CHE 111-111L
Co-requisite or prerequisite: BIO 263


Instructor: David Dunbar, Ph.D.
Office: IAD, Room 220
Telephone: 610-902-8770
Email: ddunbar@cabrini.edu

Teaching Assistant: Catherine Mageeney
Email: cmageeney@yahoo.com

Office Hours: Tuesday from 4:30-6:00, Thursday from 4:30-6:00 and Friday from 3:15-4:15 or by appointment.

Text: None Required. The materials for this lab were developed as part of the curriculum by the Dr. Sarah Elgin at Washington University at Saint Louis for the Genomics Education Partnership (GEP).

Course Description:
Major advances in the fields of genomics have led to an explosive growth in the biological information. This deluge of genomic information has, in turn, led to an absolute requirement for computerized databases to store, organize and index the data, and for specialized tools to view and analyze the data. Bioinformatics is the field of science in which biology, computer science and information technology merges to form a single discipline.
This is a research-based class run in collaboration with the Genomics Education Partnership at Washington University in St. Louis (http://gep.wustl.edu). The research that you complete during the course will be published in a peer-reviewed scientific paper, and you will be listed as a co-author. This is an excellent opportunity to work in a student-scientist partnership and gain undergraduate research experience.
We will be studying how DNA sequence affects chromosome organization by comparing the sequences of various Drosophila species. These sequences are publicly available, but they are 'draft' sequences and not highly reliable. In the first phase of the project, you will be conducting annotation, which involves identifying genes and other features in your sequences. You will do this by comparison to Drosophila melanogaster, which is much better studied so that data about gene expression is available for at least some of the genes. This is a great project to look at evolutionary questions, and to see the divergence that has occurred over a rather short time frame, between very similar species.
This course will include genome sequence acquisition and analysis sequence analysis software, pairwise and multiple, sequence alignments, database searches, and some case studies. Students will learn from extensive hands on exercises.


Course Objectives:
1. Students will actively work on nation-wide-genomic-projects through our partnership with Washington University at Saint Louis, MO. To learn more about the partnership, please visit http://gep.wustl.edu.
2. Students will apply their knowledge of basic genetics to analyze and compare fosmid library DNA of Drosophila erecta to other fly genus. In other words, students will understand and put to practice the Central Dogma information as it relates genes (nucleotide sequence) to proteins (amino acid sequence) and their homology among different species.
3. Students will be able to learn more about Sequencing, PCR experiments and blast programs among others.
4. Students will produce high quality annotations on fosmids containing D. erecta genomic sequence data.
5. Students will have the opportunity to have their complete work to be part of a peer-reviewed manuscript.


The in silico labs:

Date Class Work Homework
September 1, 2011 Syllabus, Introduction to GEP project, Pre-course Survey and Quiz Watch “Next Generation Sequencing Video” tour
September 8, 2011 Introduction to Drosophila and 4th dot chromosome, A Simple Annotation Problem Simple annotation quiz (10pts)-due Sept. 15,2011
September 15, 2011 A Difficult Annotation Problem, Intro to ChimpChunks 1. Finish Chimp Chunk tutorial
2. Harder annotation quiz (20pts)-due Sept. 22, 2011
September 22, 2011 Annotate fosmid Chimp Chunks quiz (10pts)-due Sept. 29, 2011
September 29, 2011 Annotate fosmid
October 7, 2011 Annotate fosmid
October 14, 2011 NO CLASS DEANS HOLIDAY Annotate fosmid
October 21, 2011 Annotate fosmid
October 28, 2011 Annotate fosmid
November 4, 2011 Annotate fosmid Paper Draft Due- due Nov. 4, 2011
November 11, 2011 Synteny, Clustalw Annotation Reports Due Nov. 11
November 18, 2011 Intro to consed with simple finishing problem Finishing quiz(10pts)- Nov. 25, 2011
November 25, 2011 No Class Thanksgiving
December 2, 2011 Presentations
December 9, 2011 Presentations, Post-course Survey and Quiz PAPER DUE
Week of Finals

GRADING
Point Distribution
Quizzes (5) 30% (250 pts)
Lab Notebook 15% (150 pts)
*Presentations 25% (200 pts)
*First draft papers 5% (100 pts)
*Final version papers 25% (200 pts)

Total Points 800 pts

To calculate your grade at the end of the semester, I will divide the total number of points you have by 800 points. Your letter grade will be based on that number as a percentage according to the following scale:
A = 94-100% C = 73-76.9%
A- = 90-93.9% C- = 70-72.9%
B+ = 87-89.9% D+ = 67-69.9%
B = 83-86.9% D = 60-66.9%
B- = 80-82.9% F = 59.9% or less
C+ = 77-79.9%

At the beginning of each week’s lecture, you will be given a 10 point quiz based on the previous weeks lecture material. You will have approximately 15 minutes to complete each lecture quiz and the entire class time to complete each exam, unless other arrangements have been made between you and me. Regular attendance is positively correlated with success in this and any course.

Exam and Assignment Dates: Make-up quizzes and exams will only be offered for students with extreme circumstances. Acceptable excuses include a major illness, family emergency or participation in a college-sponsored athletic competition. All valid excuses must be documented with a note from the Academic Affairs Office, a physician, or a coach or a 0 grade will be assigned. Assignments may be turned in late, but a 20% per day penalty will be assessed. If the college is closed for any reason, exams will be held and assignments due during the next scheduled class period.


Withdrawal Date: The last day to withdraw from the course is Thursday, November 4.

CENTER FOR TEACHING & LEARNING (CTL)
Iadarola Center 106 call: 610-902-8213
The CTL is a Learning Commons. We strengthen students’ academic skills by having them work closely with trained peer tutors and friendly professional coaches. We offer one-on-one coaching across all fields of study (science, language, computer science, humanities) with a special emphasis on math and writing. The following is a brief description of our student services:

• ACADEMIC COUNSELING Iadarola Center L1N call: 610-902-8567
Email: mdejesus@cabrini.edu
Advising and academic counseling are the foundation of our student support system. Our counselors work one-on-one with students to help them implement practical, proven strategies for improving their academic skills and study habits. Free counseling services are available by appointment.

• PEER TUTORING SERVICES Iadarola Center 109 call: 610-902-8213
Email: peertutoring@cabrini.edu
The peer tutoring services provide academic support across all fields of study to all students who would like additional resources. Our services focus upon specific needs, such as preparing for tests, reviewing class materials, and understanding advanced concepts. Ongoing assistance in the mastery of specific course content is also provided via classroom coaches and peer partners. Free tutoring is available by appointment and on a drop-in basis.

• MATH RESOURCE CENTER Iadarola Center 318 call: 610-902-8563
Email: mathtutor@cabrini.edu
The Math Resource Center provides individual and group tutoring to help students succeed in their required math courses. Working closely with the faculty of the Math Department, we assist students with their homework, quizzes, and test preparation. We also help with preparation for standardized tests (e.g., PRAXIS and GREs). Tutoring is offered in a relaxed setting designed to eliminate any math anxiety students might be experiencing. Free tutoring is available by appointment and on a drop-in basis.

• WRITING CENTER Iadarola Center 110 call: 610-902-8506
Email: writingcenter@cabrini.edu
The Writing Center helps students use writing as a tool for learning, reflection, and career preparation. In a comfortable, relaxed, and friendly atmosphere, we deliver individualized instruction at all stages of the writing process ─ from brainstorming, pre-writing, and drafting to revision. We have both professional and peer tutors available and eager to help. Free tutoring is available by appointment and on a drop-in basis.

Holy Spirit Library
Library Information call: 610-902-8538 and 610 902-8432
Website: www.cabrini.edu/library Email: library@cabrini.edu
Holy Spirit Library is your gateway to information. The Library staff invites students to use its facilities, resources, and services, and gladly provides assistance with research needs. The reference staff are happy to answer reference questions in person, by telephone, email, or chat. Computers are available to conduct research and to use the Microsoft Office applications. Please visit our website, send us an email or call us for more information.


Cabrini College Academic Honesty Policy
The principal objective of the Cabrini College Academic Honesty Policy is to encourage a dynamic, open, and honest intellectual climate based on the personal and academic integrity of all members. It is the responsibility of students to help maintain the community of academic integrity. Students shall not receive credit for work that is not a product of their own efforts. For a full description of the policy, please see the Academic Affairs homepage and follow the Academic Honesty link, or see the 2011-2012 Undergraduate Catalog.
Academic dishonesty includes, but is not limited to:
• Plagiarism
• Cheating
• Information falsification or fabrication
• Theft or destruction of intellectual property
• Facilitation of academic dishonesty

For a first violation, the faculty member will meet with the student or otherwise communicate the charge. The faculty member will complete an Academic Honesty Violation Charge Form, stating the violation and assigning a penalty. The student should sign and date the charge form and return it to the faculty member. The student may request a hearing before the Academic Honesty Board by indicating that option on the form. For a second violation in a given course, the faculty member will follow the same procedures as in the first incident but will assign a penalty of failure of the course without privilege of withdrawal. For any second or subsequent violation during a student’s academic career at Cabrini College, the Academic Honesty Board shall conduct a hearing.

Disability Resource Center
Cabrini College provides support services and appropriate accommodations for qualified students with documented disabilities. If you are a student who requires classroom or testing accommodations, please contact the Disability Resource Center by phone at 610-902-8572 or e-mail at drc@cabrini.edu. Please note that classroom or testing accommodations can only be provided to students who have Accommodation Notification Forms from the Disability Resource Center. Students are responsible for providing the instructor with the Accommodation Notification Forms and informing the instructor when they need academic adjustments.


Good luck and enjoy the semester!