Rebecca Burgess

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Genomics at Stevenson University

Course Overview

A 2-credit, 3 -week winter independent research course, taught by 2 faculty members. Six students are recruited from Genetics classes in the Fall, and work in pairs on annotation projects. We meet for 14 days for 4 hours at a time, with a signficant portion of the work being conducted outside of class. The minimum number of hours for this class is 85 hours. Students regularly complete up to 120 hours of research time, however. 


GEP Curriculum Used:

Intro to BLAST, Basic BLAST Exercise

Understanding Eukaryotic Genomes, Modules 1-6

Annotation of a Drosophila Gene

Lessons Learned and Future Plans

Syllabus for BIO 362: Independent Research In Biology (Winter 2017)

Dr. Rivka Glaser
Telephone number: 443-394-9644
Stevenson email:    
Best times for phone contact:  Tuesdays and Thursdays, 9:30-1:30 
Office location: Academic Center N115
Office hours:   By appointment

Dr. Rebecca Burgess
Telephone number: 443-394-9653
Stevenson email:    
Best times for phone contact:  M-F 9-10am    
Office location: Academic Center N109
Office hours: Mondays 3:30-5:00 pm, Thursdays, 2:00 pm – 3:30 pm

BIO 362: Independent Research in Biology
Section number: ON1 and ON2
Credits: 2
Prerequisite(s): A grade of "C" or better in BIO 113 and BIO 113L and permission of the faculty member who will be supervising the research.
Classroom or Studio Location: Owings Mills North, Manning Academic Center- Room TBA 
Scheduled Class Days and Time:  January 3-22nd. M-F 10-2
Course Description: Provides an opportunity to conduct independent research in an on-campus laboratory under the supervision of a Biology faculty member. This course may be repeated for credit. This course cannot be used as a substitute for the senior capstone requirement. 
Instructional Methods Used in this Course: Laboratory work, group work.
Required and Recommended Texts, Manuals, and Supplies: Printing fees are required for the poster presentation. There are no required texts, although you may find reference material from the SU library helpful, such as: Mount, David W. Bioinformatics : Sequence And Genome Analysis. n.p.: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press, c2001., 2001. ShaRC -- MIC Consortium Shared Catalog. Web.
     Your BIO 230 Genetics text (Klug 10th ed.) may be helpful as a reference, as well.
Most of the teaching materials used in the course can be found at the Genomics Education Partnership web page ( under Curriculum.
Additional information: The Genomics Education Partnership (GEP) is a national, collaborative, scientific investigation of a problem in genomics, involving wet-lab generation of a large data set (e.g., sequence improvement of genomic DNA) and computer analyses of the data (including annotation of genes, assessment of repeats, exploration of evolutionary questions, etc.). Overall, the goal of annotation is to create gene models for all the genes in a genome. The specific goal of the GEP is to annotate the genomes of several Drosophila species, using the genome of D. melanogaster as a reference genome. In particular, the GEP is focused on genomic regions in other species that correspond to chromosome four of D. melanogaster. Thus, the current research problem entails generating finished sequence from the fourth (dot) chromosome of various species of Drosophila, annotating these sequences, and making comparisons among species to discern patterns of genome organization related to the control of gene expression. In this course, we will perform the process of gene annotation to address research questions in collaboration with the Genomics Education Partnership.  Your work will be submitted to the consortium for use in their research efforts and you will be included as a co-author on future publications from this collaboration.

Course Objectives/Learning Outcomes:  At the conclusion of this course, a student will be able to:
1.    Conduct an inquiry-based scientific study
2.    Develop an understanding of the elements of experimental design.
3.    Develop the skills necessary to propose a hypothesis-driven study
4.    Augment skills required for maintaining a laboratory notebook
5.    Broaden and enhance analytical skills by analyzing empirically-derived data
6.    Broaden and enhance critical thinking skills by interpreting data and drawing conclusions about the results of a scientific study
7.    Develop an understanding of the elements of a scientific poster
8.    Explore your suitability and desire for a career in scientific research
9.    Develop an appreciation for the rigors and rewards of scientific research
To determine if this course fulfills additional program or track outcomes, please see the Academic Affairs portal page. 
We anticipate that students will become familiar with the use of commonly used DNA databases; model organism websites; genome browsers; RepeatMasker; Genscan and other gene prediction tools; BLAST, BLAT searches for similarity; Clustal for comparative analysis. As time permits and the research dictates, we may explore other databases and comparative tools.

Grading Scale:
A    93-100    4.0
A-    90-92    3.7
B+    87-89    3.3
B    83-86    3.0
B-    80-82    2.7
C+    77-79    2.3
C    73-76    2.0
C-    70-72    1.7
D+    67-69    1.3
D    60-66    1.0
F    1-59    0.0
Students must earn a minimum grade of “C” in courses that are used to fulfill the SEE requirement and major requirements.

Continuance and Progression Policies, if applicable:  Students must earn a minimum GPA of 2.00 in the major, and the lowest acceptable grade is a "C" in all major and Stevenson Educational Experience (SEE) courses. No student, regardless of major, will be permitted to take a science or math course unless he/she earns a grade of "C" or better in all prerequisite courses.

Grading Standards: Please note that the School of the Sciences policy is that final course grades are NOT rounded. Your final grade in this course will be calculated as follows:           
Journal Club Presentation     15% 
Lab Report    20% 
Poster and Presentation    20% 
Digital Lab Notebook     20% 
Research Conduct    20% 
Professionalism    5%
TOTAL    100
Course Requirements:   
JOURNAL CLUB We will have three days for journal club presentations where students give an approximately 20 min presentation of a research article from a list of relevant references, followed by discussions. The presentations can be produced in Powerpoint, Keynote, or other presentation software. Communication of findings is a key feature of all scientific careers and practicing this skill early will be instrumental for your development. Students will discuss the large-picture importance of the paper, relevant background and the experimental procedures and rationale. Rubrics for the grading of the lab meeting/research proposal can be found on Blackboard.
LAB REPORT The research you’ve performed for the semester will be written up as a research summary and submitted to the GEP.  There are examples of this paper on the GEP website. The grading rubric for the final version is on Blackboard. 

POSTER AND PRESENTATION Students completing research projects must also prepare a poster for the School of the Sciences Research Symposium in the following semester. Since the poster presentation is at the end of spring semester, students will prepare a draft poster by the end of Winterim.  The poster summarizes the research project and the student is expected to prepare the poster, with guidance from the instructor. We will work on drafts of the poster together over the course of Winterim. We will have a mini-symposium of our own at the end of the semester where each group presents their findings in a Powerpoint presentation (or other presentation software). Failure to present at the end of the winter term results in lowering of the final course grade by one letter grade. 

LAB NOTEBOOKS Lab notebooks will be electronic- students will create their own Microsoft OneNote account (if they do not already have one) using their SU email address, and then I will grant them access to the “Drosophila Genomics Research” Notebook. Students will then enter their research data into their own section (tab) of the Drosophila Genomics Research notebook using their computer/table. DO NOT USE YOUR OWN ONENOTE NOTEBOOK FOR LAB DATA- IT WILL NOT BE BACKED UP! Daily entries will be entered into a new page within your notebook tab. Pages can be made ’subpages’ for organizational purposes. Information can be handwritten with the stylus and converted to text later, but lab notebooks are for direct entry of experimental information (writing on scrap paper and then entering information later is not recommended). Pictures or voice notes can be captured with your computer/ tablet (or with smartphones) and inserted directly into the lab notebook via the OneNote app.
It is important to take very detailed notes so that research can be reproduced. Some organization after completion of the experiment is acceptable, but no changes to the previous inputs are permitted and processed data should be inserted into the entries when it is complete. Please see the SOS Student Guide for requirements and tips on keeping a lab notebook. The pages previews along the right side (or left, depending on the version) of the OneNote notebook will suffice as your table of contents. All data external to the notebook must be stored on the W: drive for backup. Other notebooks, such as protocols, will remain locked for editing, though students can view the contents for assisting them in their lab work. At the end of the semester, on the day of the poster session, the notebooks will be locked to editing for grading. A rubric for notebook grading is on Blackboard.

Students are expected to:
1. Adhere to lab safety standards at all times and be good lab citizens. This entails promptly cleaning up work spaces after completion of work.
2. Treat equipment with care and take time to exercise proper practices. Accidents happen, do not cover up or hide mistakes. Report any hazardous spills or damaged equipment immediately.
3. Handle empirical data with integrity. Ethical practices are of utmost importance in scientific pursuits. If there is any question about how statistical tests or data analysis should be performed, please discuss it with the instructor as soon as possible.
4. Perform research duties in an organized manner. Both electronic data/results and the physical samples from which they come will be kept organized on a daily basis. 
Lab conduct/practices constitute 20 percent of your grade. If a student begins to display shortcomings in these practices, weekly progress reports addressing these points and the students self-reported improvement in each will become required. Since research environment, progress, and integrity are vital components of the laboratory’s work, failure to submit required weekly reports will result in loss of all the lab conduct points for the semester.
NOTE:  We will not be in a traditional wet lab for these projects.  We will be in a computer lab.  The computers are your research tools, therefore when you are in class, you are expected to be working only on the GEP project and you should treat the computer lab as your workspace per the guidelines above.

PROFESSIONALISM As you prepare for a career in any field, it is essential that you develop professional attitudes and behaviors in addition to the cognitive (knowledge) and psychomotor (techniques) skills. Therefore, the School of the Sciences at Stevenson University encourages your development of professionalism as part of your career preparation here by requiring a grade for professional attitude and behavior in every course in the School. As a part of your professionalism requirement, your course contract must be returned to your instructor by September 1, 2016, if it is not returned by that date, 1 point will be deducted from your final Professionalism score.
Department of Biology Professionalism Objectives
The following professionalism objectives will be included and evaluated in every biology course (lecture and laboratory courses):
1. Student adheres to the attendance policies established by the course syllabus.
2. Student is consistently well prepared and submits all assignments according to deadlines set by the instructor and the course syllabus.
3. Student demonstrates a respectful attitude and professional demeanor with faculty and peers.
4. Student demonstrates flexibility with changes to the course schedule.
5. Student demonstrates the ability to follow verbal and written instructions.
In every laboratory course, the following criterion will be added to those above:
6. Student complies with all safety regulations

Communication: Each student has been given a Stevenson University email address.  It is expected that students will check their SU email account and Blackboard every day to look for important announcements and information. Students are responsible for information sent to their Stevenson University email address and/or posted on their courses’ Blackboard sites.  
If you have questions or concerns about the course itself or the material covered, the best way to discuss it is to see one of us.  If you cannot see us in person, you may e-mail us and we will do my best to respond to your e-mail within 24 hours.  See Instructor Information section for office hours, e-mail address, etc.                                                                                                                                                           
In the event of Stevenson University Closure:  Should SU experience an unplanned closure during the semester for any reason, faculty will continue to provide instruction to students through Blackboard and/or via email.  If you foresee a problem with internet access, please speak with your instructor at the beginning of the semester.  Please keep in mind that SU computers or computer laboratories may be impacted by whatever conditions led to the closure, which means that you must let your instructor know if you are relying solely on the University’s computers (i.e. if you do not have a computer of your own).  If at any time you have a problem with internet access, it is your responsibility to contact your instructor immediately.  It is acceptable to leave a voice mail for your instructor if you are unable to communicate in person or via the internet. 
Submission of Assignments or Projects:  
Turning in written work:
All written work for BIO 362 MUST be submitted in class on the day it is due in the appropriate format (i.e. typed or handwritten, hard copy or e-mail).  Multiple pages must be stapled together.  Assignments consisting of multiple pages that are not stapled together will not be accepted.  If the assignment is to be submitted electronically, then it should be uploaded to the Blackboard site as a file. It is the student’s responsibility to make sure that the assignment is complete before submitting it.  Save your work in the event that it needs to be resubmitted.
A failure of a personal computing device will not be an acceptable excuse for missed academic or University deadlines.

Late Work:
•    All assignments are due by the end of class on the scheduled date.
•    A 5% deduction of points will occur for every day that the work is late.  A day means a day, not the next class period.  After one week, late assignments will not be accepted.  
•    If you miss a deadline due to an absence, you must submit your work at the earliest opportunity by any of the methods listed above or point deductions will accumulate. Assignments late due to sickness are due as soon as you are well enough to attend class.

Policy on Challenging Grading: All requests to review the grading on assignments must be submitted in writing within one week of the grades being available.  

Classroom Policies:  
Conduct in Class:
Students must come to class prepared to learn, participate, and ask questions.  The following policies have been developed to allow everyone in class to benefit from the instruction offered and to minimize disturbances to the class as a whole:
o    We will be using computers extensively in this bioinformatics-based research course, lab it will serve as your lab manual and digital lab notebook. We will be working in a computer lab, but you are welcome to bring your laptop as well, so that you can use one for reading instructions and the other for completing analyses and for the lab notebook.
o    Students will be allowed to use computers in lectures for the purpose of note taking and in. 
o    If computers are used for checking e-mail, social media sites, or anything else other than note taking, the instructor reserves the right to rescind the privilege of using your personal laptop. All cell phones, iPods, etc. must be TURNED OFF during class and lab.  
•    No side conversations are allowed when the instructor is talking or animations/videos are being shown.  
•    Students may not work on assignments for any course during class time, unless that time period has been specifically designated for this purpose.  
•    Students who do not comply with these policies be asked to leave the classroom or laboratory.  

Laboratory Safety: Since this Winterim course uses only in silico methods (computer based work), the regular lab safety training does not apply.  Students will, however, still need to take the CITI Training (see below) if they have not done so before. 

Other Course Requirements:
1.    Students will engage in research for a minimum of 135 hours over the course of the semester.  Failure to complete at least 135 hours will result in the student earning a grade of “F” for the course. 
a.    We will be meeting face to face for 13 days, 4 hours a day (52 hrs).  In order to attain the 135 hrs needed, it is expected that students work outside of class time on their project and report their hours honestly to the instructors.
2.    Students will also present their research findings in class.  If not, the course grade will be lowered by one letter grade.  
3.    Students must submit their lab notebook (or other lab records, data etc.) to the instructor to keep at the end of the semester.  These records are essential and belong to the mentor.  Failure to do so will result in earning a grade of “F” for the course.

CITI Training: A course on Responsible Conduct of Research must be completed within the first two days of the start of the semester.  Students who wish to complete this course before the semester starts may do so.  This requirement can be satisfied by taking the Collaborative Institutional Training Initiative (CITI) online course.  Directions for course registration are available in this packet and on the Office of Sponsored Programs and Research (OSPR) website:  Complete the RCR course for Students (see below for instructions).  A cumulative score of 80% on the quiz is required.

CURE Survey: As part of your independent course study in the School of the Sciences, we would like you to you have been asked by your course instructor to complete an independent assessment survey. This CURE survey (classroom undergraduate research experiences) captures the pattern of reported learning gains from a variety of pedagogies. It allows students to evaluate their independent research experience and will provide us with data that will assist us in reviewing these courses and our research opportunities in general.
The CURE survey has two components for students:
1)            A pre-course survey to be completed by the students in the course or lab. 
Access the CURE pre-course survey here. 
2)            A post-course survey to be completed by the student in the course or lab. 
Access the CURE post-course survey here. 
Depending on the course you are taking, please use the following identifiers so that we can track Stevenson University data. Please substitute your initials for XX below. (The identifiers are not case sensitive.)
For BIO 365 – use “SUbio-XX”    For ENV 365 – use “SUenv-XX”
For more information about CURE please see
Let Mrs. Michelle Schwartz ( know if you have any questions, or you can contact for survey-related questions.

Diversity Statement 
Stevenson University commits itself to diversity as it relates to awareness, education, respect, and practice at every level of the organization. The University embraces people of all backgrounds, defined by, but not limited to, ethnicity, culture, race, gender, class, religion, nationality, sexual orientation, gender identity or expression, age, physical ability, learning styles, and political perspectives. The University believes its core values are strengthened when all of its members have voice and representation. The resulting inclusive organizational climate promotes the development of broad-minded members of the University who positively influence their local and global communities.

Each student is responsible for his or her own class attendance and regular attendance is expected. Every student is responsible for the material covered or the skills exercised during scheduled classes. Grades will be based on demonstrated achievement of the objectives of the course, not on attendance in class as such. Students who stop attending and fail to officially withdraw from a class will be given a grade of "FX" which calculates as an "F" in the GPA.

Standards of Academic Integrity
Stevenson University expects all members of its community to behave with integrity. Honesty and integrity provide the clearest path to knowledge, understanding, and truth – the highest goals of an academic institution. For students, integrity is fundamental to the development of intellect, character, and the personal and professional ethics that will govern their lives and shape their careers. Stevenson University embraces and operates in a manner consistent with the definitions and principles of Academic Integrity as set forth by the International Center for Academic Integrity.

Students are expected to model the values of academic integrity (honesty, trust, fairness, respect, responsibility, and courage) in all aspects of this course.  

Students will be asked to assent to and to uphold the University Honor Pledge:  
“I pledge on my honor that I have neither given nor received 
unauthorized assistance on this assignment/exam.”
Suspected violations of the Academic Integrity Policy will be reported and investigated as outlined in the Policy Manual, Volume V.  

Disability Services
The Office of Student Success facilitates equal access for every student who self-identifies as having a disability. If you are a student with a disability who needs accommodations in this class, please contact Abby Hurson, Director of Disability Services at / (443) 352-4920. Once accommodations are authorized by OSS, please provide me (your instructor) with your approved accommodations memo as soon as possible. Accommodations are not retroactive. This is the link to the University’s Disability Support Services:

In addition to meeting during my office hours, the following resources are available for academic support:
•    The Academic Link, located on Greenspring (KH 201) and Owings Mills (Caves 249), provides free tutoring. If you are having difficulty understanding the material, seek help immediately. Tutoring often makes the difference in a student’s grade. For more information regarding hours, scheduling appointments and helpful study strategy links visit:
•    The SU Library provides electronic and print resources to support your coursework. Subject specific Research Guides and Databases by subject can be found on the library home page as well as brief tutorials and directions to assist you in using these resources. 
• is an online learning resource available to all Stevenson students. On students can view video tutorials for hundreds of computer applications, including the Adobe Creative Suite.

Course Calendar: Subject to change, please refer to Blackboard for the most up-to-date schedule.
Date    Topic    Assignments and activities
Jan 3    Introduction to course

Introduction to the scientific question

BLAST Walkthrough: An Introduction to NCBI BLAST
    Pre-course participant survey (GEP and CURE) and quiz

GEP website navigation

BLAST exercise #1 Detecting and Interpreting Genetic Homology

Option: Basic BLAST and Annotation Exercises (Series of 4)
Jan 4    Transcription and mRNA splicing

Lecture:  Eukaryotic Genomes and Chromatin Structure
    Module 2: Transcription, Part I: From DNA sequence to transcription unit

Module 3: Transcription, Part II: What happens to the initial transcript made by RNA pol II?

Module 4: Removal of introns from pre-mRNA by splicing

Jan 5    Translation and alternative splicing

Lecture:  Heterochromatin formation
    Module 5: Translation: The need for an Open Reading Frame

Module 6: Alternative splicing

Journal club article – Comprehensive analysis of chromatin landscape
Jan 6    Introduction to ab initio and Evidence-based Gene Finding

Primer on RNA-Seq Data
    BLAST Exercise #2 Using mRNA and EST Evidence in Annotation

Exercise: Browser-Based Annotation and RNA-Seq Data

Jan 9    Introduction to annotation- Primer on Annotation of Drosophila genes

Lecture:  Fourth Chromosome Organization and function

Annotation work     Annotation tutorials:
Simple annotation problem

Annotation of a Drosophila gene

Select and begin annotation projects

Use of digital Lab Notebooks (DLN) for annotation notes
Jan 10    Repetitious DNA/Design and Use of RepeatMasker
Annotation work    Journal Club presentations 
Jan 11    Annotation discussions/
problem solving as a group    Journal Club presentations
Jan 12    Annotation discussions/
problem solving as a group    Journal Club presentations
Jan 13    Annotation discussions/
problem solving as a group    Initial gene models due for check
Jan 16    University closed- Martin Luther King Jr. Day
Jan 17    Searching for Transcription Start sites    Annotation of Transcription Start Sites in Drosophila

Jan 18    Transcription start site discussions/
problem solving as a group    Final gene models due for check
Jan 19    Transcription start site discussions/
problem solving as a group    Written annotation reports due
Jan 20    Student presentations (electronic poster)
    Student presentations due

Post-course surveys (GEP and CURE) and post-course quiz

Graded Assignments: See “Course Requirements” section for details and schedule (above)  
Journal Article Summary (Journal Club)
Lab Report (Annotation Report)
Poster and Poster Presentation
Notebook or Records/Methods/Data    
Lab/Research Conduct
Other requirements:
Pre-course CURE Survey – Completed on first day
Pre-course GEP survey- Completed on first day
CITI Responsible Conduct of Research – Needs to be completed by first day of class 
Poster and Poster Presentation – Mock poster session- Jan 20th. Spring SOS poster session- TBA
Post-course CURE Survey – Completed on last day
Post-course GEP survey- completed on last day
CITI Responsible Conduct of Research Training Information

CITI (Collaborative Institutional Training Initiative)
Responsible Conduct of Research 
Social and Behavioral Research
Course-Based Research
Conflict of Interest (Financial Conflict of Interest)

The CITI Program, run through the University of Miami, provides a customized online curriculum for faculty, staff, laboratory workers and students who will be conducting research.  Certification, good for three years, will be received for courses taken.   These courses are open to all Stevenson University faculty, staff, administrators, and students. 

To register:
Go to  and click on the Register button located in the blue log in box to the right of the homepage.

1.    Select Stevenson University from a list of participating institutions.
2.    Scroll down to the bottom of this page and Continue to Step 2.
3.    Enter your name and SU email address and Continue to Step 3.
4.    Create a user name and password.  Select and answer a security question, then Continue to Step 4.
5.    Answer questions about gender, ethnicity (optional) and race.  Continue to Step 5.
6.    Answer the question about receiving continuing education unit credits (CEU) for completed CITI program courses with “yes” or “no.” Answer the survey questions as necessary and Continue to Step 6.
7.    Answer the following questions, leaving the rest of the page blank:

Institution email:  Use your SU email address
Gender:  (optional)
Highest degree:  (optional) Select high school from drop down menu
Department:  Select the department of your major - biology, chemistry or nursing
Role in research:  Select from the drop down box.  Students should select “student researcher undergraduate” and Continue to Step 7

8.    Click on all courses that apply.  While you may leave the response blank in number one, you must click “yes” or “no” under Conflict of Interest (number three).   Click on Complete Registration.
9.    The next screen will have two choices.  Click on the one that says:  Finalize your Registration.  A confirmation email will be sent to your SU email address.  You must respond to this email to complete your registration.  Once confirmed, go back to and sign in.  You may then select and complete the course(s) you need.
10.    A copy of the scores for each module in a completed course will be sent to Diane Payne, the CITI administrator for Stevenson University.  Please direct any questions to her at 


SU Goal No. 1: Intellectual Development (ID)
The SU graduate will use inquiry and analysis, critical and creative thinking, scientific reasoning, and quantitative skills to gather and evaluate evidence, to define and solve problems facing his or her communities, the nation, and the world, and to demonstrate an appreciation for the nature and value of the fine arts.
SU Goal No. 2: Communication (C)
The SU graduate will communicate logically, clearly, and precisely using written, oral, non-verbal, and electronic means to acquire, organize, present, and/or document ideas and information, reflecting an awareness of situation, audience, purpose, and diverse points of view. 

SU Goal No. 3: Self, Societies, and the Natural World (SSNW)
The SU graduate will consider self, others, diverse societies and cultures, and the physical and natural worlds, while engaging with world problems, both contemporary and enduring. 

SU Goal No. 4: Experiential Learning (EL)
The SU graduate will connect ideas and experiences from a variety of contexts, synthesizing and transferring learning to new, complex situations.

SU Goal No. 5: Career Readiness (CR)
The SU graduate will demonstrate personal direction, professional know-how, and discipline expertise in preparation for entry into the workplace or graduate studies.

SU Goal No. 6: Ethics in Practice (EIP)
The SU graduate will practice integrity in the academic enterprise, professional settings, and personal relationships.

For more information about the SU learning outcomes and goals, please see the Stevenson catalog. 

Course Contract
Drs. Glaser and Burgess
Winterim 2017

Your signature below indicates your acceptance of the following statements:

•    I have read and understood the entire course syllabus for BIO362-ON1/ON2 Independent Research in Biology  

•    I understand, accept and will abide by the terms detailed in the course syllabus for BIO362-ON1/ON2 Independent Research in Biology  

Student’s printed name: _______________________________________        

Student’s signature: _______________________________________ Date: _________________