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Portland Campus · School of Medicine

Research Methods/Bioinformatic

  • Winter 2020
  • 1-2 Credits
  • 01/06/2020 to 03/20/2020
  • Modified 02/18/2020


The Research in Bioinformatics course is designed to give students a foundation in general research approaches with specific application to bioinformatics, computational biology, and clinical informatics. This is the first in a two-part course, with the second part of the course being taken in the Spring. This course will focus on developing the critical thinking and evaluation skills necessary to be successful in the field. Special emphasis will be placed on critical evaluation of the literature, and preparing to do a project in the Spring term course.

This syllabus is forBMI 552A PDX W20,BMI 652A PDX W20

Contact Information

Eilis Boudreau, M.D., Ph.D., [email protected]

Office Hours: by appointment

Meeting Times

This course will meet 9:30-11:30 am on six Fridays during the term per the table below.



Week #














Course Coordination:

The course Website will be the central location for the distribution of course materials and assignment listing. For any technical questions or if you need help logging in, please contact the Sakai Help Desk.


Hours: Sakai Help Desk is available Mon – Thurs., 8 am – 7 pm, Fridays 8-5, and Sundays 12 pm – 5 pm, Pacific Time.

Contact Information:

(Toll-free) 877-972-5249

(Email) [email protected]


ReferenceText (will be in library on reference reserve if you don’t want to purchase one of these manuals): or

Reading Material: Relevant literature from the fields of biomedical research, bioinformatics, and computer science.

Course Goals

Course Competencies, Outcomes, and Objectives

  • If presented with a research idea, be able to identify informatics issues relevant to the problem and be able to develop and articulate appropriate approaches to finding solutions to these problems.
  • Critically develop a research idea (hypothesis), including complete a thorough background evaluation of the literature relevant to this idea.
  • Understand basic principles of project management and be able to develop a simple project plan.



This course is given for a letter grade. The final grade will be based on 100 points. The number of points assigned to each activity is as follows: 40 points for your written bibliography, 30 points for your in class bibliography presentations, and 30 points for your Specific Aims Rewrite. All written assignments should be submitted through Sakai and grades for written assignments will be posted in Sakai no later than two weeks after the assignment due date (for assignments submitted late, grades will be posted no later than two weeks after the assignment is submitted).



# Points

Due Date/Time

Written bibliography.


2/20/20, 11 PM (submit to Sakai)

Bibliography presentations.


In class

Rewrite Sample Specific Aims Page


3/19/20, 11 PM (submit to Sakai)

Complete OHSU IRB training


3/20/20, 11 PM

Final Class Grade




Late Submissions

The assignments will be marked down by 1 point per day if you have not obtained prior permission to delay submission from the instructor. An assignment is considered late if submitted anytime after the Sakai deadline. For example, if a written assignment is due at 11 PM and you submit it at 11:05 PM you will lose 1 point. If the assignment still has not been submitted by the following day by 11 PM, you will lose another point. A one-point loss will continue to occur for each day late until the assignment has been submitted.


Class Participation

While you will have some lectures during the term, a significant amount of class time is devoted to interactive in-class exercises. Therefore, it is very important that you come to all class sessions on time. If for some reason you must miss a class, please let the instructor know in advance (or in the case of an emergency as soon as possible after the class is missed). In these cases, you may be given a make-up exercise if appropriate to do on your own. Repeated tardiness to class may also result in the loss of 1 point on your final grade for each class session for which you are late.


Grades are assigned based on the following criteria:

A             93-100

A-           90-92.99

B+           87-89.99

B             83-86.99                                                                             

B-            80-82.99                    

C+           77-79.99                    

C             73-76.99                    

C-            70-72.99                    

F              <70        

Course & Instructor Evaluations



class #




--Course Introduction

-- Development of a research question

-- Accurate documentation of your scientific work

--Using a bibliography to trace lineage of an idea




--Introduction to the Specific Aims page

--Reference Management Best Practices (with guest reference librarian)




Using a Bibliography to Trace Lineage of an Idea (includes time to interact with archivist, and identify and review archival materials

Meet in Old Library Building in Historical Archives; be ready to do primary archival research


--Introduction to Institutional Review Board (IRB)

--In-class bibliography presentations



--In-class bibliography presentations




--Discussion of Specific Aims Pages rewrites

--Discussion of Spring Term projects

--Class wrap-up



Week 1

  • Course Introduction, accurate documentation of your scientific work
  • Using a bibliography to trace lineage of an idea, intro to development of an scientific question
  • Introduction to the Institutional Review Board (IRB)

Week 1 Assignments:

  • Reading: UW-Madison Writing Center document on acknowledging sources (
  • Reading in The Grant Application Writer’s Workbook on developing a scientific idea and preparing a Specific Aims page
  • Complete required training for OHSU IRB. All units must be completed by the last day of class (see table of assignment due dates/times).
  • Begin preparation of a bibliography based on the topic of your choice. Although you will have 6 weeks to complete this project, it requires iterative work and you should plan to spend some time on it every week. This bibliography will be the tool by which you trace the lineage of a key idea(s) in your chosen area. This literature review should go back AT A MINUMUM to 1900. As part of this exercise, you will choose a reference manager and prepare the bibliography using a common reference format of your choosing. Please list on the bibliography which reference manager that you used to prepare the document. For each reference cited, you must have reviewed a copy of the actual reference. It is insufficient to cite a reference for which you have not been able to obtain a copy of the actual article or for older literature, the book which you are citing. To accomplish this exercise, you will need to cite between 10 – 15 references. However, during the course of the exercise you will need to review significantly more papers or resources in order to identify the most significant ones. In general, these references should cover the whole time period equally (eg. do not cite 8 references from the past 10 years and then only a few covering the previous 100 years). If there is a large time gap of 20 years or greater, during which no major developments occurred in the field, then you must note this in your bibliography and briefly state why you think progress in the area was stagnant. Each reference should be followed by a few sentences that describe what the paper contributes to the field. Lastly, at least one of the references you cite must be considered archival material. This material may predate 1900. We will be spending the entire third class in the OHSU library archives, where you will be given an introduction to these resources and provided with an opportunity to review some archival materials. Feel free to be creative with this assignment (eg. you may insert 1-2 pictures or diagrams but only use them if they really support and enhance the bibliography).


Your bibliography should minimally include the following:

  • Documentation of the reference manager used and demonstration that this reference manager was used to generate the bibliography.
  • Coverage of the literature on the topic back to at least 1900 with no gaps longer than 20 years. If there are truly no major developments in the area for over 20 years, then insert a line or two in the bibliography hypothesizing why this gap in development occurred.
  • Citation of at least one archival reference that you have personally reviewed.
  • A succinct paragraph after each reference describing what that reference contributed to the body of literature on the subject and/or how the reference represented a paradigm shift in the field.

In class we will spend about 20 minutes on each bibliography (10 minute presentation followed by discussion for the remainder of the time). This presentation should focus on how your bibliography delineates the lineage of the core idea(s) you’ve studied. You may bring a copy of your bibliography with you for your class presentation for reference but you will not need to prepare handouts or slides.  During your presentation, you should not just read your bibliography to the class. You should come to class prepared to tell a engaging story to your classmates about the development of the idea(s) you researched. Some of the ideas you present may have also been cited by others in the class during their bibliography presentations so you may be interrupted during your presentation to comment on the overlap.

The course of science is often impacted by external forces such as the politics of the era (eg. bans on certain experiments, war, etc.) and the personalities of the individuals engaged in research (eg. individuals working in isolation or those with such difficult personalities that they were ostracized by colleagues). If you feel that a particular discovery was substantially influenced by one of these factors, then you should be prepared to weave this into the story you create around your bibliography. You may also want to note these factors on your written bibliography, as they may be relevant to the development of a particular paper or may be the reason why there was a prolonged gap in the development of a key idea.


Week 2

  • Introduction to the Specific Aims page
  • Reference Management Best Practices (with guest reference librarian)


Week 2 Assignment:

  • Complete required training for OHSU IRB. All units must be completed by 11 PM on the last day of the term.
  • Work on bibliography project.
  • Submit any requests to archival librarian to pull special materials for you at least 1 week before class #3.


Week 3 (Meet in Old Library Historic Archives Room)

  • Using a bibliography to trace lineage of an idea (includes time to interact with archivist and review archival materials
  • Random partner assignments


Week 3 Assignment: work on bibliography project.


Week 4 Bibliography presentations.

            Week 4 Assignment: work with assigned class partner on identifying areas of overlap between your two bibliography projects.



Week 5 Bibliography presentations.

Week 5 Assignment: Work on assigned Specific Aims page rewrite


Week 6

  • Discussion of Specific Aims pages rewrites
  • Discussion of Spring Term projects
  • Class wrap-up







Course Policies and Resources

School Policies and Resources

Graduate Studies Guidelines:

Students are responsible for following all OHSU School of Medicine, Graduate Studies, and program/department guidelines & policies. For more information, please visit here. For program/department guidelines & policies, please inquiry with the program/department director and/or coordinator.

School of Medicine Conduct Policy (housed under the graduate studies guidelines section)

Students are responsible for their own academic work. Students are expected to have read and practice principles of academic honesty, as presented in the Graduate Studies Student Handbook.

The School of Medicine reserves the privilege of retaining only those students who, in the judgement of the faculty, satisfy the requirements of scholarship and clinical performance necessary to maintain the highest standards. The Student Handbook has information about academic standards and probation and dismissal policies.

Grading Criteria, Academic Standards, & Release of Final Grades:

Graduate Studies in the OHSU School of Medicine is committed to providing grades to students in a timely manner. Course instructors will provide students with information in writing at the beginning of each course that describes the grading policies and procedures including but not limited to evaluation criteria, expected time needed to grade individual student examinations and type of feedback they will provide.

All coursework applied towards degree requirements must meet the minimum cumulative grade point average of at least 3.0.

Refer to the School of Medicine Graduate Studies Forms & Policies for withdraw, incomplete, and in-progress grading standards. Final course grades will be posted with the OHSU Registrar the Monday following the last day of the term. On those occasions when a grade has not been submitted by the deadline, the following procedure shall be followed:

  1. The Department*/Program** Coordinator will immediately contact the Instructor requesting the missing grade, with a copy to the Program Director and Registrar.
  2. If the grade is still overdue by the end of next week, the Department*/Program** Coordinator will email the Department Chair directly, with a copy to the Instructor and Program Director requesting resolution of the missing grade.
  3. If, after an additional week the grade is still outstanding, the student or Department*/Program** Coordinator may petition the Office of Graduate Studies for final resolution.

*For courses that are run by a specific department.

**For the conjoined courses (course number is preceded by CON) that are run by Graduate Studies.

Graduate Studies Inclement Weather Procedures

Inclement weather procedures can be found here. In the case of inclement weather, the faculty member will email or place a voice-mail greeting on her/his office telephone number by 6:00am on the day of the clinical or class to give instructions to students about the class schedule.

Graduate Studies Copyright Information

Every reasonable effort has been made to protect the copyright requirements of materials used in this course. Class participants are warned not to copy, audio, or videotape in violation of copyright laws. Journal articles will be kept on reserve at the library or online for student access. Copyright law does allow for making one personal copy of each article from the original article. This limit also applies to electronic sources.

DMICE Communication Policy

  1. If the syllabus directs the student to contact the TA before contacting the instructor, the student should do so. Otherwise, the student should contact the instructor and allow 2 business days (not including weekends) for a response.
  2. If the student does not receive a response from the instructor within 2 business days, s/he should contact the TA (if there is one). When contacting the TA s/he should cc the instructor and Diane Doctor at [email protected].
  3. If a student does not receive a response from the TA within 1 business day (not including weekends), s/he should contact Diane Doctor at [email protected] and cc the instructor and the TA.
  4. If Diane does not reply within 1 business day (not including weekends), the student should contact Andrea Ilg at [email protected].
  5. Students having difficulties with Sakai should contact the Sakai Help Desk at [email protected] or at (877) 972-5249. Sakai help is available M-F from 8am to 10-pm and weekends from Noon to 5pm. Do not contact the instructor.

When Problems Arise

It is critical to contact the appropriate person when problems arise:

  • For basic Sakai problems and course issues (e.g., cannot log in, after-hours technical assistance, Course Materials or Forum not available/accessible during regular business hours/days), contact the Sakai Help Desk: Toll-Free - (877) 972-5249; email - [email protected] Sakai help is available M-F from 8 am to 9 pm and weekends from Noon to 5pm.

  • For questions about course content (e.g., do not understand a topic or disagree with homework quiz answer), contact the Teaching Assistant, who will be announced at the beginning of the course: go to the Email Tab after logging into the course and choose “Associate” role to send message to the TA or post a question in the Forums.

Examination Policy

It is OHSU policy that any exam offered online and worth more than 10% of the final course grade must be virtually proctored. In this course, we will be using the services of Examity, a remote proctoring services company. You will be required to schedule your exam three (3) weeks ahead of time. There is no cost to the student. More information will be provided to you regarding setup, scheduling, and requirements in the Course Materials.

Policy number: 02-70-050

Turn It In

In an effort to uphold the principles and practice of academic honesty, faculty members at OHSU may use originality checking systems such as Turnitin to compare a student’s submitted work against multiple sources. To protect student privacy in this process, it will be necessary to remove all personal information, i.e. student name, email address, student u-number, or any other personal information, from documents BEFORE submission.

Sakai and TLC Help Desk

You will learn through the Sakai learning management software at The online component includes reading material, lectures (including streaming presentations and handouts), project material, learning assignments, and online discussions.  If you have any technical questions or if you need help logging in, please contact the Sakai Help Desk, which is open Mon – Fri, 8 am – 9 pm and weekends 12 pm – 5 pm, Pacific Time.

Contact Information:

(Toll-free) 877-972-5249


(Email) [email protected]

Online Etiquette

Please use professional etiquette when communicating with peers and the instructor. This means avoiding aggressive or offensive language, showing respect for others’ opinions and positions, and conducting yourself as if you were face to face with them. Please pay special attention to etiquette in class forums and when using email. If you notice someone violating this policy, please make the instructor and TA aware of the problem.

School Competencies

OHSU Competencies

List of OHSU Graduation Core Competencies
  1. Professional Knowledge and Skills
  2. Reasoning and Judgement
  3. Evidence-Based Practice and Research
  4. Lifelong Learning
  5. Communication
  6. Professionalism and Ethics
  7. Teamwork
  8. Safety and Quality Improvement
  9. Systems
  10. Patient/Client-Centered Care (Clinical)
To access a descriptive list of OHSU Graduation Core Competencies:  OHSU Graduation Core Competencies

Institutional Policies and Resources

Statement Regarding Students with Disabilities:

OHSU is committed to inclusive and accessible learning environments in compliance with federal and state law. If you have a disability or think you may have a disability (mental health, attention-related, learning, vision, hearing, physical or health impacts) contact the Office for Student Access at (503) 494-0082 or OHSU Student Access to have a confidential conversation about academic accommodations. Information is also available at Student Access Website. Because accommodations may take time to implement and cannot be applied retroactively, it is important to have this discussion as soon as possible.

Portland State students also have similar resources available via the PSU Disability Resource Center (website ). Please contact the DRC at tel. (503) 725-4150 or email at [email protected]

Student Evaluation of Courses:

Course evaluation results are extremely important and used to help improve courses and the learning experience of future students. Responses will always remain anonymous and will only be available to instructors after grades have been posted. The results of scaled questions and comments go to both the instructor and their unit head/supervisor. Refer to Student Evaluation of Courses and Instructional Effectiveness, *Policy No. 02-50-035.

*To access the OHSU Student Evaluation of Courses and Instructional Effectiveness Policy, you must log into the OHSU O2 website.

Copyright Information:

Copyright laws and fair use policies protect the rights of those who have produced the material. The copy in this course has been provided for private study, scholarship, or research. Other uses may require permission from the copyright holder. The user of this work is responsible for adhering to copyright law of the U.S. (Title 17, U.S. Code). To help you familiarize yourself with copyright and fair use policies, the University encourages you to visit its Copyright Web Page

Sakai course web sites contain material protected by copyrights held by the instructor, other individuals or institutions. Such material is used for educational purposes in accord with copyright law and/or with permission given by the owners of the original material. You may download one copy of the materials on any single computer for non-commercial, personal, or educational purposes only, provided that you (1) do not modify it, (2) use it only for the duration of this course, and (3) include both this notice and any copyright notice originally included with the material. Beyond this use, no material from the course web site may be copied, reproduced, re-published, uploaded, posted, transmitted, or distributed in any way without the permission of the original copyright holder. The instructor assumes no responsibility for individuals who improperly use copyrighted material placed on the web site.

Syllabi Changes and Retention:

Syllabi are considered to be a learning agreement between students and the faculty of record. Information contained in syllabi, other than the minimum requirements, may be subject to change as deemed appropriate by the faculty of record in concurrence with the academic program and the Office of the Provost. Refer to the *Course Syllabi Policy, 02-50-050.

*To access the OHSU Course Syllabus Policy, you must log into the OHSU O2 website.

Commitment to Diversity & Inclusion:

OHSU is committed to creating and fostering a learning and working environment based on open communication and mutual respect. If you encounter sexual harassment, sexual misconduct, sexual assault, or discrimination based on race, color, religion, age, national origin, veteran’s status, ancestry, sex, marital status, pregnancy or parenting status, sexual orientation, gender identity, disability or any other protected status please contact the Affirmative Action and Equal Opportunity Department at 503-494-5148 or [email protected]. Inquiries about Title IX compliance or sex/gender discrimination and harassment may be directed to the OHSU Title IX Coordinator at 503-494-0258 or [email protected]

Modified Operations, Policy 01-40-010:

Portland Campus:  Marquam Hill and South Waterfront

Students should review O2 or call OHSU’s weather alert line at 503-494-9021 for the most up-to-date information on OHSU-wide modified operations which include but are not limited to delays or closures for inclement weather.

If your home institution is not on the Portland campus (Marquam Hill or South Waterfront, contact your home institution for more information.

OHSU Resources Available to Students*:

Registrar’s Office
Mackenzie Hall, Rm. 1120
503-494-7800; Email the Registrar

Student Registration Information: 
To Register for Classes

OHSU ITG Help Desk
Regular staff hours are 6 a.m. to 6 p.m., Monday through Friday, but phones are answered seven days a week, 24 hours a day. Call 503 494-2222.

Teaching and Learning Center
Academic Support Counseling and Sakai Course Management System, please contact the TLC Help Desk at 877-972-5249 or email TLC Help Desk

Concourse Syllabus Management
For help with accessing your Concourse Syllabus:  Please contact the Sakai help Desk for all other Concourse inquiries please visit the Concourse Tutorial Website or please contact the Mark Rivera at [email protected] or call 503-494-0934

Public Safety

OHSU Public Safety-Portland Campus (Marquam Hill and South Waterfront)

*Joseph B. Trainer Health & Wellness Center 
Baird Hall, Rm. 18 (Primary Care) and Rm. 6 (Behavioral Health)
503-494-8665; For urgent care after hours, 503-494-8311 and ask for the Nurse on call.
Wellness Center Information  
Wellness Center Website

If your home institution is not on the Portland campus, contact your home institution student support services for more information.

Ombudsman Office
Gaines Hall, Rm. 117
707 SW Gaines Street, Portland, OR 97239
503-494-5397; Contact OmbudsmanOmbudsman Website

Library: Biomedical Information Communication Center
BICC Library Hours of Operation

Additional Items