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OHSU Online · School of Medicine

Scientific Writing for Inform

  • Fall 2019
  • 3 Credits
  • 09/23/2019 to 12/13/2019
  • Modified 09/19/2019


The focus of this course is scientific writing and communication. Students will prepare abstracts, papers and slides as well as learn about writing theses and capstones, scientific journal articles, and grant proposals. Topics will also include bibliographic database searching and presentations and posters for scientific meetings.
Prerequisite: None
Note: Enrollment limited to admitted Biomedical Informatics students. Registration preference given to master's and PhD students. Signature Required. Course offered on a Pass/Fail basis.
Offering: Online: Fall, Spring

This syllabus is forBMI 570 OL F19,BMI 670 OL F19

Contact Information

Kathryn I. Pyle, AMLS, MA

Assistant Professor, Medical Informatics & Clinical Epidemiology

BICC 505, 503-494-6058, [email protected]

Office Hours: By phone (by appointment) or email response usually within 24 hours


Guest Lecturer: Andrew Hamilton, MLS, MS, Reference Librarian, OHSU Library

Teaching Assistant: Kelly Gossen

Meeting Times



  1. Alley, Michael. The Craft of Scientific Writing, fourth edition. New York: Springer, 2018. ISBN: 978-1-4419-8287-2
  2. Alley, Michael. The Craft of Scientific Presentations, second edition. New York: Springer, 2013. ISBN: 1441982787 ISBN-13: 9781441982780

Course Goals

  • Become more proficient in scientific writing and communication.
  • Know the basic requirements for preparing research manuscripts; writing biomedical journal articles; and preparing biomedical grant proposals.
  • Understand the basics of MEDLINE searching and citation preparation.
  • Using the principles learned in the class, prepare and revise a term paper on a biomedical informatics topic of your choice as well as prepare a presentation on the same topic.

Course Competencies, Outcomes, and Objectives


The material for each session will be posted by Monday at 5:00 am Pacific time at the latest.  Each week, in the Course Materials section of Sakai, there will be one or more lectures to watch as well as readings, short writing or grammar exercises, and Forum discussion topics.  There is also a written assignment most weeks that relates to the preparation of your term paper and slide presentation on your research topic.

The writing exercises and Forum discussion topics will be posted in the Course Materials area for that week as well as in the Submissions and Forum sections, respectively.  The written assignments are described in detail below and are also described in detail in the Submissions section of Sakai.  All written work and Forum discussion posts for a session must be submitted by 11:55 pm Pacific time on the due date to receive full credit.  It is expected that you will submit at least one Forum discussion post per session.  Written work should be submitted via the Submissions tool in Sakai.  If you have difficulties submitting work through Sakai, you may email your assignment to me at [email protected]

The primary written assignments in this course follow the iterative process of writing. Each assignment is an installment -- you will think up a fascinating health/clinical informatics or bioinfomatics topic, identify your sources, outline your structure, write an abstract, draft the first round, receive peer review, edit, finalize, et voila -- a seven-to-ten-page formal paper. 

Please select a topic related in some way to health/clinical informatics or bioinformatics and is a topic that you are not researching, developing, or writing about for another BMI course.  Also, revising a paper previously submitted in another course is not allowed.

Basic Homework Requirements:  Please name your homework file with the following convention: LastnameSessionAssignment.doc  Example: SmithSession3References.docx or Jones Session5Exercise.docx.  Please put your name and the date at the top of all written assignments. Once I download and print out an assignment for grading, I can’t tell whose it is without a name on it.  For most assignments, you can use either single or double spacing.  For the draft term paper and final version of the term paper, please use 1.5 or double spacing.



Writing Assignment

Writing Exercise

Forum Discussion Topics


7 points

Analysis of Constraints

5 points

Gunning Fog Index

1 point

Balancing precision and clarity

1 point


8 points

Summary of Paper Topic

5 points

Sentence Openers

2 points

Using familiar language

1 point


8 points

Vancouver Style References

5 points

Searching MEDLINE

2 points

Writing concisely

1 point


8 points

Outline for Paper

5 points

Preparing an abstract

2 points

Sitting down to write

1 point


12 points

Title and Abstract for Paper

10 points

Dangling and Misplaced Modifiers

1 point


1 point


2 points

No written assignment, work on draft paper

Using Transitions

1 point


1 point


16 points

Draft Term Paper

15 points

None, due to draft term paper assignment

Discussion of Thesis Presentation

1 point


7 points


Peer Review of Draft Term Paper

5 points

Faulty Parallelism

1 point

Evaluating your writing process for draft term paper

1 point


18 points

PowerPoint Presentation

15 points

Review of Eden grant proposal

2 points

Potential research topic

1 point


14 points

Final Version of Term Paper

10 points

Reviews of 3 student presentations

3 points

How has your communication changed?

1 point

Total Points


75 points

15 points

10 points


Course & Instructor Evaluations


Session One – September 23-October 2, 2019

Principles of Good Writing I

Posted by September 23rd - Due by October 2nd

Lectures: Lesson 1: Analyzing the Audience, Purpose, and Occasion; Lesson 2: Balancing Precision and Clarity; Lesson 3: Avoiding Ambiguity

Writing Exercise: Gunning Fog Index, 1 point

Forum Topic: Language goals in scientific writing, 1 point

Readings: Alley, Craft of Scientific Writing textbook, Lesson 1: Analyzing the Audience, Purpose, and Occasion; Lesson 2: Balancing Precision and Clarity; Lesson 3: Avoiding Ambiguity (pages 1-47)

Written Assignment: Analysis of Constraints Exercise, due October 2nd, 5 points

Select a recent healthcare research study (findings released within the last three years) and find both the original study published in a biomedical journal and another (non-academic) article written about the study findings (for example, a news article in the New York Times or on BBC News on the Web).

For each document, identify the following constraints:

Audience: Who is the audience? Why would they be reading the article? Purpose: Why was the article published?

Occasion: What kind of language was used in the article?  How formal is the language?

Comparison: How do the constraints differ? How do you think the writing process differed for each document?

Please discuss the original research study first and provide citations for each document.


Session Two – September 30-October 9, 2019

Principles of Good Writing II

Posted by September 30th – Due by October 19th

Lectures: Lesson 4: Sustaining Energy; Lesson 5: Connecting Your Ideas; Lesson 6: Beginning with the Familiar

Writing Exercise: Sentence openers, 2 points

Forum Topic:  Being familiar, 1 point

Readings: Alley, Craft of Scientific Writing textbook, Lesson 4: Sustaining Energy; Lesson 5: Connecting Your Ideas; Lesson 6: Beginning with the Familiar (pages 49-107)

Written Assignment: Summary of Paper Topic, due October 9th, 5 points

     Write a paragraph or two explaining the proposed topic of your term paper. Include the draft title and some proposed sources.  You can also say why you selected this particular topic, which should be related to biomedical informatics or bioinformatics in some way.  Please select a topic that can be covered appropriately in a 7-10 page paper.  I realize this is early in the term, and you may end up modifying your topic.  This assignment gives you a chance to get started on your topic and gives me an opportunity to learn more about your interests and your writing style.


Session Three – October 7-16, 2019

Bibliographic Database Searching and Citation Preparation

Posted by October 7th - Due by October 16th

Lecture: Bibliographic Database Searching and Citation Preparation, by Andrew Hamilton, MLS, MS, OHSU Library

Writing Exercise: Searching MEDLINE, 2 points

Forum Topic: Writing concisely, 1 point

Readings: Identifying and Evaluating Sources for Your Writing, References in Papers

Written Assignment: Reference List, due by October 16th, 5 points

     Using Vancouver style, create a list of 6-10 references that you might use for your term paper. You should include at least three different types of sources (for example, books, journals, and Web sites)The primary purpose of the assignment is for you to learn how to use Vancouver style, also known as Uniform Requirements for Manuscripts from the International Committee of Medical Journal Editors.  An ancillary purpose is for you to start finding source material for your term paper.  If you are not familiar with Vancouver style, which is used by many biomedical journals, please see the National Library of Medicine Web site:


Session Four – October 14-23, 2019

Principles of Good Writing III

Posted by October 14th - Due by October 23rd

Lectures:  Lesson 7: Organizing the Content for the Audience; Lesson 8: Providing Proper Emphasis; Lesson 10: Using Your Writing Time Efficiently

Writing Exercise: Preparing an abstract, 2 points

Forum Topic: Getting ready to write, 1 point

Readings: Alley, Craft of Scientific Writing textbook, Lesson 7: Organizing the Content for the Audience; Lesson 8: Providing Proper Emphasis; Lesson 10: Using Your Writing Time Efficiently (pages 109-152, 199-226)

Written Assignment: Outline of Paper, due by October 23rd, 5 points

     Please submit a one-to-two-page, logically organized outline for your paper.  You may choose the style of outline (based on those presented in the lecture).  Provide enough detail so that the major sections and structure of your term paper are clear.


Session Five – October 22-30, 2018

Preparing Research Manuscripts

Posted by October 21st - Due by October 30th

Lecture: Preparing a Research Manuscript as a Journal Article or Thesis/Capstone

Writing Exercise: Misplaced and Dangling Modifiers, 1 point

Forum Topic: TBD, 1 point

Readings: Graphs, Tables, and Figures in Scientific Publications: The Good, the Bad, and How Not to Be the Latter

Written Assignment: Abstract of Paper, due October 30th, 10 points

Please prepare a draft abstract of your paper, including a title.  Your abstract should not exceed 250 words.  You may use a descriptive, informative or structured (if applicable) abstract format.


Session Six – October 29-November 7, 2019

Preparing Biomedical Journal Articles and Peer Review

Posted by October 28th - Due by November 6th

Lectures: Preparing Biomedical Journal Articles; Peer Review of Biomedical Journal Articles

Writing Exercise: Using Transitions, 1 point

Forum Topic: TBD, 1 point

Readings: How to write an article: Preparing a publishable manuscript; Reviewing manuscripts for biomedical journals

Written Assignment: None – work on your draft paper   


Session Seven – November 4-13, 2019

Presentations and Posters

Posted by November 4th - Due by 13th

Lecture: Scientific Poster Presentations

Writing Exercise: None

Forum Topic: Presentation style of DMICE thesis defense, 1 point

Readings: Alley, Craft of Scientific Presentations, chapters 1, 2, 5; BMJ article: How Not to Give a Presentation; The Scientist: Poster Perfect; CMAJ: Effect of colour coordination of attire with poster presentation on poster popularity

Written Assignment: Draft paper due by November 13th - 15 points – give copy to assigned peer reviewer

     The first draft of your paper is due. The paper should be a minimum of seven pages and a maximum of ten pages, 1.5 or double-spaced (not counting the title page, abstract, or references). The draft should be complete (no missing sections) and include a title page, abstract and reference list. Please include page numbers.

     Please create a title page with the title of your paper, your name, and the date.  The title page does not count as one of the 7-10 pages of your paper.

     The first item on the next page should be your abstract.  An abstract is a summary of the contents of the paper: it is not a substitution for an introduction section in the paper.  You should not have any content in the abstract that is not in the paper (although the wording does not have to be identical).  Also, abstracts do not contain references; you should not begin citing reference numbers until the beginning of the paper itself.  The abstract included in the draft paper should be revised from the one submitted in Session Five, based on feedback from the instructor.

     Please use section headings in your paper.

     Please use Vancouver style for your references.  References should be numbered in the order they appear in the paper.  Each reference keeps the same number, no matter how many times it is cited in your paper.  Please use superscript numbers for your reference numbers in the body of the paper.  When using the superscript reference numbers, the number goes after a period or comma, not before.  So if the reference number is at the end of a sentence, for example, it should look like:  …according to Brown et al.15  If you have a semi-colon, the reference number would be before the semi-colon. 

     The reference list at the end of the paper should list the references in the order they were cited in the paper.  It is fine to use reference management software but please proof your list to make sure there are no errors.

     You might want to take a look at one of these JAMIA papers to see how their references are formatted.  However, please list 6 authors before “et al” instead of just 3.  Also, I like periods with e.g. and i.e.

     JAMIA bioinformatics paper sample (for formatting):  ‘N-of-1-pathways’ unveils personal deregulated mechanisms from a single pair of RNA-Seq samples: towards precision medicine

     JAMIA clinical informatics paper sample (for formatting):  A qualitative study of the activities performed by people involved in clinical decision support: recommended practices for success


Session Eight – November 11-20, 2019

Presentation Slides

Posted by November 11th - Due by November 20th

Lecture: Effective Presentations, parts 1 and 2

Writing Exercise: Faulty Parallelism, 1 point

Forum Topic: Evaluating the writing process for the draft term paper, 1 point

Readings: Alley, Craft of Scientific Presentations, chapters 3-4

Written Assignment: Review of another paper, due by November 21st, 5 points

     You will exchange draft papers with another student and provide a peer review of that person’s paper, using a peer review form.  Reviewer assignments will be made by the instructor partway through the term.  The credit for this assignment is for you doing a review of another person’s paper.  A copy of the completed peer review form must be sent to both the author of the paper and to the instructor.

Session Nine – November 18-27, 2019

Grant Proposals

Posted by November 18th - Due by November 27th

Lecture: Preparing Proposals

Writing Exercise: Review of grant proposal, 2 points

Forum Topic: Research topic, 1 point

Readings:  Alley Craft of Scientific Writing textbook, Lesson 9, pages 174-198

Written Assignment: Presentation with voiceover recorded in Echo 360 – due November 27th, 15 points

     Using Echo360, prepare an oral presentation with voiceover on your paper topic, using the Alley format presented in class (sentence headlines, images, no bullets).  You should prepare enough slides for a 7-10 minute talk, as if you were presenting at an American Medical Informatics Association meeting, and your talk should have a beginning, middle and end (summary).  More information on preparing the slides will be provided later in the term.  The slides will be posted in Sakai and you will be asked to critique other students’ presentations.  Instructions for using Echo 360 are found in Course Materials.


Session Ten – November 25-December 6, 2019

Student Presentations

Posted by November 25th - Due by December 6th

View Student Presentations

Writing Exercise: Critique of other students’ presentations

Forum Topic: How has your communication changed, 1 point

Written Assignment: Final Paper due by Friday, December 6th, 10 points

     Based on the feedback from both Kathryn and your peer reviewer, please revise your draft paper and submit it by 11:55 p.m. Pacific time on Friday, December 6th.  Remember to include a title, the abstract, and references (in Vancouver style) and number your pages.

Course Policies and Resources


Students are encouraged to download and save course content (excluding videos) from each class in Sakai while you are taking the class if you think you will want to refer to it later. This is especially important for PhD students who will need to review content prior to taking the qualifying exam.


This course will have an online component, which can be accessed through Sakai, OHSU’s online course management system. For any technical questions or if you need help logging in, please contact the Sakai Help Desk.


Hours: Sakai Help Desk is available Mon – Fri, 8 am – 9 pm, and weekends, 12 pm – 5 pm, Pacific Time.

Contact Information:

Phone (toll-free): 877-972-5249


Email:  [email protected]

School Policies and Resources

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 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.

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.

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.

School Competencies

OHSU Competencies

OHSU Graduation Core Competencies

1.  Professional Knowledge and Skills

Demonstrate competence in the core knowledge, skills, and practices as defined by degree programs and relevant professional licensing and credentialing boards.

2.  Reasoning and Judgement

Demonstrate the ability to identify and define problems, critically compare options, make timely decisions or recommendations, identify uncertainties, and use findings to improve outcomes in light of evolving evidence.

3.  Evidence-Based Practice and Research

Demonstrate the ability to access, evaluate, and apply relevant science knowledge to support evidence-based health care, disease prevention, health promotion and discovery.

4.  Lifelong Learning

Demonstrate the ability to recognize gaps in knowledge and experience through informed self-assessment and reflective practices, and take actions to address those gaps.

5.  Communication

Demonstrate active listening and oral and written communication skills with diverse individuals, communities, and colleagues to ensure effective, culturally appropriate exchange of information.

6.  Professionalism and Ethics

Demonstrate integrity, honesty, knowledge of ethical principles and the standards of professional conduct, and the ability to apply ethical principles in clinical care, research, education or community service.

7.  Teamwork

Demonstrate the abilities required to foster and work effectively within collaborative, team-based environments.

8.  Safety and Quality Improvement

Demonstrate the ability to identify situations that compromise safety and participate in risk reduction and continuous quality improvement.

9.  Systems

Demonstrate an appropriate understanding of evolving health care systems, health and science policy, and resource allocation in order to optimize human health and scientific discovery.

10. Patient/Client-Centered Care

Additionally, clinical degree program graduates will be able to...

Demonstrate the ability to collaborate with diverse individuals, families, and communities to provide quality care that is respectful of and responsive to their preferences, needs, attitudes, beliefs and values.

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:

Students should review the Student Portal, 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. For specific campus information, outside of Portland, check the following sites:

OHSU Learning 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 Sakai 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

Office of Public Safety

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

*Exceptions include Public Health students who have selected PSU as their primary providers and students whose home campus is a satellite campus or online. 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 Ombudsman; Ombudsman Website

Library: Biomedical Information Communication Center
BICC Library Hours of Operation

Additional Items