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OHSU Online · School of Medicine

Comp Science/Prog Clin Inform

  • Fall 2018
  • 3 Credits
  • 09/24/2018 to 12/14/2018
  • Modified 09/22/2018


BMI540 provides an introduction to computer science and programming demonstrated through the Python programming language.  In addition, the course includes the presentation of computer science principles, including spreadsheets, representation and storage of data, architecture, operating systems, and algorithms.  The goal of this class is to expose clinical informatics students to programming in Python for common data manipulation and analysis tasks.

Offering: On Campus: Fall; Online: Fall

Note: Enrollment limited to admitted Biomedical Informatics students who have completed the introductory computer programming prerequisite.


Prerequisite: Prior college-level computer programming course and successful completion of a pretest.


Contact Information

Instructor: Dr. Michelle R Hribar

The best way to reach me is by email, even if you'd prefer to talk with me.  We can set up times to meet virtually, on the phone, or in person.


Think Python, How to Think Like a Computer Scientist

  • Author: Allen B. Downey
  • Publisher: O'Reilly Media
  • Edition: 2nd
  • ISBN: 1491939362

Python for Everybody

  • Author: Charles Severance
  • Publisher: CreateSpace Independent Publishing Platform
  • ISBN: 1530051126

Available for free online at:

Computer Science: An Overview

  • Author: Glenn Brookshear & Dennis Brylow
  • Publisher: Pearson
  • Edition: 12
  • ISBN: 1292061162
  • Optional

Optional text.  Any edition >= 11 is sufficient.

Course Goals

The main goal of BMI 540 is to introduce students to the fundamentals of computer science and programming in Python that are relevant to clinical informatics. Specific topics for BMI 540 include:

  • The history of computing
  • Representation and manipulation of data
  • Operating systems
  • Algorithms, iterative and recursive structures, efficiency and correctness
  • Fundamental data types, such as strings, integers, floats, etc.
  • Control structures, such as if-then, while, etc.
  • Objects and Functions
  • Simple I/O from files.
  • Computer Architecture
  • Networks
  • Data manipulations such as filtering and sorting
  • Data visualization


There will be 6 assignments. They will be a combination of programs and problem sets.  There will be 2 quizzes and a final exam.

Course & Instructor Evaluations

You will be asked to evaluate the course at the end of the term, but there will also be opportunities during the course to provide feedback.


Tentative--may change as course progresses.

Course calendar and related activities
When Topic Notes
Week 1
Computer Overview & Computer History

Prepping for spreadsheets assignment

Week 2
Data manipulation, graphing in spreadsheets & data storage, memory

Spreadsheets assignment & binary conversion problem set

Week 3
Python Overview & Computer Architecture

Program 1

Week 4
Conditional Expressions, Iteration, Lists

Quiz 1

Week 5
Dictionaries, Tuples, Files & Algorithms

Program 2 & Algorithms problem set

Week 6
Objects & Operating Systems
Week 7

Quiz 2

Week 8
Data Manipulation in Python

Program 3

Week 9
Graphing in Python

Thanksgiving holiday

Week 10
Data visualization

Program 4

Week 11

Final Examination

Course Policies and Resources

Computer Environment

Students will be using their own computers to develop code in Python.  Instructions will be given for accessing an online development environment.

Instructions for turning in your work will be provided with each exercise and must be followed exactly for full credit.


The class will require completion of weekly homework assignments and two examinations. There will be discussions in the forums as well. The final grade will be determined with an approximate weighting of

Participation 10%

Homework 40%

Quizzes 20%

Final Exam 30%

Participation is defined as contributing to the discussion forums. Homework assignments must be turned in by the due date. Only assignments that are correct and complete upon submission by the original due date will receive full credit.

Learning to program can be very time consuming and frustrating, but the only way to learn is by doing. It is in your best interests to keep up with the homework assignments and the reading, as it is easy to get hopelessly behind. To encourage everyone to keep up, assignments that are not submitted on time will be penalized. Late assignments will be downgraded up to10% per day.  Assignments that are more than 10 days late will not be accepted.

Final grades are determined at the end of the quarter and usually are assigned as follows:

A 94 – 100

A- 90 – 93

B+ 87 – 89

B 83 – 86

B- 80 – 82

C+ 77 – 79

C 73 – 76

C- 70 – 72

D/F < 70

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