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Portland Campus · School of Medicine

Research Methods/Bioinformatic
BMI-552B

  • Spring 2019
  • 1 - 2 Credits
  • 04/01/2019 to 06/21/2019
  • Modified 04/11/2019

Description

The Research in Bioinformatics course is designed to give students (Masters, Ph.D., and fellows) a foundation in general research approaches with specific application to bioinformatics and medical informatics. This is the second of a two-part course which will focus on developing the critical thinking and evaluation skills necessary to be successful in this field. The emphasis this term will be on executing an informatics project and preparing a Specific Aims page using the skills developed during the first part of the course.

Requisites

Prerequisites: Acceptance into the DMICE bioinformatics track or instructor permission and completion of Bioinformatics 552A/652A.

Contact Information

Instructors:

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

Deborah Woodcock, M.B.A. [email protected]

 

Office Hours: by appointment

Meeting Times

One Credit Hour

Spring, Fridays 10:30 AM – 12:30 PM*

*Course Meeting Time: Class meets for two hours on six Fridays (4/5/19, 4/12/19, 4/26/19, 5/17/19, 5/31/19, 6/7/19).

BICC 124

Materials

Texts: The Grant Application Writer’s Workbook, available at http://www.grantcentral.com/workbook_nih_sf424_shortened.html

 

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

Course Goals

Course Competencies, Outcomes, and Objectives

Course 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), and complete a Specific Aims page which outlines an approach to testing this hypothesis.
  • Develop and execute an informatics project plan and complete a project for a design challenge.
  • Understand how a grant proposal is prepared and evaluated.

 

Assessment

COURSE GRADING POLICY:

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: 35 points for your project management deliverables; 30 points for your Specific Aims page; 12.5 points for your AMIA project submission write-up (or equivalent if doing an alternate challenge); 12.5 points for your final project presentation; 10 points for your primary grant reviewer summary statement. All written assignments should be submitted through Sakai and grades for written assignments will be posted in Sakai two weeks after the assignment due date or completion of presentations (for assignments submitted late, grades will be posted two weeks after the assignment is submitted).

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

Schedule

Task

Points

Due Date

Post in Project Management and term projects forum: Thesis project work plan 

5

Thursday 4/11/19 @ 11:55 PM

 

Submit in Sakai: Term project team charter

5

Thursday 4/18/19 @ 11:55 PM

Submit to Sakai: Draft term project charter/SOW

5

Thursday 4/25/19 @ 11:55 PM

Bring a near-final draft of Specific Aims page to class.

N/A

Friday 4/26/19

Submit to Sakai: Final term project charter/SOW and initial/high-level project work plan

10

Thursday 5/2/19 @ 11:55 PM

Submit to Sakai your Final Specific Aims page

20

Friday 5/10/19

(10:30 AM)

Post your final Specific Aims page to Forum section of Sakai

N/A

Friday 5/10/19

(10:30 AM)

Do primary grant review using your assigned SA page; come prepared to class ready to lead discussion on your assigned SA page

N/A

In-class Friday 5/17/19 (you may not present until 5/31/19 but all reviewers must be prepared for possible review presentation by 5/17/19)

Submit to Sakai your Primary Reviewer Summary Statement

10

1 PM on the day after assigned in-class grant review completed (either Saturday 5/18/19 or 6/1/19 at 1 PM)

Submit to Sakai: Updated/detailed project work plan

5

Thursday 5/23/19 @ 11:55 PM

Submit to Sakai: Final project presentation (copy of your slides and link to site where the beta version of your project can be accessed)

Present in class

10

Friday 6/7/19 @ 10 AM

 

Submit to Sakai: Final project write-up

25

Friday 6/14/19 @ 5 PM

Submit to Sakai: Project reflections

5

Friday 6/14/19 @ 5 PM

Final Class Grade

100

 

Course Outline:

 

Week 1 (4/5/19; room 124)

  • Course Introduction
  • Project Management: Organizing & Preparing - Deb Woodcock

Week 1 Assignments:

  • Working individually, create a thesis project work plan based on the WBS your group developed in class (stickies exercise). Each person should submit their own work plan. Post your work plan in the Thesis project work plan forum on Sakai by Thursday 4/11/19 at 11:55 PM.
  • Identify a topic for your specific aims page. This can be written on a topic related to your project or another area of your choosing. Some students may choose to do it on a topic related to their research.

 

Week 2 (4/12/19; room 124):

  • Project Management: Executing and Closing – Deb Woodcock
  • Project kickoff
  • NIH Grant Review Process

Week 2 Assignment:

  • Convene your project team and develop a team charter for your project. The team charter should clearly identify how each project team member will individually contribute to the completion of the project. You'll create this document as a group, but each team member should submit a copy of the files in Sakai by Thursday 4/18/19 at 11:55 PM. ​All members of the team should review and agree upon this file prior to submission.
  • Convene your project team, define your project, and begin to draft your project charter/SOW. Your charter/SOW should follow project management best practices as discussed in class, and include as much detail as you can provide, based on your initial understanding of the project. You'll create this document as a group, but each team member should submit a copy of the files in Sakai by Thursday 4/25/19 at 11:55 PM. ​All members of the team should review and agree upon this file prior to submission.
  • Bring at least one copy of your near final draft Specific Aims page to class on Friday 4/26/19. You will be using this draft for the in-class exercise. Based on the feedback you get in class, you will be able to make corrections and then submit your final Specific Aims page to Sakai by Friday 5/10/19 at 10:30 AM. In addition to submitting to Sakai, please also post a copy of your FINAL Specific Aims page to the Forums section by Friday 5/10/19 at 10:30 AM. Each class member will be assigned to be the primary reviewer for one Specific Aims page for our Mock Grant reviews. You will be able to download your assigned Specific Aims page from the Forum’s section of Sakai. Reviewer assignments will be made in class on 4/26/19.

 

Week 3 (4/26/19; room 124):

  • In-class review of Specific Aims pages
  • Five-minute project updates

Week 3 Assignment:

Convene your project team to 1) finalize your project charter and 2) develop a high-level work plan for your project. Your plan should be based on your charter, follow project management best practices as discussed in class, and include as much detail as you can provide, based on your initial understanding of the project. You'll create these documents as a group, but each team member should submit a copy of the files in Sakai by Thursday 5/2/19 at 11:55 PM. ​All members of the team should review and agree upon these files prior to submission.

 

Week 4 (5/17/19; room 124):

  • Mock Grant Reviews
  • Five-minute project updates     

Week 4 Assignment:

  • Continue executing your project and refining your work plan.
  • Submit your updated/more detailed work plan by Thursday, 5/23 at 11:55 PM.

 

Week 5 (5/31/19, room 124):

  • Mock Grant Reviews

Week 5 Assignment:

  • Continue executing against your work plan.
  • Submit your project presentation slides and a link to your demo-able final project deliverable by Friday, 6/7/18 at 10 AM. Each group will do a project presentation. The focus should be on the problem/gap your project addressed and what your solution was. Each member of the team is expected to do part of the presentation. Each member of the team may use 1-slide or graphic, with the total time for the group presentation being 5 min. You must demo a working version of your project during the presentation. You will be graded on the clarity of your presentation and slide, demonstrating that you at least have a working beta version of your product, how well you stick to the time-limit, and how well your presentations coordinate with your team members’ presentations. In general, each team member should do an equal part of the presentation. Each group project presentation will be videoed and we will play back the video in class immediately after each group presentation. This exercise is designed so that you can get constructive feedback on your presentations.

                                                              

Week 6 (6/7/19; room 124):

  • Final Project Presentations

Week 6 Assignment:

  • Close your project.
  • Submit your final project write-ups by Friday 6/14/19 at 5 PM.
  • Submit your project reflections by Friday 6/14/19 at 5 PM.

 

 

Course Policies and Resources

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 any time after the Sakai deadline. For example, if a written assignment is due at 10 AM and you submit it at 10:05 AM, you will lose 1 point. If the assignment still has not been submitted by the following day at 10 AM, 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.

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 http://sakai.ohsu.edu. 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

(Web) http://atech.ohsu.edu/help

(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

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 http://www.pdx.edu/drc ). 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 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

SOU - Ashland Campus Public Safety

  • For Emergencies dial 911
  • Officer Assistance: (541) 552-6911

WOU - Monmouth Campus Public Safety

  • Emergency: 503-838-9000
  • Main Office (Open 24/7): 503-838-8481

EOU - La Grande Campus Public Safety

  • Emergency: 911
  • Camus Security Non Emergency: 541-962-3911

OIT - Klamath Falls Campus Public Safety

  • Emergency: 911 or 541-885-0911
  • Camus Security Non Emergency: 541-885-1111

*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

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