Portland Campus · School of Medicine
Readings in Bioinformatics
- Spring 2019
- 1 Credits
- 04/01/2019 to 06/21/2019
- Modified 02/19/2019
Single Cell Genomics: Technologies, Analysis, and Applications
This course is a weekly seminar course that will cover selected readings in a focused topic in bioinformatics. This year’s topic is Single Cell Genomics: Technologies, Analysis, and Applications. Single-cell genomics allows us to interrogate cell-to-cell differences and uncover the roles of cell-specific populations in disease. This term we will cover single cell sequencing technologies and data generation, computational analysis, and open challenges for a variety of applications, including transcriptomics, imaging, rare cell subsets, cell fate, and cancer heterogeneity. In addition to critically reading and assessing papers in the field, students will each lead a weekly paper discussion to develop and hone presentation skills
Prerequisite: DMICE BCB track or instructor permission.
Offering: On Campus: Spring
Tuesdays 12:30 -1:30pm
Required Textbook and Reading Material:
Presentation Zen: Simple Ideas on Presentation Design and Delivery by Garr Reynolds (2011). New Riders Press.
Weekly readings and presentation assignments will be assigned in the first week of the course.
Course Competencies, Outcomes, and Objectives
Grading for this course is on a letter grade scale. Grades will be based on the following:
Letter Grade Assignments
Course & Instructor Evaluations
Tues, April 2
Introduction, Presentation Zen,
Tues, April 9
Tues April 16-
Tues June 18
Course Policies and Resources
Attendance and Participation
Students are expected to critically read the weekly assigned literature. In-class participation will include guided discussion of the assigned readings, responses to presenter questions, and completing constructive weekly evaluations for student presenters.
Student presenters will be responsible for presenting the material for their assigned week to the class and leading discussion on a critical analysis of the assigned paper(s). This includes relevant background information, methods, key results, and major conclusions. Presenters should be comfortable explaining and discussing all figures, tables, and methods (including information in supplementary methods/materials as necessary). Assigned reading material should be reviewed in full with sufficient time to clarify any issues with the mentored teaching assistant and/or instructor as needed.
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:
- The Department*/Program** Coordinator will immediately contact the Instructor requesting the missing grade, with a copy to the Program Director and Registrar.
- 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.
- 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
- 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.
- 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].
- 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.
- If Diane does not reply within 1 business day (not including weekends), the student should contact Andrea Ilg at [email protected].
- 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.
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.
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.
(Email) [email protected]
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.
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.
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.
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.
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.
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 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*:
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
- Emergency on Campus: 503-494-4444 (Portland)
- Non-emergency: 503-494-7744; Contact Public Safety
- For Emergencies dial 911
- Officer Assistance: (541) 552-6911
- Emergency: 503-838-9000
- Main Office (Open 24/7): 503-838-8481
- Emergency: 911
- Camus Security Non Emergency: 541-962-3911
- 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.
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