Bio/Comp Biomed I: Algorithms
BMI-550

The course will be a problem-driven examination of the algorithmic and quantitative issues in computational biology. The course assumes basic background in algorithms. The emphasis is on algorithm development and application to biological problems, particularly those from multi-omics studies. This will enable the student to evaluate algorithms, as well as assess computational considerations for development and implementation. Topics include: global and local alignment, Scoring functions, suffix trees, Next Generation Sequencing Algorithms, Genome Alignment, Database search, Phylogeny, Multiple sequence alignment, motif finding, and genome rearrangements.
Prerequisite: None.
Offering: On Campus: Fall

This syllabus is for BMI 550 PDX F21, BMI 650 PDX F21

James Jacobs, MD
Department of Medical Informatics and Clinical Epidemiology
[email protected]
Office hours: By appointment

Shannon K. McWeeney, Ph.D., Professor
Head, Division of Bioinformatics and Computational Biomedicine,
Department of Medical Informatics and Clinical Epidemiology
Phone: (503) 494-8347
E-mail: [email protected]
Office hours: By appointment

No formal decision has been made yet regarding in-person vs. online courses for the Fall of 2021.

If classes are in-person, BMI 550/650 will be in BICC 124.

If classes are online, synchronous Webex sessions can be accessed directly through the Course Site on Sakai.  There is a Webex tab on the left-hand side that will open a link to each week’s class. 

Required

Compeau, P and Pevzner P. Bioinformatics Algorithms An Active Learning Approach 3rd Edition but 2nd edition is also ok.

Note: We will augment this text with papers from primary literature for topics not covered in the text.

Additional Reading (Not required)

Di Pierro, Massimo. Annotated Algorithms in Python: with Applications in Physics, Biology, and Finance 2013

 For non-biologists: Brown, TA. Genomes 2nd Edition (available online)

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=genomes.TOC&depth=2

For non-computer scientists: Jones NC and P Pevzner. An Introduction to Bioinformatics Algorithms (Computational Molecular Biology) 2004

CORE COMPETENCIES, OUTCOMES AND OBJECTIVES:

1. Understand the difference between a brute force approach vs. a refined computationally plausible algorithm. Use big-O notation to describe the computational demands of an algorithm. 
2. Know the difference between global and local alignment of genomic sequences and be able to describe the issues related to each.
3. Learn to store, extract and search information in the form of suffix trees and suffix arrays and then abstract these concepts to that of genome alignment using the Borrows Wheeler Transform.
4. Understand the technologies – as well as inherent biases and limitations – involved in massively paralleled sequencing.
5. Develop an understanding of the concept of a genomic “motif” and learn the basic algorithmic techniques for motif discovery.

Students will be evaluated on in-class preparation/participation (10%), homework assignments (35%), a mid-term exam (25%) and a final programming project (30%).  Late assignments will not be accepted.

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 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.

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.

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.

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].
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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.

Policy number: 02-70-050

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.

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]

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’s Respect for All app helps students, faculty, and staff educate themselves about sexual misconduct and harassment as well as their reporting responsibilities. To download the app, open the link below in Chrome, Firefox, Edge, Safari or Opera. It does not work in Internet Explorer.

 https://ohsurespectforall.com/

List of OHSU Graduation Core Competencies

• Professional Knowledge and Skills
• Professionalism
• Information Literacy
• Communication
• Teamwork
• Community Engagement, Social Justice and Equity
• Patient Centered Care

To access a descriptive list of OHSU Graducation Core Competencies:  OHSU Graduation Core Competencies

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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]

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 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.

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].

Portland Campus:  Marquam Hill and South Waterfront

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

Remote Learning Resources
The Remote Learning webpage on O2 contains concise, practical resources, and strategies for students that need to quickly transition to a fully remote instructional format.

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Mackenzie Hall, Rm. 1120
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Academic Support Counseling and Sakai Course Management System, please contact the TLC Help Desk at 877-972-5249 or email TLC Help Desk

Student Academic Support Services
For resources on improving student’s study strategies, time management, motivation, test-taking skills and more, Please access the Student Academic Support Services Sakai page. For one-on-one appointments or to arrange a workshop for students, please contact Emily Hillhouse.

Confidential Advocacy Program
Support for OHSU employees, students, and volunteers who have experienced any form of sexual misconduct, including sexual harassment, sexual assault, intimate-partner violence, stalking, relationship/dating violence, and other forms — regardless of when or where it took place. Contact Us.

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 Support - Sakai 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)

• Emergency on Campus: 503-494-4444 (Portland)
• Non-emergency: 503-494-7744; Contact Public Safety

Student 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.

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Gaines Hall, Rm. 117
707 SW Gaines Street, Portland, OR 97239
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Library: Biomedical Information Communication Center
BICC Library Hours of Operation

Students may be asked to take classes remotely through videoconferencing software like WebEx. Some of these remote classes will be recorded. Any recording will capture the presenter’s audio, video, and computer screen. Student video and audio will be recorded if and when you unmute your audio and share your video during the recorded sessions. These recordings will not be shared with or accessible to the public without prior written consent.