Portland Campus · School of Medicine
Bio/Comp Biomed I: Algorithms
- Fall 2021
- 4 Credits
- 09/27/2021 to 12/17/2021
- Modified 08/12/2021
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.
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
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.
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)
For non-computer scientists: Jones NC and P Pevzner. An Introduction to Bioinformatics Algorithms (Computational Molecular Biology) 2004
Course Competencies, Outcomes, and Objectives
CORE COMPETENCIES, OUTCOMES AND OBJECTIVES:
- 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.
- Know the difference between global and local alignment of genomic sequences and be able to describe the issues related to each.
- 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.
- Understand the technologies – as well as inherent biases and limitations – involved in massively paralleled sequencing.
- 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.
Course & Instructor Evaluations
Course Policies and Resources
School Policies and Resources
Graduate Studies Guidelines:
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School of Medicine Conduct Policy (housed under the graduate studies guidelines section)
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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.
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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:
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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].
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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.
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List of OHSU Graduation Core Competencies
- Professional Knowledge and Skills
- Information Literacy
- Community Engagement, Social Justice and Equity
- Patient Centered Care
To access a descriptive list of OHSU Graducation Core Competencies: OHSU Graduation Core Competencies
Institutional Policies and Resources
Statement Regarding Students with Disabilities:
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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.
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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.
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Modified Operations, Policy 01-40-010:
Portland Campus: Marquam Hill and South Waterfront
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Remote Learning Resources
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Privacy While Learning Remotely
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.