Bioinfo Programming/Scripting
BMI-565

: The purpose of this course is to equip research scientists with computational skills necessary to create and automate tools to analyze biological data. The course is divided into four sub-topics: Python programming, scripting in Unix/Linux, the BioPython library, and computational workflows. Python will be used to solve simple to sophisticated programming problems and to review general programming language paradigms such as problem abstraction, data types, file I/O, iteration, functions, and objects. There will also be an emphasis on writing Unix/Linux operating system shell scripts to automate repetitive tasks and connect multiple bioinformatics tools using files and pipes. In addition, students will learn to access public repositories to perform basic bioinformatics tasks such as annotating gene products, sequence searching, and functional queries. This course is designed to be a first year requirement for students in the Bioinformatics and Computational Biology graduate program in Biomedical Informatics.
Offering: On Campus, Fall

This syllabus is for BMI 565 PDX F21, BMI 665 PDX F21

No Required Textbook

Recommended Reference: Python for Bioinformatics, 2^nd Edition by Sebastian Bassi. CRC Press, 2017.

Other Resources:

• Think Python by Allen B. Downey, http://www.greenteapress.com/thinkpython/
• Python for Informatics: Exploring Information by Charles Severance, http://py4inf.com/book.php
• Google's Python Class, https://developers.google.com/edu/python/
• Learn Python the Hard Way by Zed A. Shaw, http://learnpythonthehardway.org/book/
• Problem Solving with Algorithms and Data Structures Using Python by Brad Miller and David Ranum, http://interactivepython.org/courselib/static/pythonds/index.html
• Python Cookbook by David Beazley and Brian K. Jones, 3^rd, O’Reilly Media, 2013
• Python for Data Analysis by Wes McKinney, O'Reilly Media, 2012
• Python Essential Reference by David Beazley, 4th Ed., 2009

All lecture notes are available on GitHub: https://github.com/mooneymi/bioinformatics_programming

Course Objectives:

• Working with Problems Algorithmically: Be able to create and automate bioinformatics tasks using a high level programming language.
• Working with Pipelines: Using scripting in a Linux operating system to execute and connect previously written bioinformatics tools in a workflow
• Working with Files and Public Repositories: Read and write text data in files, and access data and annotations from common bioinformatics public repositories.
• Working with Bioinformatics Data: Be able to perform basic data processing tasks and create a graphical representation of results.

Prerequisites:

An introductory programming class (or equivalent work experience) covering the following concepts: data types, control structures (e.g. loops), I/O, functions, and basic algorithms.

Course Grading Policy:

Grades will be based on scores from examinations, weekly programming assignments, and a final research project.  The point breakdown is as follows:

Programming assignments will be released through Sakai. Late assignments will not be accepted. Research projects will involve the analysis of a high throughput dataset over the last 2 weeks of class and will require a 2-3 page write-up. All assignments and the research project should be submitted through Sakai.

Attendance policy:

If possible…don’t miss class!  Consider getting notes from a kind fellow student. 

All students are strongly encouraged to complete the course/instructor evaluations at the end of the term. Results from the evaluations are critical for improving the course for future students. Additional information can be found in the "Institutional Policies and Resources" section below.

Tentative Class Schedule:

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].
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.

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

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]

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

Students should review 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.

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.

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

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.

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

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.