Academic/Operating Unit
Department/Center/Institute/Program
SYLLABUS
BSGP 7030
Introduction to Data Science in Biomedical Science
Research
College of Medicine
Biomedical Science Graduate Program
Summer 2023 – Online
Credit Hours 2
Instructor: Michael A. Freitas
Email address: michael.freitas@osumc.edu
Phone number: 614-688-8432
Office Hours: Arranged by appointment
Days and Times:
Second Term Summer 2022
June 20, 2022 - July 28, 2022
Tuesday / Thursday 11:00am-1:00pm*
*(time subject to change to accommodate student schedules, check with the instructor if time
overlaps with other required courses)
Course Policies:
All College and Program course policies apply to this course.
See OSU BSGP Handbook for Related Policies and Procedure.
This syllabus, the course elements, policies, and schedule are subject to change.
Course description
BSGP 7030 is a course that teaches how to apply principles of data science to the analysis of
biomedical data. The goal of the course is to introduce students to tools that are used by data
scientists, build skills in quantitative data analytics, and to promote rigor and reproducibility in
data analysis.
Course learning outcomes
By the end of this course, students should successfully be able to:
• Develop familiarity with scripting languages: R, Python, Bash
• Develop proficiency in building and using container-based software environments
• Develop proficiency in building and using scientific workflows
• Develop proficiency using data science notebooks
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HOW THIS COURSE WORKS
Mode of delivery: This course is taught as a100% synchronous online course.
Credit hours and work expectations: BSGP 7030 is a 2-credit hour course. We will meet every
Tuesday and Thursday for two hours. It is expected that each student will work 4-6 h per week
outside of class in order to pass. Each student enrolled in BSGP 7030 will participate in small
group assignments focused on developing the necessary skills to apply data science to
biomedical and biological research problems. To demonstrate these skills students will perform
and independent project during the class where they will build and test an end-to-end analysis
pipeline for a project of their choice. Students are allowed to work in groups, share ideas and
collaborate freely on problems but the final graded project must demonstrate the students’
individual work. Any students that turn in duplicated work will receive zero credit for duplicated
portions of the assignment.
Attendance and participation requirements: Because this is an online course, your
attendance is required for every class. Class participation is encouraged.
Missed Class: Students unable to make class must schedule a makeup session with instructor
in advance. All sessions will be recorded. Students will be required to watch the recorded
sessions and complete a makeup assignment in addition to other work. Students can only
makeup 1 missed class. Missing more than two classes will result in an incomplete grade for
the class.
Online Structure: This course will be conducted in a distance-learning, online format. All
materials will be provided via Carmen and all assignments will be completed via Canvas file
upload. All necessary materials will be provided in the content section of Carmen. A tutorial is
available at https://ocio.osu.edu/audience/students.
Notices about this course will be sent to your name.#@buckeyemail.osu.edu or
firstname.lastname@osumc.edu account. All students must have an active OSU email account
and remain electronically connected to OSU. Please contact the Help Desk for more information.
Safety and health requirements: All teaching staff and students are required to comply with
and stay up to date on all University safety and health guidance, which includes wearing a
facemask in any indoor space and maintaining a safe physical distance at all times. Non-
compliance will be warned first and disciplinary actions will be taken for repeated offenses.
Group Discussion: One class every four weeks will be dedicated to critically reviewing and
reflecting on the prior week’s seminars. Students will update their IDP and discuss with the class
their short term (predoc), medium term (postdoc) and long-term career goals.
Biomedical Workforce Topics: These sessions will be dedicated to presentation by OSU
faculty, visiting faculty, alumni or other external speakers. The topics will vary but will be cover
biomedical careers in academia, medicine, industry, and entrepreneurship. There will be
evaluations after each presentation that must be completed to receive credit for attending the
class.
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COURSE MATERIALS AND TECHNOLOGIES
Course Materials
Learning Resources:
• RECCOMENDED BUT OPTIONAL The Biostar Handbook: 2nd Edition
(https://www.biostarhandbook.com/) Student Edition is $25 for a subscription that covers
the term of the course (Bulk subscriptions can be purchased for less provided multiple
students coordinate purchase)
• DataCamp (access provided for enrolled students for no cost)
Course technology
For help with your password, university email, Carmen, or any other technology issues,
questions, or requests, contact the Ohio State IT Service Desk. Standard support hours are
available at ocio.osu.edu/help/hours, and support for urgent issues is available 24/7.
• Self-Service and Chat support: ocio.osu.edu/help
• Phone: 614-688-4357(HELP)
• Email: [email protected]
• TDD: 614-688-8743
BASELINE TECHNICAL SKILLS FOR ONLINE COURSES
• Basic computer and web-browsing skills
• Navigating Carmen: for questions about specific functionality, see the Canvas Student
Guide.
REQUIRED TECHNOLOGY SKILLS SPECIFIC TO THIS COURSE
• CarmenZoom virtrual meetings
• Recording a slide presentation with audio narration
• Recording, editing, and uploading video
REQUIRED EQUIPMENT
• Computer: current Mac (OS X) or PC (Windows 7+) with high-speed internet connection
• Webcam: built-in or external webcam, fully installed and tested
• Microphone: built-in laptop or tablet mic or external microphone
• Other: a mobile device (smartphone or tablet) or landline to use for BuckeyePass
authentication
REQUIRED SOFTWARE
• Microsoft Office 365: All Ohio State students are now eligible for free Microsoft Office 365
ProPlus through Microsoft’s Student Advantage program. Full instructions for
downloading and installation can be found at go.osu.edu/office365help.
CARMEN ACCESS
You will need to use BuckeyePass multi-factor authentication to access your courses in Carmen.
To ensure that you are able to connect to Carmen at all times, it is recommended that you take
the following steps:
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• Register multiple devices in case something happens to your primary device. Visit the
BuckeyePass - Adding a Device help article for step-by-step instructions.
• Request passcodes to keep as a backup authentication option. When you see the Duo
login screen on your computer, click Enter a Passcode and then click the Text me new
codes button that appears. This will text you ten passcodes good for 365 days that can
each be used once.
• Download the Duo Mobile application to all of your registered devices for the ability to
generate one-time codes in the event that you lose cell, data, or Wi-Fi service.
If none of these options will meet the needs of your situation, you can contact the IT Service
Desk at 614-688-4357 (HELP) and IT support staff will work out a solution with you.
GRADING AND FACULTY RESPONSE
This course will be graded from A-E, based 75% on assigned problems and 25% on the
independent study assignment.
Incomplete: An Incomplete grade indicates specific requirements of the Seminar Series Course
are not yet met. Examples of requirements not met are:
o Class is not attended.
o Assignments are not completed.
Late Assignments: the max points available for Late assignments will be reduced by 10%. Any
assignment not turned in by the end of class will be given zero.
The Graduate School requires graduate students to maintain a graduate cumulative point-hour
ratio (CPHR) of 3.0 or better in all graduate credit courses. Any student receiving a B- [82.9%],
or lower, in any course, may be required to complete remedial work as assigned by the
program. The decision regarding whether repetition or remediation is required is at the
discretion of the course director(s) with input and final approval from the BSGP Leadership.
Grievances and Solving Problems: Please see the BSGP Handbook for Policy and
Procedures. In general, a student should meet with the instructor of record for the course first
and then, should then take any problem or grievance to the BSGP Director(s).
Instructor feedback and response time
I am providing the following list to give you an idea of my intended availability throughout the
course. (Remember that you can call 614-688-HELP at any time if you have a technical
problem.)
• Grading and feedback: You can generally expect grading rubric feedback within 7 days.
• Email: I will reply to emails within 24 hours on days when class is in session at the
university.
OTHER COURSE POLICIES
Discussion and communication guidelines
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Let's maintain a supportive learning community where everyone feels safe and where people
can disagree amicably. Remember that sarcasm doesn't always come across online.
Academic integrity policy
POLICIES FOR THIS ONLINE COURSE
In general, you are prohibited in university courses from turning in work from a past class to your
current class, even if you modify it. If you want to build on past research or revisit a topic you've
explored in previous courses, please discuss the situation with me.
OHIO STATE’S ACADEMIC INTEGRITY POLICY
Academic integrity is essential to maintaining an environment that fosters excellence in teaching,
research, and other educational and scholarly activities. Thus, The Ohio State University and
the Committee on Academic Misconduct (COAM) expect that all students have read and
understand the university’s Code of Student Conduct, and that all students will complete all
academic and scholarly assignments with fairness and honesty. Students must recognize that
failure to follow the rules and guidelines established in the university’s Code of Student
Conduct and this syllabus may constitute “Academic Misconduct.”
The Ohio State University’s Code of Student Conduct (Section 3335-23-04) defines academic
misconduct as: “Any activity that tends to compromise the academic integrity of the university or
subvert the educational process.” Examples of academic misconduct include (but are not limited
to) plagiarism, collusion (unauthorized collaboration), copying the work of another student, and
possession of unauthorized materials during an examination. Ignorance of the university’s Code
of Student Conduct is never considered an excuse for academic misconduct, so I recommend
that you review the Code of Student Conduct and, specifically, the sections dealing with
academic misconduct.
If I suspect that a student has committed academic misconduct in this course, I am
obligated by university rules to report my suspicions to the Committee on Academic
Misconduct. If COAM determines that you have violated the university’s Code of Student
Conduct (i.e., committed academic misconduct), the sanctions for the misconduct could include
a failing grade in this course and suspension or dismissal from the university.
If you have any questions about the above policy or what constitutes academic misconduct in
this course, please contact me.
Other sources of information on academic misconduct (integrity) to which you can refer include:
• The Committee on Academic Misconduct web pages (COAM Home)
• Ten Suggestions for Preserving Academic Integrity (Ten Suggestions)
• Eight Cardinal Rules of Academic Integrity (www.northwestern.edu/uacc/8cards.htm)
Diversity:
"The Ohio State University affirms the importance and value of diversity in the student
body. Our programs and curricula reflect our multicultural society and global economy
and seek to provide opportunities for students to learn more about persons who are
different from them. We are committed to maintaining a community that recognizes and
values the inherent worth and dignity of every person; fosters sensitivity, understanding,
and mutual respect among each member of our community; and encourages each
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individual to strive to reach his or her own potential. Discrimination against any individual
based upon protected status, which is defined as age, color, disability, gender identity or
expression, national origin, race, religion, sex, sexual orientation, or veteran status, is
prohibited."
Statement on Title IX
All students and employees at Ohio State have the right to work and learn in an environment
free from harassment and discrimination based on sex or gender, and the university can arrange
interim measures, provide support resources, and explain investigation options, including
referral to confidential resources.
If you or someone you know has been harassed or discriminated against based on your sex or
gender, including sexual harassment, sexual assault, relationship violence, stalking, or sexual
exploitation, you may find information about your rights and options at titleix.osu.edu or by
contacting the Ohio State Title IX Coordinator at titleix@osu.edu. Title IX is part of the Office of
Institutional Equity (OIE) at Ohio State, which responds to all bias-motivated incidents of
harassment and discrimination, such as race, religion, national origin and disability. For more
information on OIE, visit equity.osu.edu or email equity@osu.edu.
Counseling and Consultation Services – Your Mental Health
As a student you may experience a range of issues that can cause barriers to learning, such as
strained relationships, increased anxiety, alcohol/drug problems, feeling down, difficulty
concentrating and/or lack of motivation. These mental health concerns or stressful events may
lead to diminished academic performance or reduce a student's ability to participate in daily
activities. The Ohio State University offers services to assist you with addressing these and other
concerns you may be experiencing. If you find yourself feeling isolated, anxious or overwhelmed,
please know that there are resources to help: ccs.osu.edu. You can reach an on-call counselor
when CCS is closed at (614) 292-5766 and 24 hour emergency help is also available through
the 24/7 National Prevention Hotline at 1-(800)-273-TALK or at suicidepreventionlifeline.org.
The Ohio State Wellness app is also a great resource available at go.osu.edu/wellnessapp.
ACCESSIBILITY ACCOMMODATIONS FOR STUDENTS WITH DISABILITIES
Requesting accommodations
The university strives to make all learning experiences as accessible as possible. If you
anticipate or experience academic barriers based on your disability including mental health,
chronic or temporary medical conditions, please let me know immediately so that we can
privately discuss options. To establish reasonable accommodations, I may request that you
register with Student Life Disability Services. After registration, make arrangements with me as
soon as possible to discuss your accommodations so that they may be implemented in a timely
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Avenue.
Accessibility of course technology
This online course requires use of Carmen (Ohio State's learning management system) and
other online communication and multimedia tools. If you need additional services to use these
technologies, please request accommodations with your instructor.
• CarmenCanvas accessibility
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• Streaming audio and video
• CarmenZoom accessibility
• Collaborative course tools
COURSE SCHEDULE
Date
Topics
Week 1
Data science notebooks
Scripting R, Python, Bash
Week 2
Basic Algorithms
Week 3
Software environments
Docker / Singularity
Week 4
Scientific workflows
Bioconductor
Week 5
Data Science Dashboards
Week 6
Independent Study Project
Copyright disclaimer
The materials used in connection with this course may be subject to copyright protection and
are only for the use of students officially enrolled in the course for the educational purposes
associated with the course. Copyright law must be considered before copying, retaining, or
disseminating materials outside of the course.
