Last Updated: 2023-02-06

SYLLABUS

BIOL 1555 / PHP 2561: Methods in Informatics and Data Science for Health
Spring 2023

Day, Time: Mondays 3:00pm-5:30pm ET

Location: CIT Center (Thomas Watson CIT) 227

Google Classroom
[Link]
(join by link: [Link]

Instructors: Liz Chen, PhD, FACMI liz_chen@[Link]

Neil Sarkar, PhD, MLIS, FACMI, ACHIP neil_sarkar@[Link]

TAs: Hannah Hiraki hannah_hiraki@[Link]

Lindsey Ross lindsey_ross@[Link]
Deniz Toruner merih_toruner@[Link]
Harshini Venkatachalam harshini_venkatachalam@[Link]

Office Hours: Tuesdays 11:00am-12:00pm (Lindsey, Zoom)

5:00pm-6:00pm (Deniz, Zoom)
Wednesdays 11:00am-12:00pm (Deniz, Zoom)
8:00pm-10:00pm (Harshini, Zoom)
Thursdays 9:30am-11:30pm (Lindsey, Zoom)
4:30pm-6:30pm (Hannah, Zoom)
Fridays 11:00am-12:00pm (Lindsey, Zoom)
12:00pm-1:00pm (Harshini, Zoom)
Additional hours by appointment

Override Requests
The 2023 offering of this course is full. No additional overrides will be given.

COURSE DESCRIPTION

The goal of this course is to develop a functional solution that uses informatics and data
science approaches to address a biomedical or health challenge. Particular emphasis

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will be given to formalisms and algorithms used within the context of biomedical
research and health care, including those used in electronic health records, clinical
decision support, and public health surveillance. General programming language skills
will be taught (in Julia and Python) within these contexts. This course will provide a
functional overview of methods commonly used to address challenges in biomedical
and public health contexts.

Mastery of informatics and data science skills will be assessed by a final project done
within a biomedical or health context. In pursuing the project, students will gain
experience in the design, implementation, and evaluation of how a biomedical or health
challenge can be addressed using informatics and data science. This course was
developed as a Course-based Research Experience (CURE) and is designated as a
Collaborative Research and Scholarly Experiences (COEX), where students will gain
experience with the scientific method, its application, and presentation. Undergraduate
students will develop a team poster and one-page abstract. For graduate students and
capstone requirements, the final products of this course include a team poster and full
manuscript.

PREREQUISITES

Course is designed for students who have completed a course in introductory statistics
(e.g., BIOL 0495) or statistical programming (e.g., PHP 2560). Other students may
enroll with instructor permission.

ENROLLMENT

Course enrollment is limited to the number of students listed on Courses@Brown.

Auditors are not permitted.

COURSE GOALS & OBJECTIVES

The goal of this course is for students to master fundamental informatics and data
science principles within the context of biomedicine and health. By the end of the
course, students will have gained the needed knowledge to leverage informatics and
data science approaches in support of biomedical and health research.

Specific learning objectives are thus to:

1. Understand principles of informatics and data science, as used across the
spectrum of biomedicine and health
2. Demonstrate competency in informatics and data science skills through the use
and adaptation of existing tools and algorithms in biomedical research and health
settings

CORE COMPETENCIES

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Primary Competencies
1. Acquire knowledge and skills in research methodologies to collaborate with
substantive investigators
2. Apply programming skills to analyze data and develop simulation studies
3. Attain proficiency in management and documentation of data for use in
practical analytic studies

Refresher Competencies
1. Identify and implement analytic techniques and models for analysis of data
2. Effectively function in an interdisciplinary, collaborative environment
3. Develop proficiency in making oral, written, and poster presentations of work to
computational, statistical, and non-technical colleagues
4. Review and evaluate the use of analytic methods in public health and
biomedicine
5. Build productive collaborations across public health and biomedicine

COURSE MATERIALS

Required

● Assignment readings
● Biomedical Informatics and Data Science Skills (BIDSS) Manual

Optional

● Sarkar, Indra Neil (Ed). Methods in Biomedical Informatics. Academic Press

(2014). ISBN: 9780124016781**
● Secondary Analysis of Electronic Health Records [Internet]. Cham (CH):
Springer; 2016. Available from: [Link]
doi: 10.1007/978-3-319-43742-2
● Lauwens, Ben and Downey Allen B. Think Julia How to Think Like a Computer
Scientist. O’Reilly Media (2019). ISBN: 9781492045038
● Downey Allen B. Think Python How to Think Like a Computer Scientist. O’Reilly
Media (2016). ISBN: 9781491939369

Freely accessible with Brown email address (on campus or on Brown VPN)**

Google Classroom and Apps

All course materials, including assignments and reading material, will be distributed
through Google Classroom. Notes will be done group style using a shared Google Doc.

Computing
Students will be required to access a laptop that can connect to the Internet (a laptop
that can be used during lectures and connect to the Brown VPN is ideal). Any Brown
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University recommended version of MacOS, Linux, as well as Windows with PowerShell

5.0 can be used for this course.

GRADING CRITERIA / ATTENDANCE POLICY

The graded elements of the course and their contribution to the final grade are:

Assignments 30%
Midterm 10%
Final Team Project 60%

Specific criteria details:

● Attendance is mandatory and is subject to be taken at a random moment during
each lecture. Unexcused absences will result in a 10% deduction in overall
course grade (i.e., five unexcused missed lectures will result in a failing grade).
A Zoom link will be available for students who are unable to attend in person
(e.g., due to being COVID-19 positive or other extenuating circumstance). This
Zoom link should only be used with prior approval from an instructor.
● Weekly Assignments will be assigned at the end of each class and must be
turned in on specified due dates (generally the start of the next lecture). Late
submissions will not be accepted.
● A Midterm will be assigned before Spring Break and due two weeks thereafter.
This assignment should be done independently.
● A Final Team Project will be submitted at the end of the course that is designed
to bring together applicable concepts to address a challenge in biomedical
research or public health. Components of the project:
○ A Proposal Presentation consisting of the background and motivation for
the final project and expected goal.
○ A Poster summarizing major aspects of the project and 5-minute Final
Presentation describing the project as a team.
○ A Report providing more details about the project
▪ For Undergraduate Students: 1-page abstract
▪ For Graduate Students and Capstone Requirements: 5-10 page
manuscript formatted for a MEDLINE-indexed conference
proceeding or peer-reviewed journal
○ All Code and Documentation associated with the project.

CLASSROOM ENVIRONMENT EXPECTATIONS

All lectures will be done in traditional format along with hands-on exercises. Students
are expected to contribute to discussions and actively participate in exercises during
class (see Grading Criteria/Attendance Policy above). In addition to the three hours of
weekly class time, students will be expected to spend an average of 10-12 hours a
week outside of class to complete assignments and the final project.
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As a guide, the minimum number of hours a student should expect to spend on each
major task for this course is summarized below:

Task Hours
Class Time 40
Assignments / Readings 80
Final Project 60
Total 180

COMMUNICATION

The course Slack workspace (Methods 2023; click here to join) should be
used for questions about the class, assignments, and projects. Use of threads is
encouraged rather than direct messages.

SCHEDULE OF TOPICS

The course will consist of “Theory” (didactic lectures) and “Practice” (interactive labs
and project work). Computers will be needed for all lectures.

Day Date Type Topic

Theory Introduction to Biomedical Informatics and Data Science
1 Jan 30
Practice Computing Environment Setup
Theory Data and Data Standardization
2 Feb 6
Practice Unix - Basics; GitHub Setup
Theory Software Engineering
3 Feb 13
Practice UML and Julia - Basics
- Feb 20 NO CLASS Long Weekend
Theory Knowledge Discovery
4 Feb 27
Practice Julia - File I/O and Structures (Arrays & Dictionaries)
Theory Information Retrieval and Natural Language Processing
5 Mar 6
Practice Julia - Packages, Web Services, RegEx
Theory Databases
6 Mar 13
Practice SQL and Julia - DataFrames
Practice Project Description: Process and Data Sources
7 Mar 20 Practice Python - Basics
MIDTERM ASSIGNMENT AVAILABLE (Julia and Python)
- Mar 27 NO CLASS Spring Recess
8 Apr 3 Practice Project Planning
Practice Proposal Presentation
9 Apr 10
Theory Project Management and Agile Methodology

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MIDTERM ASSIGNMENT DUE

Theory Machine Learning; Julia Stats & MLJ
10 Apr 17
Practice Update #1 (Data Review) and Working Session
Theory Team Science and Open Science
11 Apr 24
Practice Update #2 (UML Review) and Working Session
May 1 Theory Clinical Decision Support and Learning Health System
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(Reading Period) Practice Update #3 (Code Review) and Working Session
May 8
13 FINAL Project Presentations
(Reading Period)
May 17
14 (Final Exam FINAL Project Materials due by 11:59pm
Period)

ACADEMIC INTEGRITY

Please familiarize yourself with Brown’s Academic Code and the Graduate Student
edition. Avoid unintentional plagiarism by properly citing your sources. Intentional
plagiarism is a deliberate violation of the academic code.
(Academic Code, p. 5) “A student’s name on any exercise (e.g., a theme, report,
notebook, performance, computer program, course paper, quiz, or examination) is
regarded as assurance that the exercise is the result of the student’s own thoughts and
study, stated in his or her own words, and produced without assistance, except as
quotation marks, references, and footnotes acknowledge the use of printed sources or
other outside help.”
(Academic Code Graduate Edition, p.4) “Academic achievement is evaluated on the
basis of work that a student produces independently. A student who obtains credit for
work, words, or ideas which are not the products of his or her own effort is dishonest.
Such dishonesty undermines the integrity of academic standards of the University.
Infringement of the Academic Code entails penalties ranging from reprimand to
suspension, dismissal or expulsion from the University. Brown students are expected to
tell the truth. Misrepresentation of facts, significant omissions or falsifications in any
connection with the academic process (including Change of Course permits, the
academic transcript, or applications for training or employment) are violations of the
Code. This policy also applies to alumni, insofar as it relates to Brown transcripts and
other records of work at Brown. Misunderstanding the Code will not be accepted as an
excuse for dishonest work. If a student has questions on any aspect of the Academic
Code as it relates in a particular course or as it may be interpreted in practice, he or she
should consult the instructor in the course or one of the deans of the Graduate School
so as to avoid the serious charge of academic dishonesty.”

STUDENTS WITH SPECIAL NEEDS

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Brown University is committed to full inclusion of all students. Please inform the
instructors early in the term if you have a disability or other conditions that might require
accommodations or modification of any of these course procedures. You may speak
with the instructors after class or during office hours. For more information, please
contact Student and Employee Accessibility Services at 401-863-9588 or
SEAS@[Link].

DIVERSITY STATEMENT

This course is designed to support an inclusive learning environment where diverse

perspectives are recognized, respected and seen as a source of strength. It is our intent
to provide materials and activities that are respectful of various levels of diversity:
mathematical background, previous computing skills, biomedical or health knowledge,
gender, sexuality, disability, age, socioeconomic status, ethnicity, race, and culture.
A list of learning support resources can be found here.

EXPENSES AND FINANCIAL CONCERNS

Undergraduates with concerns about the non-tuition cost(s) of this course, may apply to
the Dean of the College Academic Emergency (E-Gap) Fund to determine options for
financing these costs (while ensuring their privacy). The fund can be found in the
Emergency Funds, Curricular & Co-curricular Gap (E-Gap) Funds in UFunds.
Information and procedures are available at this link: [Link]