585.788.8VL - Foundations of Computational Biology and Bioinformatics

Expanded Course Description

This course establishes a basic working knowledge of statistical and algorithmic approaches for bioinformatics, and computational biology that utilizes genomic sequenced-based information. Approaches include sequence alignment, machine learning, probabilistic thinking, and empirical-based predictive modeling. The course incorporates lectures and training on these approaches to applied learning assignments that are assessed throughout the course. Each week will consist of an in-person lecture and an in-person practical session where you will work in groups on assigned work based on the lectures. Lastly, a topic-based group project will be completed that represents the capstone of the course. 

Course Structure

The course runs for 14 weeks/modules. For 8 of those weeks, I will deliver lectures and you will have individual assignments/practicums based on the lecture. During the other weeks, class will meet as usual. These classes are also considered mandatory. The time is designated for you to work in your assigned groups on the course project. Myself and the teaching assistants will be available to answer questions and provide guidance. 

The Course Outline provides specific dates for all activities and deliverables. Please also check the Course Calendar and Announcements in Canvas on a regular basis.

Course Topics

• Pairwise Sequence Alignment Algorithms
• Machine Learning Fundamentals
• Cancer genomics
• Probabilistic Thinking
• Hidden Markov Models I
• Bayesian Modeling for Bioinformatics 
  
• Metagenomics

Course Goals

• Gain solid overview of computational molecular biology and its applications to medicine
• Solidify required computer skills
• Improve analysis and algorithmic skills
• Improve professional researcher’s skill set
– Problem solving
– Team work
– Writing up results effectively
– Presenting scientific results to a group

Course Learning Outcomes (CLOs)

• Apply current techniques, skills, and tools necessary for biological sequence computing practice
• Apply knowledge of computing and mathematics appropriate to basic problems in bioinformatics and computational biology
• Analyze a problem, and identify and define the computing requirements appropriate to its solution
• Design and implement a computer-based system, process, component, or program to meet the desired needs of selected biological problems
• Take part in groups problem solving efforts using basic approaches in computational biology

Textbooks

This course does not use a textbook.

Other Materials & Online Resources

Recommended supporting material can be found at the NCBI bookshelf:

Computational Biology - NCBI Bookshelf (nih.gov)

Required Software

VirtualBox 6.1.32
Ubuntu 20.04 LTS

Student Coursework Requirements

• 8 Practicals/Assignments (60%) - The primary course content will be comprised of a 8 lectures and 8 practicals. During each week in which there are two in-person/live virtual meetings, the lecture will be the first meeting of the week, while the practical will be the second. The practicals will comprise 60% of their grade. 
• Quizzes (10%) - There will be graded quizzes in modules 2, 8, and 10.
• Group Project (30%) - One final group project will be required. In these projects, students will work as a team to research a project topic, propose it, and execute it. You will be assessed by each group giving a 20-minute presentation on their project. 

Grading Policy

EP uses a +/- grading system (see “Grading System”, Graduate Programs catalog, p. 10).

Academic Policies

Deadlines for Adding, Dropping and Withdrawing from Courses

Students may add a course up to one week after the start of the term for that particular course. Students may drop courses according to the drop deadlines outlined in the EP academic calendar (https://ep.jhu.edu/student-services/academic-calendar/). Between the 6th week of the class and prior to the final withdrawal deadline, a student may withdraw from a course with a W on their academic record. A record of the course will remain on the academic record with a W appearing in the grade column to indicate that the student registered and withdrew from the course.

Academic Misconduct Policy

All students are required to read, know, and comply with the Johns Hopkins University Krieger School of Arts and Sciences (KSAS) / Whiting School of Engineering (WSE) Procedures for Handling Allegations of Misconduct by Full-Time and Part-Time Graduate Students.

This policy prohibits academic misconduct, including but not limited to the following: cheating or facilitating cheating; plagiarism; reuse of assignments; unauthorized collaboration; alteration of graded assignments; and unfair competition. Course materials (old assignments, texts, or examinations, etc.) should not be shared unless authorized by the course instructor. Any questions related to this policy should be directed to EP’s academic integrity officer at ep-academic-integrity@jhu.edu.

Students with Disabilities - Accommodations and Accessibility

Johns Hopkins University values diversity and inclusion. We are committed to providing welcoming, equitable, and accessible educational experiences for all students. Students with disabilities (including those with psychological conditions, medical conditions and temporary disabilities) can request accommodations for this course by providing an Accommodation Letter issued by Student Disability Services (SDS). Please request accommodations for this course as early as possible to provide time for effective communication and arrangements.

For further information or to start the process of requesting accommodations, please contact Student Disability Services at Engineering for Professionals, ep-disability-svcs@jhu.edu.

Student Conduct Code

The fundamental purpose of the JHU regulation of student conduct is to promote and to protect the health, safety, welfare, property, and rights of all members of the University community as well as to promote the orderly operation of the University and to safeguard its property and facilities. As members of the University community, students accept certain responsibilities which support the educational mission and create an environment in which all students are afforded the same opportunity to succeed academically. 

For a full description of the code please visit the following website: https://studentaffairs.jhu.edu/policies-guidelines/student-code/

Classroom Climate

JHU is committed to creating a classroom environment that values the diversity of experiences and perspectives that all students bring. Everyone has the right to be treated with dignity and respect. Fostering an inclusive climate is important. Research and experience show that students who interact with peers who are different from themselves learn new things and experience tangible educational outcomes. At no time in this learning process should someone be singled out or treated unequally on the basis of any seen or unseen part of their identity. 
 
If you have concerns in this course about harassment, discrimination, or any unequal treatment, or if you seek accommodations or resources, please reach out to the course instructor directly. Reporting will never impact your course grade. You may also share concerns with your program chair, the Assistant Dean for Diversity and Inclusion, or the Office of Institutional Equity. In handling reports, people will protect your privacy as much as possible, but faculty and staff are required to officially report information for some cases (e.g. sexual harassment).

Course Auditing

When a student enrolls in an EP course with “audit” status, the student must reach an understanding with the instructor as to what is required to earn the “audit.” If the student does not meet those expectations, the instructor must notify the EP Registration Team [EP-Registration@exchange.johnshopkins.edu] in order for the student to be retroactively dropped or withdrawn from the course (depending on when the "audit" was requested and in accordance with EP registration deadlines). All lecture content will remain accessible to auditing students, but access to all other course material is left to the discretion of the instructor.