605.751.81 - Algorithms for Structural Bioinformatics

Expanded Course Description

Course Structure

The course materials are divided into modules which can be accessed by clicking Course Modules on the left menu. A module will have several sections including the overview, content, discussions, and assignments. You are encouraged to preview all sections of the module before starting. Most modules run for a period of seven (7) days, exceptions are noted on the Course Outline page. You should regularly check the Calendar and Announcements for assignment due dates.

Course Goals

To familiarize students with the principals and wide range of algorithmic techniques utilized in structural bioinformatics.

Course Learning Outcomes (CLOs)

• Explain the basic concepts, principles, various computational algorithms, and methods of structural bioinformatics.
• Perform sequences alignment and database searches.
• Predict the secondary/tertiary structures of proteins.
• Analyze the sequences and structures of proteins.
• Demonstrate a broad understanding of structural biology.

Textbooks

Optional

Jones, N.C. & Pevzner, P.A. (2004). An introduction to bioinformatics algorithms. Cambridge, MA: The MIT Press.

ISBN-10: 0262101068
ISBN-13: 978-0262101066

Textbook information for this course is available online through the appropriate bookstore website: For online courses, search the MBS website at http://ep.jhu.edu/bookstore.

Required Software

There is no required software for this course; however, if you decide to use MATLAB for your assignments, you can access it free through the JHU Software Catalog.

Visit your myJHU Portal, log in, and look for Technology on the left-hand menu. From there, select mySoftware, and then follow the link to access the Software Catalog. In the Software Catalog, search for MATLAB. Click on MATLAB in the search results and follow the instructions provided.

Student Coursework Requirements

It is expected that each module will take approximately 6–15 hours per week to complete. Here is an approximate breakdown: watching course lecture videos (approximately 2–3 hours per week), reading the assigned sections of the texts as well as outside reading (approximately 1–3 hours per week), participating discussions (approximately 1 hours per week), and completing assignments (approximately 2–8 hours per week).

This course will consist of three basic student requirements:

Module Discussions (15% of Final Grade Calculation)

There are Discussions in every module of the course. Refer to the specific module for instructions regarding each Discussion question(s).

You are required to post a Discussion Response that addresses the module Discussion question(s) and reply to at least two classmates’ threads by Day 7 of each module. To facilitate this, it is required that you post your response to the prompt by Day 4 of the module to give your classmates enough time to reply to your post by the end of the module. Just posting your response to a discussion question is not sufficient; we want you to interact with your classmates. Be detailed in your postings and in your responses to your classmates' postings. Feel free to agree or disagree with your classmates. Please ensure that your postings are civil and constructive.

Refer to the Discussion Guidelines for more detailed requirements and grading information.

Assignments (65% of Final Grade Calculation)

Most of the course modules will contain Assignments with problems sets that you will complete individually. A maximum of 100 points per Assignment can be earned, with partial credit given as discussed below. Each problem set will be due by Day 7 of the module in which they are assigned. No late problems sets will be accepted without prior approval.

These assignments will be returned weekly, providing frequent feedback to the student. Problems will be a mixture of exercises from the course text, other texts, or created by the instructor. Some are to be worked out by hand, and will require creating and running programs. For problems required programming, both the result of the program and the program itself must be turned in.

Refer to the Assignment Guidelines for more detailed requirements and grading information.

Final (Team or Individual) Project (20% of Final Grade Calculation)

As part of this course, you are required to complete a project in a small group (2-3 people). If you prefer, you may also complete the project individually, although working as a team is recommended so that you can complete all the components in time. The project is to select a biological question or an algorithmic challenge and address it by using the methods and algorithms learned inside and outside the course.

The Final Project is worth 100 points.

Refer to the Final Project Guidelines for more detailed requirements and grading information.

Grading Policy

Assignments are due according to the dates posted in your Blackboard course site. You may check these due dates in the Course Calendar or the Assignments in the corresponding modules. I will post grades one week after assignment due dates.

I generally do not directly grade spelling and grammar. However, egregious violations of the rules of the English language will be noted without comment. Consistently poor performance in either spelling or grammar is taken as an indication of poor written communication ability that may detract from your grade.

A grade of A indicates achievement of consistent excellence and distinction throughout the course—that is, conspicuous excellence in all aspects of assignments and discussion in every week.

A grade of B indicates work that meets all course requirements on a level appropriate for graduate academic work. These criteria apply to both undergraduates and graduate students taking the course.

Final grades will be determined by the following weighting:

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.