605.657.81 - Statistics for Bioinformatics

Course Structure

The course materials are divided into 14 modules which can be accessed by clicking Course Modules on the left menu. A module runs for 7 days starting Tuesday. The main part of a module is the PDF lecture; it can be found in the Lectures and Content folder. Inside the PDF lecture, you will find the problems that you will need to solve to complete this module (they are named "question 1", "question 2", etc.).

Please submit the answers to the problems in the Submit All Solutions section of a module and post one solution to the Post One Solution forum. The requirements are specified in the Student Coursework Requirements section below. If you have a question, for example, if you need a clarification on a problem, you can post it at the Questions forum or email me.

The Readings section lists the readings. Some readings are suggested readings; you may be able to solve the module problems without these readings if you have a strong background in the corresponding area. Other readings are required and then they are also mentioned in the PDF lecture. The PDF lecture is the starting point of each module as it specifies the recommended sequence of readings, videos, etc.

Course Topics

• Basic Probability Laws
  
• Probability Distributions
  
• Application of Probability Distributions to RNA-Seq
  
• Markov Chains
  
• Markov Chains in Biology & Bioinformatics
  
• Hidden Markov Models (HMMs)
  
• Applications of HMMs to Bioinformatics
  
• Bayesian Statistics
  
• Bayesian Networks
  
• An Application of Bayesian Statistics to Bioinformatics
  
• Bayesian Networks -- Learning from Complete Data
  
• Bayesian Networks -- Learning from Incomplete Data
  
• An Application of Bayesian Networks to RNA-Seq
  
• Bayesian Networks in Bioinformatics
  

Course Goals

Students will learn the principles behind Markov chains, Hidden Markov Models, Bayesian statistics and Bayesian networks and how these methods are applied in bioinformatics research.

Course Learning Outcomes (CLOs)

• Apply Markov chains to solve bioinformatics problems.
• Apply Hidden Markov Models (HMMs) to solve bioinformatics problems.
• Apply Bayesian statistics and Bayesian networks to solve bioinformatics problems.
• Analyze the statistical methods used in bioinformatics research articles.

Textbooks

There is no single textbook. The readings are listed in the Readings section of each module and they can be accessed online through the Course Reserves link on the left menu.

Required Software

You will need to install the R language environment on your computer. R is a free programming language and software environment that is available for Windows, Mac and Linux. It can be downloaded from here: http://cran.r-project.org.

Student Coursework Requirements

There are two requirements:

1. Submit your answers to the questions/problems via an online form.
2. Post solutions to one of these problems on the discussion forum AND reply to at least two solutions posted by other students.

Problem Sets - Submit All Solutions (approximately 80-85% of the final grade)

The problems can be found in the lecture PDF, they are named "question 1", "question 2", etc. Please enter the answers to all problems in the Submit All Solutions section of the module. After clicking Submit All Solutions, click Begin to start, enter the answers, then click Save All Answers to save your work in progress and return to it later. Don’t forget to submit your work when you are finished. If you submit your work more than once (in order to change your answers), the last submission before the deadline will be graded. You are welcome to use the solutions posted by other students on the discussion board, but keep in mind that there is no guarantee that they are correct.

Problem sets are due on Monday, before midnight, Eastern Standard Time (at 11:59pm Monday at the latest). Full solutions will be available after all homework assignments have been graded.

Forum Posts - Post One Solution (approximately 15-20% of the final grade)

Please select one of the questions from the module problem set that has not been answered on the discussion board yet and post your complete solution (not just the answer). Create a separate thread and name it "Question ", for example, "Question 3". Please use this exact format for the thread name as uniform format allows one to sort questions on the forum by clicking on the header of the "Thread" column, making it easy to see which questions have already been answered.

If you’d like to ensure that nobody answers the question you have selected while you are writing up the solution, you can "reserve it" for 2 hours by creating a thread using the format described above. Your "reservation" is valid for 2 hours and you can only make one reservation per module. After 2 hours, the question can be "reserved" or answered by other students. Once you have posted your solution, you can delete the "reservation" post you made earlier.

After you have posted your solution, reply to two or more threads started by other students. You can confirm that you agree with the solution or explain why you disagree or ask a clarifying question about the solution or answer another student’s question. Replies can be brief, "I agree" is acceptable, but, if you disagree with the solution, please explain why and provide your solution. Please only start one thread on each Post One Solution forum (an abandoned "reservation" doesn’t count), but feel free to reply to as many threads as you like (two is the minimum).

As a courtesy to other students, please answer the questions about your solution that others posted (unless it has already been answered by somebody else). Everybody’s schedule is different and questions may be posted after you have completed your work on the module, so it is OK to answer these questions the following week.

The initial discussion post with a solution is due on Saturday, before midnight, Eastern Standard Time (EST) (at 11:59pm Saturday at the latest). Replies are due on Sunday, before midnight EST (at 11:59pm Sunday at the latest). One extra-credit point is added if the initial discussion post with a solution is made before Thursday at midnight EST.

Grading Policy

Problem Sets - Submit All Solutions

Problem sets are graded based on whether or not the answer is correct. Unless specified otherwise, there is no partial credit. The correct answer gets the full credit; an incorrect answer gets a zero, even if it is just a rounding error. Please do not round any intermediate calculations unless you are sure it won’t affect the final answer. Please check your math for the problems that are worth more than one point. The number of points is specified near each question. If the number of points is not specified, the question is worth 1 point.

Forum Posts - Post One Solution

The only requirement for a solution posted on the discussion board is that it is explained in detail and that the question has not already been answered by another student. A solution does not have to be correct to get the full discussion forum credit. The full credit for the discussion board participation (one post with a solution and two or more replies to other students’ solutions) is 10 points. One extra-credit point is added if you post your solution no later than Thursday, Eastern Standard Time.

Academic Integrity Policy

No collaboration is allowed on the problem sets aside from the public discussion on the class discussion board. The answers/solutions to the problems must represent an individual effort by you alone. Please note that collaboration (or use of someone else's work) is easy to detect – all correct answers are the same, but incorrect answers are often unique and allow for the identification of the source. If similar answers to problems not discussed on the forum are repeatedly submitted by two (or more) students, both students will receive a zero on the assignment(s) and the matter will be referred to the Program Chair.

Late Work Policy

Students who register after the class has started can request an extension on module 1. All other late work will have points deducted. 10% of the score is deducted if a problem set is submitted late and 20% if it is submitted more than 24 hours late. 10% of the score is deducted if a discussion post or reply is late; a discussion post or reply that is more than 24 hours late gets a zero. Late work is not accepted for module 14. The only exception to this rule is a documented illness or other documented exceptional circumstances. Computer problems and internet outages are not valid excuses for late work. Please plan for such emergencies and submit your work well before the due date.

Please note that submitting a problem set after the due date is only possible if you have not submitted it before the due date, i.e., it's not possible to submit some problems before the due date and other problems after the due date because, if work is submitted, the correct answers are automatically revealed shortly after the due date.

If you expect to have a busy week and would like to start working on the next module ahead of time, you are welcome to request the next module’s problem set after you have completed all or almost all the work for the current module. However, any materials and info that are provided before the official module release are preliminary in nature and it is your responsibility to ensure that you are using the officially released version when submitting/posting your solutions.

Final Grade

The final grade is based upon accumulated points as follows:

If your score is below 83%, you are welcome to contact me for hints on current module problems. However, by doing so, you are forfeiting any chance of getting any grade above "B" in this class. This courtesy does not extend to students who repeatedly miss or are late with problem sets or discussion posts.

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.