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CS618 - Computational Biology

Spring 2022

Syllabus and Information

Table of Contents

Table of Contents
General Information
Contact Your Instructor
Lecture, Exam, Office Hours
Prerequisites
Standard text
Course Announcements
Classroom conduct
Course Description
Course Outline
Learning Outcomes
Grading and Assignments
Late Homework
Start Homework Early
Expected Amount of Work
Grade Cutoffs
Canvas
Lectures (using Zoom)
Office hours (using Teams)
Online
CS Course Policies
COVID-19 Information
Academic Integrity
Special Needs
Disclosures Regarding Sexual Misconduct

General Information

Contact Your Instructor

Name: Jeff Kinne
Email: jkinne@cs.indstate.edu
Office: Root Hall A-142 and in Teams
Office: 812-237-2126
Instructor Office Hours: M-F 11-noon, 2-3pm (see syllabus for how office hours will work)

Lecture, Exam

Lecture: F 3:00-4:00 in . See syllabus for information on joining lectures by Zoom or watching recordings Zoom
Exams:

Lab help: We have a few graduate assistants who are available to help students in beginning computer science courses. Please see https://cs.indstate.edu/wiki/index.php/Unix_Lab_and_Help for details. The lab hours are in a calendar on the CS homepage, at http://cs.indstate.edu/info/index.php#lab_hours. You can join the lab when working on your programs. You can ask the lab assistants to look at your programs, and you can work with any other CS students that are there (you could use the lab as a regular meeting place to work with your classmates).

Prerequisites

Permission of instructor (often taken by both CS and Biology students)

Standard text

Free online sources

Course Announcements

Announcements regarding the course will be made both during class and via email to your @sycamores.indstate.edu email address. You should regularly check this email account or have it forwarded to an account that you check regularly. You can set the account to forward by logging into your indstate.edu email from Internet Explorer (the "light" version of the webmail client that opens up from Firefox or Chrome does not give the option to forward email).

Classroom conduct

You may not use cell phones, iPods/music players, etc. during class. You should be civil and respectful to both the instructor and your classmates, and you should arrive to class a few minutes before the scheduled lecture so you are ready for lecture to begin on time. You may use your computer during class if you are using it to follow along with the examples that are being discussed. You may not check email, Facebook, work on other courses, etc. during class.

Course Description

The catalog description for this course is: "An introduction to computational biology. Topics may include principles and methods used for sequence alignment, motif finding, structural modeling, structure prediction and network modeling, as well as currently emerging research areas. A focus is placed on the computational cost of solving problems ­ in terms of CPU time, memory, and disk space. Study of the core algorithms used to solve problems."

We will take some time to go through fundamental CS (terminal/linux, programming, program analysis, etc.) and biology (experimental validation, maybe some others) concepts. We then focus on computational biology problems that are parts of research at ISU. We will study different types of biological sequencing and algorithms for dealing with these. We will also survey clustering algorithms and see their application to research. We will use ISU research (the instructor's, and students' research if you would like) as case studies throughout. Other topics may be covered as time allows and depending on interests of the class.

Course Outline

** Unit 1

  • Foundations
    • Terminal - linux shell, mac OS terminal, Windows command prompt, text editors, utilities
    • Programming languages used in computational biology
      • R
      • Python
      • Bash
      • Perl
      • C
      • LaTex
    • Program analysis
      • Basic computer architecture, tradeoffs - CPU, GPU, memory, SSD, HDD, tape
      • Asymptotic notation/rules - running time, memory usage
        • Some classic examples - linear/binary search, insertion/quick sort, array/hash table/BST
      • Multi-CPU / multi-threaded, GPU programs
    • Statistics
    • Software Testing - spiked/fake data, unit testing, pre/post specifications, opaque/clear box testing
    • Biological Validation - types of error, types of controls
    • Online datasets, Tools
  • Sequencing Data, Algorithms, Tools
    • Types of Sequencing - DNA, RNA, protein
      • Technology, types of error, data formats, quality control
    • Sequencing problems - multiple/single alignment, genome assembly
  • Machine learning
    • Goals/framework - classification, clustering, training / validation
    • Clustering - hierarchical, k-means, k-nearest neighbor, self organizing map, etc.
    • Classification - decision tree, neural networks, support-vector machines, naive bayes, logistic regression
  • Test Cases
    • Identifying important genes for cardiogenesis (using RNAseq data from cardiomyocytes, mice)
    • Identifying novel transmembrane proteins (using whole genomes, annotated genes, protein structure prediction)
    • Identifying mutations to transcript factor binding sites (PBM and gene sequence data)
    • Identifying important genes for skin pigmentation (using RNAseq data from fish)
    • Application to molecular folding (algorithms/optimization of a sub-case of an NP-complete problem)
    • Your project
  • In the news
    • AlphaFold, TensorFlow, numpy, pandas

Learning Outcomes

  • Able to use the terminal to run tools, programming languages, and look at / edit files - both on your personal computer and in linux on ISU systems (CS server).
  • Basic understanding of programming languages commonly used in computational biology - what each is used for, ability to compile/run programs in each, able to make small-ish changes to programs given to you.
  • Can explain fundamental concepts in computer science and apply these to problems/algorithms covered in the course - running time, memory usage, asymptotic analysis, multi-CPU and GPU programs, software testing.
  • Can explain fundamental concepts in biology and apply these to problems/algorithms covered - experimental errors, experiment design, basic statistics, central dogma of genetics, sequencing technologies and data formats.
  • Can explain and use a variety of classification and clustering algorithms (strengths, weaknesses, uses) as well as key concepts in machine learning.
  • Can run bioinformatics tools to process biological data, perform analysis, and interpret the results.

Grading and Assignments

Late Homework

All homework assignments will be given a preferred due date. Assignments can be turned in past the preferred due date, but any assignments turned in late will have their value multiplied by 80% (so the highest grade you can get on a late assignment is 80%). Any assignment discussed in depth in class are effectively closed and no credit will be given.

Start Homework Early

I suggest attempting a homework assignment the day it is given, or the day after, so that if you have a problem you can ask early. If you continue to have problems in trying to complete the assignment, you will have time to ask again. Many of the homework assignments require thought and problem solving, which takes "time on the calendar" not just "time on the clock". By that I mean that spending an hour on 3 consecutive days is likely to be more productive than trying to spend 3 hours at once on the assignment.

Expected Amount of Work

My expectation is that an average student will spend about 10 hours OUTSIDE of class each week (that is in addition to class time) WORKING PRODUCTIVELY/ EFFICIENTLY (not just staring at the computer) to complete their coursework for this class. Some students may spend less time than this, and some students will spend more.

Grade Cutoffs

Homework assignments and exams are designed so that a standard cutoff for grades will be close to what you deserve. After the first exam I will create a grade in Canvas called "Letter Grade" that is what your letter grade would be if the semester ended today. Initially, I will assign the following grades: 93-100 A, 90-93 A-, 87-90 B+, 83-87 B, 80-83 B-, 77-80 C+, 73-77 C, 70-73 C-, 67-70 D+, 63-67 D, 60-63 D-, 0-60 F

My goal is that the different grades have the following rough meaning.

A+/A
You understand everything and probably could teach the course yourself.

B+/A-
You understand nearly everything, and should be all set to use this knowledge in other courses or in a job.

C/C+/B-/B
Some things you understand very well and others you don't (more towards the former for a B and more towards the latter for a C).

D-/D+/C-
You did put some effort in, and understand many things at a high level, but you haven't mastered the details well enough to be able to use this knowledge in the future.

F
Normally, students that get an F simply stopped doing the required work at some point.

Canvas

The course has a canvas site. Click https://indstate.instructure.com/ to go to canvas. You should see this course listed under your courses for the current term. The canvas site is used for giving you your grades, for quizzes/exams, and for getting to online lectures (which are done using Zoom). Announcements will be sent through canvas and to your university email. Links and such will be kept on this website.

Lectures (using Zoom)

Here at ISU section numbers starting with the number 3 (e.g.3xx: 301, 302, etc.) are generally online sections. There are 2 types of online sections, synchronous online and asynchronous online. Sections that are synchronous must be joined at the regularly scheduled time of the course, whereas sections that are asynchronous must keep up with the material independently without regularly scheduled meetings. In general async sections are more difficult, and require a great deal of self-discipline (it is much easier to think "I can watch the videos tomorrow" and just get behind). So if you are in one of these sections make sure you get off to a strong start, and ask for help sooner rather than later. Check your course schedule for course meeting times, and if you have a meeting time, then your section is synchronous, otherwise it is asynchronous (or there is an error in the system).

This course has a 301 section (asynchronous online) with recorded lectures and meeting times arranged so all can attend.

For ISU's links to information on getting started with Zoom, see https://indstate.teamdynamix.com/TDClient/1851/Portal/KB/ArticleDet?ID=109823. You can also see the information at https://www.indstate.edu/fcte under the heading/link "Student Resources". You will get to the lectures for this course by going to Canvas for this course, and click on "Zoom - for lectures" on the lefthand menu (or click on Tools and scroll down to Zoom). Once there you should see a schedule of lectures and be able to view recorded lectures. Note that you should install the Zoom application for your computer, and you will need to be logged into to Zoom with your ISU credentials to be able to connect. Also note that the lectures are recorded and only available to those in our class.

Office hours (using Teams)

Office hours will be through Microsoft Teams by default. If you would like to meet in person you should reserve an appointment using http://cs.indstate.edu/scheduler to reserve an in person meeting with Jeff Kinne. For meeting through Teams, you should start Teams in your browser or start the application. You should be logged in using your ISU credentials. Once you have Teams open you can message me to ask me questions or to ask to talk. We can use Teams to message (better than emailing back and forth repeatedly if you have questions about something that you just want to write about) or to talk and share screens (e.g., to take a look at your code). I normally have Teams open on my computer all of the time, including during my office hours. During my office hours I will normally reply right away; at other times I will reply when I get a chance.

Participating online

If you are participating online, please see the information at https://www.indstate.edu/fcte under the heading/link "Student Resources". You are expected to either join lectures live through Zoom or watch the recordings once they are available. You will complete assignments, quizzes, and exams on the same schedule as the rest of the class. For quizzes and exams you will normally have a 24 hour period during which to take the quiz/exam (note that different students will have slightly different questions and any communication between students about quiz/exam content is academic misconduct).

CS Course Policies

Note that this course follows all standard CS course policies. In particular, (a) cheating/plagiarism by graduate students results in an F in the course, (b) missing 20% of the classes results in an F for any student, and (c) there will be no makeup exams. See http://cs.indstate.edu/info/policies.html for details.

COVID-19 Information

Information specific to CS courses - start of term announcements.

Standard ISU language required in all syllabi (read this all once, then skim for your other courses)...

Students are expected to adhere to course attendance policies, as stated in the course syllabus. Students must complete the Sycamore Symptom Assessment by email before arriving on campus each day unless they have documented their COVID immunization and have been exempted from the program. Documented COVID-related absences will be treated like any other serious medical issue. Following University policy, students with a documented, serious medical issue must contact the Office of the Dean of Students for assistance. The Office of the Dean of Students will supply documentation for faculty. Students with a documented serious medical issue should not be penalized and will be given a reasonable chance to complete exams or assignments. Once notification is made, faculty will make reasonable efforts to accommodate the student’s absence and will communicate that accommodation directly to the student. Please note that faculty are not required to accommodate a serious medical issue with virtual content options, like streaming or recorded lectures. Students who have been notified by contact tracers of a close contact who has tested positive for COVID must abide by their instructions, which will include a mandatory period of quarantine, especially if the student is unvaccinated, and/or mandatory testing. To avoid the potential of missing significant class time, students are strongly encouraged to receive the COVID vaccination that has been made available on campus. For more information about the vaccines or to find a vaccination site, go to: ourshot.in.gov. The ISU Health Center also administers COVID-19 vaccines by appointment.

Students should contact the Office of the Dean of Students with questions by calling 812-237-3829.

The information provided in this section of the syllabus is subject to modification based on guidance by public health authorities. Please follow this link for updated information on ISU’s Fall 2021 requirements.

Masks on campus: All faculty, staff, and students are required to wear face coverings anytime they are in public spaces. In classrooms they are required of faculty, staff, and students. Failure to comply with this policy will be treated, by policy, as would any student disruption of class. (A refusal or failure to properly wear an appropriate mask will result in the faculty member asking the student to do so. A refusal of that request may result in the student being asked to leave the class for that period. A refusal of that request may result in the faculty member cancelling class and referring the matter to the Office of Student Conduct and Integrity.) A failure of a faculty member to wear an appropriate mask/shield should be reported to the Chairperson of the faculty member.

Face coverings will be worn by all students and faculty in classrooms as well as in buildings (unless you are alone in an office). What is said/printed on a mask will be held to the same Student Code of Conduct standard as if it were printed on a shirt or hat. As a result, a political statement such as MAGA, BIDEN2020, or BLM is not grounds for demanding that it be removed/replaced. In judging what constitutes an offensive statement on a mask, the determination will be made by Student Affairs using the Student Code of Conduct. If there is a question about a mask, the faculty member will refer the matter to Student Affairs and only insist upon its immediate removal if there is no doubt that it violates the Code. Medical waivers will be made through Student Affairs and students with such a waiver are expected to carry the documentation with them and present it when asked.

Academic Integrity

Please follow these guidelines to avoid problems with academic misconduct in this course:
  • Homework: You may discuss the homework assignments, but should solve and finish them on your own. To make sure you are not violating this, if you discuss with someone, you should DESTROY any work or evidence of the discussion, go your separate ways, SPEND at least an hour doing something completely unrelated to the assignment, and then you should be able to RECREATE the program/solution on your own, then turn that in. If you cannot recreate the solution on your own, then it is not your work, and you should not turn it in.
  • Note on sources: if you use some other source, the web or whatever, you better cite it! Not doing so is plagiarism.
  • Exams: This should be clear no cheating during exams. The exams will be closed-book, closed-notes, no computer, and no calculator. You may be allowed one sheet of 8.5" by 11" piece of paper with hand-written notes to use as a crib-sheet for your tests.
  • Projects: You should not copy from the Internet or anywhere else. The project should be your own work. It will be fairly obvious to me if you do copy code from the Internet, and the consequences will be at the least a 0 on the project.

If cheating is observed, you will at the least receive a 0 for the assignment (and may receive an F for the course), and I will file a Notification of Academic Integrity Violation Report with Student Judicial Programs, as required by the university's policy on Academic Integrity. A student who is caught cheating twice (whether in a single course or different courses) is likely to be brought before the All University Court hearing panel, which can impose sanctions up to and including suspension/expulsion. See the http://www.indstate.edu/sjp/docs/code.pdf and http://www.indstate.edu/academicintegrity/ for more information.

Please ask the instructor if you have doubts about what is considered cheating in this course.

Special Needs / Disability Services

Standard ISU language required in all syllabi...

Indiana State University recognizes that students with disabilities may have special needs that must be met to give them equal access to college programs and facilities. If you need course adaptations or accommodations because of a disability, please contact us as soon as possible in a confidential setting either after class or in my office. All conversations regarding your disability will be kept in strict confidence. Indiana State University's Student Support Services (SSS) office coordinates services for students with disabilities: documentation of a disability needs to be on file in that office before any accommodations can be provided. Student Support Services is located on the lower level of Normal Hall in the Center for Student Success and can be contacted at 812-237-2700, or you can visit the ISU website under A-Z, Disability Student Services and submit a Contact Form. Appointments to discuss accommodations with SSS staff members are encouraged.

Once a faculty member is notified by Student Support Services that a student is qualified to receive academic accommodations, a faculty member is obligated to provide or allow a reasonable classroom accommodation under ADA.

Disclosures Regarding Sexual Misconduct

Standard ISU language required in all syllabi...

Indiana State University Policy 923 strictly prohibits discrimination on the basis of: age, disability, genetic information, national origin, pregnancy, race/color, religion, sex, gender identity or expression, sexual orientation, veteran status, or any other class protected by federal and state statutes in ISU programs and activities or that interferes with the educational or workplace environment.

Title IX of the Educational Amendments of 1972 prohibits discrimination based on sex, including sexual harassment. Sexual harassment includes quid pro quo harassment, unwelcome verbal or physical conduct, sexual assault, dating violence, domestic violence, and stalking.

If you witness or experience any forms of the above discrimination, you may report to:

Office: Equal Opportunity & Title IX; (812) 237-8954; Rankin Hall, Room 426
Email: ISU-equalopportunity-titleix@mail.indstate.edu
Online: https://cm.maxient.com/reportingform.php?IndianaStateUniv&layout_id=10

Disclosures made to the following confidential campus resources will not be reported to the Office of Equal Opportunity and Title IX:

ISU Student Counseling Center: (812) 237-3939; Gillum Hall, 2nd Floor
Victim Advocate: (812) 237-3829; HMSU 7th Floor
UAP Clinic/ISU Health Center: (812) 237-3883; 567 N. 5th Street