Overview

This course is designed to be a capstone course in the bioinformatics program, as well as be a service class to students in the disciplines contributing to bioinformatics. It integrates material in the life sciences, computational science, and mathematics. The course introduces problems and major concepts in bioinformatics, trains students in a variety of basic techniques, and introduces terminology. It also illustrates the value of, and need for, cooperation, teamwork, and multi-disciplinary collaboration in areas such as bioinformatics.

Instructor

Tony Kusalik
email: kusalik‍@‍cs‍.usask‍.ca
office: Thorv S424 (in the Spinks Addition)
telephone: 966-4904

Office Hours

I will be in S341 from 12:00 to 13:00 on Fridays. In addition, you can contact me by e-mail at any time or post a message in one of the class discussion forums. I am also readily available before and after the class. We can meet at other times too; just make an appointment.

Logistics

Class: Monday, Wednesday, Friday. 10:30 a.m. - 11:20 a.m. Thorvaldson S311 (in the Spinks Addition)

Lab: Friday. 3:30pm-4:50pm Thorvaldson S311 (in the Spinks Addition)

Prerequisites

The prerequisites for BINF 200 are CMPT 111 and BMSC 200 (or BIOCH 200). It is your responsibility to insure that you have met these prerequisites. If you don't, and you are in Arts & Science, you will not get credit for the course.

Syllabus and Readings

The following table provides a tentative schedule of high level topics for the class, and when approximately that topic will be covered. Chapter numbers under the "Readings" column refer to chapters in the Xiong textbook, while those under the "Supplementary Material" heading refer to the Wünschiers text.

Class Format

In general, the class will involve lectures, in-class demonstrations, guided tutorials, lab exercises, assignments, and written examinations.

The course will be divided into a number of topic areas. Through lecture, the instructor will provide essential background information (either in Molecular Biology or Computer Science) on starting each area. Afterward, techniques and detailed subject material will be presented, either through lecture or demonstration. Any required demonstrations will be on the equipment in the classroom. Finally, students will be required to complete laboratory exercises and assignment problems. The solution of these exercises and problems will be key to students' learning in the course. Through them students will learn more about the computer science techniques involved, the biological problem being tackled, and the use of existing applicable (software) tools.

There will be a distinction between lab exercises and assignments. Specifically, the former are intended for practice with basic bioinformatics tools and gaining experience with basic concepts and tools in an environment where a lab attendant is available. They are intended to be completed in about 1 to 2 hours of work. Assignments, on the other hand, are intended to develop a deeper understanding of issues. Solutions to assignment problems will require more thought and preparation. Both lab exercises and assignments are to be completed on an individual basis. However, it is possible to discuss solution strategies with others.

A midterm will be held as well as a two-part final exam. The date of the midterm is tentatively March 2. It will be a closed-book exam. The final exam will consist of both a written portion and an in-lab portion. Both portions of the final exam will be "open book".

Grade Allocation

Important Notes

• The participation mark will be based on whether or not the student has made any postings to the forums for the class.
• Laboratory exercises and assignments are required elements of the class and a significant majority of the lab exercises and assignments must be completed in order to achieve a passing grade (specific numbers under given in the sections on "Instructional Laboratory" and "Assignments"). Items 1.1.3.c.ii and 1.4.7.a.ii of the University examination regulations will apply if these required elements are not completed. This policy means, for instance, that students who skip labs or don't bother doing assignments will not pass the class no matter how well they "ace" the exams. With this in mind, if a student is unable to complete an assignment or lab due to extenuating circumstances, he or she should promptly contact the professor to make necessary alternate arrangements.
• The written final exam is another required element of the class. Failure to write that exam will result in failure of the course.
• Students must have a combined average of at least 30% on all other class work and in-term exams to be eligible to write the final exams.
• If a student does not write the lab final exam or midterm exam, the corresponding portion of the final grade allocation will be re-assigned to the written final exam.
• It is preferable that students complete labs and assignments even if it means submitting them late; the potential for knowledge gain is more important than strict enforcement of submission deadlines. However, it is not fair to other students or to the marker if some students are allowed to submit late assignments with no consequences. Hence, late assignments and labs will be accepted, but they will be docked a penalty which will grow exponentially with the duration late.
• As mentioned above, the date of the midterm is tentatively March 2.

Texts and Library Materials

Textbooks

The required textbook for the class is:
Essential Bioinformatics, by J. Xiong (published by Cambridge University Press, 2006).

There is also a recommended textbook for the class, which has supplemental material. It is:
Computational Biology: Unix/Linux, data processing and programming by Wünschiers (published by Springer-Verlag).

Both textbooks for the class (the required one and the recommended one) are available in the Bookstore and in the Library.

References in the Library

Texts from previous offerings of the course are also on Reserve in the library, and may prove valuable references and study aids.

The University libraries have large collections of books covering the areas of bioinformatics, using LINUX, and programming in Perl. Students are encouraged to make use of them. Many of the items are "E-books".

Instructional Laboratory

As described under "Class Format", the laboratory session is for gaining practical experience in the application of concepts introduced in the lectures. The lab periods are 90 minutes in length. An initial portion of the lab time may be devoted to providing introductory information. The remainder of the period will be for completion of the laboratory exercise. The lab instructor will be available during this time to provide assistance as necessary.

Students are required to attend the weekly laboratory session. Each week's lab component is to be completed in the time period specified and a solution either shown to the instructor for immediate evaluation, or submitted electronically. A grace period, beyond the end of the laboratory session, for submission of the solution will be given. The duration of the grace period will be specified as part of the lab specification. Beyond the grace period, late submissions will be accepted, though they will be subject to an exponentially increasing penalty.

Important Note

• For the purposes of University Examination Regulations on Incomplete Coursework if more than 2 labs are missed, a student will be deemed to have not successfully completed a required element of the class and will not receive a passing grade in the course. That is, unless special provisions have been arranged, no more than 2 labs can be missed for a student to pass the class.

Teaching Assistant

Name: Brett Trost
E-mail: brt381‍@‍mail‍(.usask.ca)

Assignments

There will be about 4 assignments in the class. They will not be long assignments, though the problems will be harder than those in the laboratory. Students will typically have 2 weeks to complete each assignment. Assignment solutions will be submitted electronically. Late submissions will be accepted, though they will be docked accordingly. The late penalty will be determined using an exponential function.

Important Note

• For the purposes of University Examination Regulations on Incomplete Coursework, if more than one assignment is missed a student will be deemed to have not successfully completed a required element of the class and will not receive a passing grade in the course. That is, unless special provisions have been arranged, no more than one assignment can be missed for a student to pass the class.

Academic Honesty

• All students must be properly registered in order to attend lectures and receive credit for this course.
• The standard University of Saskatchewan Department of Computer Science Academic Honesty Policy and the University's regulations on academic conduct apply in this course.
• All assignments and laboratory exercises are to be completed on an individual basis, unless specified otherwise. For the purposes of this class the interpretation of what constitutes "an individual basis" is:
  • You may work on an assignment or laboratory as a member of a group. However, if you work as a member of a group, you are required to clearly identify the other members of the group in your submission.
  • You may work within a group to verify that the members of the group have understood the problem. You may even confirm your design, approach, and results together. However, each of you must perform the operational or implementational phase independently. That means, for example, that you must write your own programs or scripts.
  • For a programming problem, you may work within a group on testing strategies and criteria for the selection of test cases. However, each of you must perform the testing phase independently.
  • For a programming problem, each student must compose their own documentation (internal documentation, external documentation, and testing documentation) independently.
  • The preparation of an lab exercise submission or assignment submission must be performed independently.
• Please understand that, without the practical experience gained when performing the laboratory exercises or solving the assignment problems, you will be at a significant disadvantage in your examinations when compared to those students who did. It will also be a serious detriment to you in subsequent courses, and in an employment or research situation.

Laboratory Resources

The main computational resources for this course will be the Mac OS and LINUX operating systems, the EMBOSS package of bioinformatics software, the Perl scripting language, and various other bioinformatics software packages.

Students will have accounts in the Computer Science computing laboratories (e.g. rooms THORV S311, S320, S360). The class will make use of the Apple Macintosh workstations in S311. However, any of the LINUX or Mac OS X workstations on the 3rd floor can be used at other times. For remote access (e.g. from home) to a LINUX system, log in to tuxworld.usask.ca using the ssh program or a virtual terminal program which supports the ssh protocol. Information on how to set up remote access to any of the Computer Science Department's computational lab resources can be found at http://www.cs.usask.ca/resources/computing/remote.php.

On-Line Resources

On-line forums on topics related to the class are hosted on the moodle pages for the class.