Computer Science 857 - Readings in Bioinformatics

Course Description

Reviews and discusses recent advances and issues in Bioinformatics through paper presentation by students. Topics will range from computational biology to artificial life and biological computation. Students will be evaluated based on their presentations and participation, as well as a small project.

Cmpt857 is designed to be a multi-disciplinary course allowing students from a wide range of disciplines to explore bioinformatics. The topics covered will depend on the interests of the professor and the students in the class.

Course Offering

The details of the current course offering can be found here.

Overview

Cmpt857 is designed to be a multi-disciplinary course allowing students from a wide range of disciplines to explore bioinformatics, where "bioinformatics" encompasses topics ranging from biological applications of information technology and computer science to models of computation inspired by biological systems. The topics covered will depend on the interests of the professor and the students in the class. The course is useful to students with prior schooling in bioinformatics, as well as students who are interested in bioinformatics but are uncertain that they have the necessary background to take a more traditional bioinformatics course (e.g. BINF 200 or CMPT 830).

Note: this is not a class on how to get / install / use particular software in biological applications. Rather, through readings of research papers, it will explore ideas behind such software and new ways of making use of computer science techniques in the procurement, analysis, and exploitation of biological data. It will also explore how ideas from biology can be used to perform computations in interesting new ways.

Instructors

Professor: Tony Kusalik
Office: Spinks 424
Phone: 966-4904
e-mail: kusalik‍@‍cs.usask.ca

Professor: Joe Angel
Office: HSB A4.2
Phone: 966-4361
e-mail: Joseph.Angel‍@‍usask.ca

Scheduling Details

Time: The time for the class is Tuesdays and Thursdays from 10:00 until 11:20.
Room: Thorv S386 (in the Spinks Addition)

First Meeting: Tuesday, September 7, 2010

There is no "required" text for the class, though there are three "recommended" ones.

In the "quick reference" category are:

• Instant Notes in Bioinformatics 2nd. edition, by Hodgman, French, and Westhead, published by Taylor & Francis, 2010, ISBN 978-0-415-39494-9, and
• Dictionary of Bioinformatics and Computational Biology edited by Hancock and Zvelebil, published by Wiley, 2004, ISBN 0-471-43622-4.

These titles should be in the UofS bookstore, and are also available in the Library. Students interested in a thorough grad-level textbook on Bioinformatics are advised to order (e.g. through the campus bookstore or through amazon.ca):

• Understanding Bioinformatics by Zvelebil & Baum, published by Garland Science, 2008, ISBN 978-0-8153-40024-9. This is currently the premier reference text in the field.

Syllabus

The following is a list of possible topics that could be covered by papers taken up in the course.

• From the computer science perspective, application of techniques from the following areas to biological information:
  • computational linguistics, languages, and grammars
  • simulation
  • vision and image analysis
  • graphics and visualization
  • symbolic logic
  • databases, information management
  • machine learning and artificial intelligence
  • probabilistic methods
  • operations research
  • computer networks
  • graph theory
  • parallel computation
  • novel models of computation
  • algorithms
• From a biological perspective, computer science techniques applied to:
  • DNA, RNA, and protein sequence analysis
  • DNA sequence assembly
  • gene or protein expression analysis
  • protein folding prediction, protein structure determination
  • ligand-protein binding prediction
  • genome evolution and taxonomy
  • interaction networks
  • systems biology
  • cell differentiation
  • (molecular) physiology
  • probe and primer design
  • localization
  • diagnosis
  • literature search

Given the above, a particular topic or paper typically has two categorizations: one from a biological perspective and another from a computer science perspective.

Important note: this class is not intended as a course in any of the computer science disciplines or techniques listed above. Neither is it meant to be a course addressing specific biological ideas or problems listed. Students will be assumed to either know the particular technique, idea, problem, etc., or be willing and able to learn about it from relevant sources.

Class Format

Because of the nature of this class (multidisciplinary, and having no stringent prerequisites in either Computer Science or the life sciences), students in this class usually come with a wide range of backgrounds.

For the most part, the course will be readings-based. That is, most of the instruction will come through reading, presentation, discussion, and review of (research) papers. This allows students to build on their particular expertise, while learning new concepts in less familiar areas. In addition to research papers, students may also be required to complete a small software project or construct an "index web page". Occasionally, but especially near the beginning of class, there may be supplementary lectures given to provide background material (e.g. on local and global sequence alignment). Finally, there will be a take-home final exam. These components of the class are discussed further below.

A significant part of this course will involve study and presentation of research papers. In particular, students in the class will be expected to read all selected papers, take their turn presenting papers, participate in the discussion of all papers, and compose a review of each paper. The papers covered (discussed) will be selected by the students and made available well in advance of their presentation. All members of the class will be responsible for reading each paper (prior to its presentation!) and -- except for the presenter -- formulating discussion-oriented questions. The presenter will chair the discussion of the paper. If necessary he or she may provide some background information for members of the class not familiar with an area. Students are welcome to ask their prepared questions during the discussion. Finally, students will be required to submit a review of the entire paper, or on a major theme from the subsequent discussion.

As for deadlines and due dates,

• each paper to be taken up must be made available to the class at least one week prior;
• prepared questions on a specific paper are due at the start of the class where it is to be discussed; and
• reviews are due one week after the the presentation being reviewed.

Each paper covered (discussed) will be selected by a student, but subject to approval of the instructors. Students should thoroughly read their prospective choice prior to approaching the instructors for consent since the quality of the papers selected contributes to the final grade.

Towards the end of the semester students may have the opportunity to complete a small project. This may involve experimentation with existing software, software development (programming), or installation and a "demo" of new software. The intent is to provide students with an opportunity explore and gain experience with state-of-the-art bioinformatics software, and to explore the principles behind such software. In all cases, the software system involved must be nontrivial and fall into the category of bioinformatics, and a written report describing the project must be submitted. This type of project may also be performed in small multidisciplinary teams. Students must get prior approval of their prospective project from the instructors before commencing work on it.

Alternatively, a student's project may be the construction of a web page which acts as an annotated index to resources on the web in a particular bioinformatics area. Here the motivation is an in-depth exploration of a particular bioinformatics topic, and developing skills necessary to filter and evaluate the myriad of information on the web on even a single topic. The student's index page can be constructed at any site (server) he or she chooses -- the only restrictions are that it be in HTML form, accessible to the instructor, and of the student's own composition. To construct the web page, the student will have to

• decide on a topic area
• explore the web for relevant information and links
• organize the information
• add necessary annotations, descriptions and discussion and links into a comprehensible and useful form.

The decision as to whether there will be a project component to the class will be made mid-way through the term, and will be dependent on the wishes of the students as well as the availability of sufficient time in the schedule of presentations.

The final exam will be of the "take home" variety with discussion-style questions that will be answerable by anyone who actively participated in the class and regardless of background discipline.

Questions, reviews, and reports may be submitted in hard copy or electronic form. If the latter, they should be either in a universal format such as raw text, PDF, PostScript, RTF, or HTML. Application-specific files, such as MicroSoft Word documents (.doc files), will not be accepted.

Grade Allocation

• paper presentations: 60%, apportioned as follows
  • selection of good-quality papers: 7%
  • presentation of papers and leading discussions: 20%
  • preparatory questions: 8%
  • reviews: 25%
• project: 15%
• participation in discussion of papers: 5%
• final exam: 20%

• paper presentations: 68%, apportioned as follows
  • selection of good-quality papers: 8%
  • presentation of papers and leading discussions: 25%
  • preparatory questions: 8%
  • reviews: 27%
• participation in discussion of papers: 7%
• final exam: 25%

Academic Integrity

This course will conform to the academic requirements and standards for graduate courses, including the rules of Student Appeals in Academic Matters and Academic Honesty.