Instructors may make some changes to their outlines; the official outlines will be handed out at first class. Expand to read Plant Ag and UofG Academic Misconduct policy.
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Academic Misconduct

University Policy

Academic misconduct is behaviour that erodes the basis of mutual trust on which scholarly exchanges commonly rest, undermines the University's exercise of its responsibility to evaluate students' academic achievements, or restricts the University's ability to accomplish its learning objectives.

The University takes a serious view of academic misconduct and will severely penalize students, faculty and staff who are found guilty of offences associated with misappropriation of others' work, misrepresentation of personal performance and fraud, improper access to scholarly resources, and obstructing others in pursuit of their academic endeavours. In addition to this policy, the University has adopted a number of policies that govern such offences, including the policies on Misconduct in Research and Scholarship and the Student Rights and Responsibilities regulations. These policies will be strictly enforced.

It is the responsibility of the University, its faculty, students and staff to be aware of what constitutes academic misconduct and to do as much as possible through establishment and use of policies and preventive procedures to limit the likelihood of offences occurring. Furthermore, individual members of the University community have the specific responsibility of initiating appropriate action in all instances where academic misconduct is believed to have taken place. This responsibility includes reporting such offences when they occur and making one's disapproval of such behaviour obvious.

University of Guelph students have the responsibility of abiding by the University's policy on academic misconduct regardless of their location of study; faculty, staff and students have the responsibility of supporting an environment that discourages misconduct. Students should also be aware that if they find their academic performance affected by medical, psychological or compassionate circumstances, they should inform the appropriate individuals,(instructors, program counsellors, graduate advisors) and follow the available procedures for academic consideration outlined in the University's calendars.

» http://www.uoguelph.ca/registrar/calendars/diploma/current/c08/c08-amisconduct.shtml

Department Policy

1. No Quotation and references. Plagiarism has occurred if the author does not place quotation marks around word-for-word copying of print or electronic format source material even if the source is correctly cited. To further reduce the possibility that a quotation will be misrepresented or mistaken as one's own work, instructors may request that quotations be italicized or double indented.

2. Degree of fidelity to source. Plagiarism has occurred if the author's writing is clearly recognizable as essentially derived from cited or uncited print or electronic format sources, even though the author has altered the original source material by inverting word or sentence order, or substituting synonyms. Authors should summarize and synthesize ideas and concepts rather than interchange words.

3. Group projects. Teams working on group projects should practice group dynamics (such as meetings of the whole group, review of each other's work and discussion of academic misconduct) that will discourage individuals from contributing plagiarized material. Groups may bear collective responsibility for the academic integrity of their project.

4. Identical individual projects. Plagiarism will be strongly suspected if two or more students submit individual projects that are substantially identical.

5. Editing answers. It is an improper academic practice to add, delete, or edit answers after the exam period has concluded, or using prohibited materials during an exam.

**BIOL*3300** Applied Bioinformatics

UNDERGRADUATE/GRADUATE
Graduate students must write two critical reviews of published papers. The first one is due before winter break. The second is due before the final exam. Graduate student presentations are separate from undergraduate presentations. Otherwise, the course is the same. New molecular genetic and information technologies have enabled biologists to produce and to access large and informative data sets. This course will provide an introductory understanding of the databases and methods used in computational molecular data analysis. Topics covered will include introducing the UNIX-related operating system, reviewing major molecular databases and their structures, constructing sequence alignments, constructing phylogenies, and finding motifs and genes in biological sequences. Lab sessions will include an introduction to Unix and Perl for the biologist and hands-on use of several molecular data analysis programs.

Instructor

TBA

Teaching Assistant

TBA

the following is for archival purposes representing past curriculum to give an example of the past course structure. Dates, times and locations are incorrect. Course content may change when the new lecturer is announced.

Time

Lectures: MWF 0830-0920, AXEL259 (2009)

Labs: (2009)
Tuesday, 9:30-11:20, SCIE1306
Tuesday 11:30- 1:20, SCIE1306

Objectives

Bioinformatics is an integral part of the biological sciences. The goal of this course is to
understand how fundamental methods in bioinformatics work and to understand how to
use them. We will focus on biological questions in current research, and students will
present papers to the class that utilize bioinformatics to address key and current
biological questions.

As much as possible, bioinformatics methods will be presented within the context of
application. The key areas of bioinformatics that we will cover are: database content,
access, and understanding; genetic and physical mapping; genome sequencing; pairwise
and multiple sequence alignment methods; sequence motif analysis methods; and
phylogenetics.

Textbooks

There is no textbook.
The class is primarily based on lecture notes and primary literature.
Lecture notes and papers will be available on Blackboard.
In addition, several supporting texts are available for additional information.
I especially recommend Bioinformatics and Molecular Evolution by Higgs and Attwood.

Other texts are:

A Primer of Genome Science by Greg Gibson and Spencer Muse
Bioinformatics: Sequence and Genome Analysis by David Mount
Biological Sequence Analysis by Richard Durbin, Sean Eddy, Anders Krogh, and Graeme Mitchison
Bioinformatics edited by Andreas Baxevanis and B.F. Frances Ouellette
Developing Bioinformatics Computer Skills by Cynthia Gibas and Per Jambeck
Elementary Sequence Analysis by Brian Golding and Dick Morton
Molecular Evolution: a Phylogenetic Approach by Roderic Page

All texts (with the exception of Elementary Sequence Analysis) are on reserve at the
library. Elementary Sequence Analysis is available free of charge from Dr. Brian Golding
at McMaster University http://helix.biology.mcmaster.ca/courses.html

Grades

Marks will be determined by:

Quizzes (3 quizzes, 45 points).
Satisfactory completion of lab assignments (15 points)
A class presentation (15 points: 10 points presentation and review; 3 points questions
answered; 2 points questions posed). All material is due within one week of presentation.
A cumulative final exam (25 points).

The final mark will be at least the number of marks earned. Except where noted, all work
handed in for a mark must be ones own. Please see U of G policy on academic integrity.

Initial Topics

Introduction and Overview of Topics

Case Study #1- Identifying key genes important in agriculture and evolution.

Key papers:

et al.

Science

et al.

Nature

Key concepts:

Case Study #2- sRNA Part 1: miRNAs, a major new class of regulatory molecules.

Key papers:

Key concepts:

Case Study #3- sRNA Part 2: siRNAs, methylation and the diversity of sRNA pathways.

Key papers:

Key concepts:

Case Study #4: Criminal justice and molecular evolution.

Key papers:

Key concepts:

Important Dates

Jan. 12th (Mon)	Presentation sign-up.
Jan. 30th (Fri)	Presentations start
Jan. 28th (Wed):	Quiz #1
Feb. 16th – Feb 20th	Winter break.
Feb. 27th (Fri):	Quiz #2
Mar. 23 (Fri)	Quiz #3
Apr. 3rd (Fri)	Last Class
Apr. 8th (Wed, 8:30- 10:30AM):	Final Exam

NOTE: I will be gone Jan. 21 and 23 and have guest lectures. I may be gone Mar. 13.

Student Presentations

Each student will work with one or two other students to present a research paper to the class for 30 minutes. Each student will also write a 2-3 page critical review of the research paper. The presentation should be a joint effort, but each person must write her or his own review. In the presentation, students will give the background of a research question and present the paper that addressed this question. The presentation will be uploaded to Blackboard. People in the class are responsible to know a summary of the paper for quizzes and the final and to hand in questions after the presentation. Students are welcome to address a topic of interest to them, or I can suggest a paper. I will distribute a list to sign up next Monday. Please give your preferred partners if you have them. I will assign partners to those who do not have them.

Lab Topics

Labs will cover the use of major data analysis programs discussed in lecture. These will include CLUSTAL, BLAST, the PHYLIP or MEGA suite, BIOCONDUCTOR (part of the R statistical package) for microarray data analysis, and FASTA for sequence analysis. Basic PERL and shell scripting will be introduced for text manipulation. The first lab is in the second week of class. Shuhua Zhan will give you details about lab credits.

Academic Misconduct

University Policy

Department Policy

BIOL*3300 Applied Bioinformatics

Instructor

Teaching Assistant

Time

Objectives

Textbooks

Grades

Initial Topics

Introduction and Overview of Topics

Case Study #1- Identifying key genes important in agriculture and evolution.

Case Study #2- sRNA Part 1: miRNAs, a major new class of regulatory molecules.

Case Study #3- sRNA Part 2: siRNAs, methylation and the diversity of sRNA pathways.

Case Study #4: Criminal justice and molecular evolution.

Important Dates

Student Presentations

Lab Topics

**BIOL*3300** Applied Bioinformatics