Graduate Course Listings 2019-20

Note: Subject to change. Please refer to the Graduate Calendar for confirmation of fall/winter offerings listed below.

Biol-860-Biol-865 inclusive - these courses are also CAPPED at 12 and require written permission from the course coordinator.  Only the Biology Graduate  Assistant will register you into any of these courses once the permission has been received by her.   

All courses are half-courses (3.0 credit units) which are offered either in the fall or winter term.  

 

Biol-812
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Biol-812 Programming for Biologists

Description/Outline:  Programming for Biologists

This hands-on course introduces students to modern computational methods for biology with an emphasis on emerging standards of Open Science and Reproducible Research. No prior programming experience is assumed. In coordination with Queen’s University Centre for Advanced Computing (CAC), the content of this course is intended to teach core-competency in the following areas:

1. Programming basics: regular expressions, flow control, file manipulation, custom functions.

2. Unix/Linux command-line programming and shell scripting on CAC infrastructure (SLURM).

 

R with GitHub, R Markdown, and the tidyverse (dplyr, %>%, tidyr, ggplot2) for seamless reproducible data management, analysis and production of publication-ready graphics.

3. Introduction to some standard formats (e.g. FASTA, FASTQ, SAM, BED, BAM), programs (e.g. SAMTOOLS, VCF, HISAT2), and pipelines in Unix/Linux, R and Python for reproducible analysis of data from next-generation sequencing platforms.

 

Content includes introduction to state-of-the-art methods in genomics and metagenomics, including sequence assembly, alignment, variant detection, and gene annotation. However, the majority (~3/4) of the course is devoted to learning basic computational tools that may be useful to biologists working on large datasets of any kind.

Winter 2020 R. Colautti
BIOL 819
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Biol 819 Selected Topics in Molecular Biology

Topics vary annually to reflect the latest status of the field of molecular genetics .

Winter 2020 W. Bendena
BIOL 820
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Biol 820 Commercialization of Biological Research
Current issues relating to the biotechnology industry will be dealt with in detail. Topics covered include: grant writing; patenting; circumventing patents; funding sources; business plans; venture capital investments; public awareness; public perspective; and layperson presentations. Three term hours; fall. K. Ko and V.K. Walker. PREREQUISITE: At least one of the following: BIOL-201*, BIOL-205*, MBIO-318*, BIOL-441*, BIOL-330*/430* or equivalent.
 
EXCLUSION: PHGY-801.
Fall 2019 K. Ko
BIOL 822
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Biol-822 Long-Term Environmental Change

The main focus of this course will be to review and assess the many techniques currently available to track long-term environmental change. An emphasis will be placed on biological approaches dealing with sedimentary analyses, but other proxy methods (e.g. ice cores, bore holes, etc.) will also be covered. General topics to be covered will include climatic change, acidification, eutrophication, lake and reservoir management, UV penetration, etc. Three term hours.  Fall.  J.P. Smol 

Fall 2019 John Smol
Biol-824
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Biol-824 Gateway to Graduate Studies in Biology

The overall goal of this course is to introduce intellectual and professional skills important for success in graduate school and in careers in Biology. Course structure and content is applicable to all fields of biology, from ecology and evolution to cell biology, biochemistry, and molecular biology.

Fall 2019 D. Orihel et al
BIOL 848
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Biol 848 Field Courses in Biology - Winter 2020
No description available.
Winter 2020 Lougheed
BIOL 860
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Biol 860 Introduction to Statistics

CAPPED AT 12 STUDENTS

This course is for new graduate students who are at early stages of planning their research projects and collecting data. Topics will include experimental design, matching hypotheses with appropriate statistical analyses, parameter estimation, and graphing. Statistical analyses will be based on a foundation using normal error distribution. Students will be introduced to R, a Language and Environment for Statistical Computing.

 

Fall 2019 S. Arnott
BIOL 861
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Biol 861 Introduction to Linear Models

This course is designed for Biology graduate students with a basic introductory statistics/experimental design course and a working knowledge of R, a Language and Environment for Statistical Computing. In-depth exploration of all aspects of fitting linear models to continuous and categorical data, using mainly the lm function in R. Topics include residual analysis, maximum-likelihood methods, graphical presentations, ordinary least squares, model II regression, transformations, model selection with focus on information-theoretic approaches and outlier detection.

 

Lecturer: C.G. Eckert

Winter 2020 C. Eckert (Lec)
BIOL 862
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Biol 862 Generalized Linear Models

This is a course designed to introduce students the linear model for analyzing continuous and categorical data in biology. Each session will begin with a short lecture by the faculty instructor, followed by a student presentation of homework, and a hands-on interactive session focusing on statistical computing and graphics. Each student will bring a laptop to class.

Fall 2019 Wm. Nelson
Biol-893
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Biol-893 Mentoring Experience in Biology

OUTLINE OF TOPICS:

Students will advise and train other students in biological investigations, over a two-term period.

 

METHODS OF INSTRUCTION AND HOURS PER WEEK:

Activities include guidance on research proposals, research procedures, student presentations, and drafts of student work

 

EVALUATION:

Assessment of mentoring skills as you provide guidance on research proposals, research procedures, student presentations, and drafts of student work

 

TEXTBOOK:

None

 

PREREQUISITE AND ASSUMED BACKGROUND:

Open to full-time students having completed two terms of study in Biology M.Sc. or Ph.D. programs.

 

 

Pass/Fail

 

Does not count towards degree

Fall 2019 and Winter 2020 Your Supervisor
BIOL 897
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Biol 897 Seminars in Biology

Attending a diverse array of seminars is an essential component in the development of a student.  The aim of this course is to develop skills in listening, synthesizing and critical thinking, as well as fostering the development of important oral and written communication skills.  Students are required to attend and evaluate departmental or specialized research seminars as well as to present a seminar based on their graduate thesis research.  Fall/Winter/Summer. 

Information and instructions for graduate students of MCIB and EEB faculty:  http://130.15.90.125/Bio897/index.html

Questions to Dr. Laurent Seroude (seroudel@queensu.ca).

 

Enrolment is extended over a period of SIX terms ONLY.  

 

Students must register in two academic years.  Ensure that you email the Biology Graduate Assistant (Joanne Surette) to register you for the second year.

 

 

Fall / Winter / Summer 2019-2020 L. Seroude
BIOL 831
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Biol 831 Bioremediation

Bioremediation is the use of organisms to alleviate environmental problems.  Topics will include the biology of the organisms involved and their bioremediation processes.  Plants act to absorb and concentrate heavy metals from soils whereas micro-organisms, invertebrates and plants degrade organic toxins and remove excess nutrients from soils, substrates and water.  The processes include extraction, absorption, concentration, and degradation of contaminants.

Fall 2019 Dan Lefebvre

I've spent more time than many will believe [making microscopic observations], but I've done them with joy, and I've taken no notice those who have said why take so much trouble and what good is it?

Antonie van Leeuwenhoek

It's a parts list... If I gave you the parts list for the Boeing 777 and it had 100,000 parts, I don't think you could screw it together and you certainly wouldn't understand why it flew

Eric Lander

What is true for E. coli is also true for the elephant

Jacques Monod

The world becomes full of organisms that have what it takes to become ancestors. That, in a sentence, is Darwinism

Richard Dawkins

Shall we conjecture that one and the same kind of living filaments is and has been the cause of all organic life?

Erasmus Darwin

Nature proceeds little by little from things lifeless to animal life in such a way that it's impossible to determine the line of demarcation

Aristotle

Cells let us walk, talk, think, make love, and realize the bath water is cold

Lorraine Lee Cudmore

In the distant future I see open fields for far more important researches. Psychology will be based on a new foundation, that of the necessary acquirement of each mental power and capacity by gradation. Light will be thrown on the origin of man and his history

Charles Darwin

It is my belief that the basic knowledge that we're providing to the world will have a profound impact on the human condition and the treatments for disease and our view of our place on the biological continuum

J. Craig Venter

Imagine a house coming together spontaneously from all the information contained in the bricks: that is how animal bodies are made

Neil Shubin

A grain in the balance will determine which individual shall live and which shall die - which variety or species shall increase in number, and which shall decrease, or finally become extinct

Charles Darwin

The stuff of life turned out to be not a quivering, glowing, wondrous gel but a contraption of tiny jigs, springs, hinges, rods, sheets, magnets, zippers, and trapdoors, assembled by a data tape whose information is copied, downloaded and scanned

Steven Pinker

We wish to discuss a structure for the salt of deoxyribose nucleic acid. (D.N.A.). This structure has novel features which are of considerable biologic interest

Rosalind Franklin

We are biology. We are reminded of this at the beginning and the end, at birth and at death. In between we do what we can to forget

Mary Roach

The systems approach to biology will be the dominant theme in medicine

Leroy Hood

I've always been interested in animal behavior, and I keep reading about it because it's so surprising all the time - so many things are happening around us that we neglect to look at. Part of the passion I have for biology is based on this wonderment"

Isabella Rossellini

Because all of biology is connected, one can often make a breakthrough with an organism that exaggerates a particular phenomenon, and later explore the generality

Thomas Cech

Nothing in Biology makes sense except in the light of evolution

Theodosius Dobzhansky

Biology is now bigger than physics, as measured by the size of budgets, by the size of the workforce, or by the output of major discoveries; and biology is likely to remain the biggest part of science through the twenty-first century

- Freeman Dyson

Nothing can be more incorrect than the assumption one sometimes meets with, that physics has one method, chemistry another, and biology a third

- Thomas Huxley