Graduate Courses

                                                                                                                     Updated September 3, 2017

How to Enrol

Graduate students in the Department of Ecology and Evolutionary Biology can access the Student Web Service (SWS) to change personal information (addresses and telephone numbers), view their academic record and current courses and to enrol in, request or drop courses. Note: you can only use SWS (e.g. ACORN/ROSI) to enrol in courses if you do so by the deadlines listed below. For complete information on using the SWS please view Instructions for Course Enrolment using ACORN/ROSI. It is your responsibility to ensure that course enrolment is accurate on SWS.

Graduate Student Run Non-Credit Workshops & Courses

The Department recognizes that individual graduate students have developed considerable expertise in many important research tools and concepts and it wishes to encourage such students to share their expertise with other graduate students. Accordingly, as a pilot project the Department will offer some financial support to students or student groups who volunteer to offer not-for-credit workshops or short not-for-credit courses that meet significant demand for skills or knowledge beyond what is commonly generated within study groups. To access departmental support, potential graduate student instructors or organizing groups should submit to the Grad Office a proposal that: 1) describes the need and the project designed to fill it, including giving it a descriptive name; 2) assesses the demand within the department and specifies a measure of success for the project (e.g. the number of students completing the training); 3) optionally describes a small budget (maximum $500) for supplies, course resources, and/or a small honorarium for the chief instructor; 4) provides a list of fewer than 10 questions that would constitute a suitable evaluation of the quality or success of the project in meeting student needs. The Grad Office will respond with a decision about the level of support, which may be contingent on the project meeting its specified index of success. At the end of the project we will also provide a letter of documentation to any student who leads a successful one.  

Graduate Courses Offered in 2017-2018

You may sign up for a course(s) beginning August 14, 2017 (but not before that date) on Student Web Services with ACORN or ROSI (please see the link above to the instructions) or the email you received in late July about course registration, ACORN, etc.  Please also note that, for some courses, you may sign up for a course but you will not be registered in the course until permission has been granted by the course instructor (this is normal procedure for many courses).

Deadlines: Please make sure that you have signed up for your course(s) by the following deadlines: for Fall or full-year courses, the deadline to enrol is *September 25, 2017* and the deadline to enrol in January session courses is *January 22, 2018*.

New students should consult their supervisor(s) and fellow students about the courses
most appropriate to meet their needs. 

The coursework requirements for the M.Sc. and Ph.D. programs are provided in the EEB Graduate Handbook: http://www.eeb.utoronto.ca/grad/current/grad-forms.htm 

Note: Section Code: usually F, S or Y. This indicates whether the course is offered in the fall session (F), the winter session, i.e., second term (S) or over both (Y).

PDF version of Graduate Courses offered by EEB in 2017-2018 (note: all of the information in this document is provided below)

***Note: see below for courses offered by other departments/groups that will be of interest to some EEB graduate students***

Graduate courses and seminars officially begin in the week of September 11th for September session courses (F) and January 8th for January session courses (S); however, some of the EEB graduate courses will not begin until the second week of classes and courses at UTM and UTSC may begin before the listed dates— please check with the course instructor.

EEB Graduate Courses Offered in Fall 2017:

EEB 1310H F  Philosophy & Methods [H. Rodd (team leader), Njal Rollinson, and guests] Day and Time: Thursday afternoons at St.G. campus (2:00-5:00) starting Sept 21. Location: Students enrolled in the course should have access to Blackboard for the course and will be contacted with the course schedule, room locations, etc. by email.

This course will involve a combination of (i) student-lead discussions (some topics are listed below), (ii) lectures/discussions lead by faculty designed to cover general and often controversial scientific issues frequently confronted in both ecological and evolutionary studies, and (iii) short presentations by students introducing the background and context for their proposed research. This course is recommended for students just starting an MSc or PhD, and for students in the second year of their PhD who have begun to nail down a thesis topic. It is intended to be a forum for students to enhance their current skills and understanding of how to do ‘good’ science and to discuss some issues that they will encounter as scientists. The class will read papers on and discuss topics that will include: human subjectivity and biases, and their role in science; some semi-philosophical controversies about approaches to science and research tactics; some common and important pitfalls/errors in experimental design and statistical analysis (note: a strong background in statistics is not necessary for the course, but at least one undergraduate course in statistics is recommended); brief overviews of some new statistical approaches; and a variety other issues that are important to researchers (e.g. ethics). Faculty from the department and other guests will give brief, overview lectures to provide a bit of background on some of the topics (e.g. power analysis). The major assignment for the course is an essay that aims to facilitate students’ progress in thinking broadly about their thesis research, before they write their thesis proposal; to this we ask the students to put their research questions in the context of their general field (ecology or evolution)—both historically and with respect to the exciting questions currently being asked in their discipline.

**Please see more graduate courses (with significant undergraduate content) offered in the Fall 2017 term listed below**

EEB Graduate Courses Offered in Winter 2018: 

EEB1210H S (1/4 course)  Advanced Statistics [M-J. Fortin] 6 week module (tentatively, in the second half of the Winter term)
Day & Time: TBA     Location: TBA

Biologists need to use statistical methods to test their hypotheses. Given the increasing complexity of experiments carried out by biologists, they need however to understand the limitations of these statistics and how to select the appropriate statistics for their needs and how to interpret them properly both statistically and biologically. The goal of this advanced course in statistics is to teach biologists how to choose and use statistics so that they can address relevant biological questions and test them with the appropriate methods. Specifically, an overview of advanced notions about regression and ANOVA will be presented. To do so, a combination of lectures and computer laboratory sessions will be used.

EEB1315H S (1/4 course) Professional Skills Development  [M. Sokolowski, H. Rodd and others]
Day & Time: Alternate Thursday afternoons     Location: St. George Campus, TBA

A short (0.25 FCE) graduate-level course focused on developing the academic and professional skills required to succeed during and beyond graduate education in basic life sciences, with an emphasis on ecology and evolution.  

EEB1315 will meet for approx. eight 2-3 hour sessions in alternate weeks (tentatively on Thursdays for 2017).  The sessions will run from 3-6 or 4-7 depending on the availability of the guest participants.  The class sessions will be comprised of A (see below) in some weeks and A+B in other weeks:

(A) Lecture and/or student led discussion and/or working group activities: 1-3 hours (depending on the schedule for that week).   Topics will include converting CVs to resumes, informational interviews, speaking and writing for non-specialists, time and project management.
(B) Guest Panel Discussions: 1.5 hours.  There will be 2-3 panel discussions over the duration of the course.  Guest panelists will be chosen largely from the department's graduate alumni, and they will speak about their career pathways and the skills that they developed during their graduate education that they find valuable in their careers.  They will be selected from a range of careers including government, industry, higher education; suggestions from the class will be welcome.

This course will be targeted at PhD students who have done their appraisal exam. If there is space in the class, others may be admitted and/or allowed to audit the course.

EEB1230H S Multivariate Statistics [D. Jackson]
Note: this course is only open to PhD students in Year 2+; enrolment is by permission of the instructor
Time: Mondays 9-12     Location: TBA

EEB 1360H S Special Topics in Behaviour: Integrative Biology of Behaviour with a focus on behaviour genetics, genomics and neurobiology [Mark Fitzpatrick (EEB), Tod Thiele (CSB, Neuroscience), and Blake Richards (CSB, Neuroscience), with guest lectures by Nick Mandrak (EEB) and Patrick McGowan (CSB) and perhaps TBA] 
Day & Time: TBA     Location: UTSC

EEB 1450H S Special Topics in Ecology and Evolution: Landscape Genetics [H. Wagner and M.-J. Fortin]  Day & Time: Wednesday 11:30 - 1:30, Jan 17 – May 9, with weekly readings, online lectures and local discussions
This graduate course on Landscape Genetics provides a unique opportunity for interdisciplinary training and international collaboration and will cater to students (and postdocs) coming from evolution, especially population genetics, and to those coming from ecology, especially landscape ecology and conservation. The course is the local implementation of a Distributed Graduate Seminar on Landscape Genetics that will be held concurrently at several universities in North America and Europe and is provided to individual online participants from across the globe through University of Idaho. It is possible to join the local group online (e.g. from other campuses). Credit options include either computer lab reports (using R) or participation in an online collaborative group project.

EEB Graduate Courses with Significant Undergraduate Content:

(These courses will normally constitute only a minor component of the required credits for a graduate degree)

Fall courses:

EEB 1420H F Special topics in Ecology--Models in Ecology and Conservation [P. Molnar at UTSc, lectures will be available by videoconferencing] 
Day & Time: Tuesdays 12:00-14:00 in BV 355; Tutorials on Thursdays from 13:00-15:00 in BV 471. Graduate students will be registered for the course with permission of the Instructor
Modelling is a critical tool used to address urgent resource management questions in ecology, epidemiology and conservation. This practical introduction includes approaches for modelling individuals, populations, species interactions, and communities. Applications include population viability assessments, disease eradication and climate change mitigation.  Discussion-based tutorials will supplement lectures to provide hands-on modelling experience on a variety of ecological, epidemiological, and conservation questions.

EEB 1421H F Special Topics in Ecology: Plant-animal Interactions [M. Frederickson]
Day & Time: Tuesdays & Thursdays, 1:00-2:00; Fridays 1:00-3:00
Location: St. George Campus, Tuesdays & Thursdays SS1088, Friday RW 142
Major concepts in ecology and evolution from the perspective of plant-animal interactions. The richness of interactions between plants and animals is explored including antagonistic interactions (herbivory), mutualistic interactions (pollination, seed dispersal, ant-plant associations), and interactions involving multiple species across trophic levels.

EEB 1460H F  Molecular Evolution  [D. Irwin & TBA] (up to 5 grads)
Day & Time: Wednesdays and Fridays: 10 am – 11 am;        Location: St. George Campus, TBA
Processes of evolution at the molecular level, and the analysis of molecular data. Gene structure, neutrality, nucleotide sequence evolution, sequence evolution, sequence alignment, phylogeny construction, gene families, transposition.

Winter courses:

EEB 1440H S Special topics in Evolution: Genomics  [R. Ness] at UTM. Funding for the UTM shuttle bus may be available.  
The ongoing revolution in DNA sequencing allows biologists to observe the variety of genetic and genomic structures that underpin the diversity of life. The lectures will focus on the diversity of genomic structures, their functions and evolutionary origins. The course is focused on computer-based practicals that provide hands-on training with cutting-edge bioinformatic tools for analysis of genome-scale datasets and next generation sequencing data. Students will learn basic competency in command line environments (BASH) and will further develop skills in Python. Python is required for this course; for those with no Python experience, but a desire to learn, please contact Rob Ness about completing the practicals (this will probably take 4-5 days, working intensively) for his BIO362 (Bioinformatics) course before enrolling in this course.

EEB 1443H S  Phylogenetic Principles  [S. Stefanovic] (up to 5 grads)
(2 hours, twice a week at UTM)  Funding for the UTM shuttle bus may be available.
Lectures will provide an in-depth coverage of modern methods of phylogenetic reconstruction including molecular systematics based on DNA sequences. The principles and philosophy of classification will be taught with an emphasis on ’tree-thinking’, one of the most important conceptual advances in evolutionary biology. Tutorials will focus on recent developments in the study of evolutionary patterns while gaining proficiency in reading, presenting, and critiquing scientific papers.

*Shuttle Bus (Hart House to/from UTM) stop is right in front of this building (IB).

Graduate Courses offered by other departments/groups at the University of Toronto that will be of interest to some EEB graduate students:

EEB graduate students may take a graduate course offered by other departments for credit as long as they have discussed the course with and have permission from their supervisor, and the other members of their supervisory committee, etc. (see below for more details).

EES3000H S Applied Conservation Biology [N. Mandrak] at UTSc
Canada has a complex conservation landscape. Through lectures and interactive discussions with leading Canadian conservation practitioners, this course will examine how conservation theory is put into practice in Canada from our international obligations to federal and provincial legislation and policies, and the role of environmental non-government organizations.
For more information about this and other courses offered by DPES:
http://utsc.utoronto.ca/gradpes/courses-menvsc

EES3113H S Topics in Population and Community Ecology (at UTSc)
The field of ecology is rapidly changing and this course will cover recent advances, concepts or controversies in ecology. This course will focus on specific scientific issues using current literature and the learning experience will be augmented by student presentations and discussions. The course will help ensure that students become familiar with current understanding and basic ecological concepts.  This will be an elective course, and will be especially attractive to those students who did not take advanced ecology courses during their undergraduate studies. In Winter 2017, the course topic will be announced: either Invasion Ecology taught by Sarah Bailey and/or Farrah Chan; or Ecology and Management of Protected Areas taught by Bill Crins and Al Dextrase.
For more information about this and other courses offered by DPES:
http://utsc.utoronto.ca/gradpes/courses-menvsc  

Tentative (Winter 2018 timetable is not available yet) CHL5425H Mathematical Epidemiology of Communicable Diseases (in the dept. of Public Health) [David Fisman]  You can ask Korryn Bodner and Stephanie Penk for their thoughts on the course.

R course: MSC1090H (half course) "Introduction to Clinical BioStatistics" (Quantitative Applications for Data Analysis)"
This will be a course for Inst. Med Sci and LMP students and will be of interest to some EEB students. It will include R and statistics, and also introduce one week of  Linux, as well as more advanced statistical methods, like power analysis, PCA, machine learning, experimental design, etc. Note: only PhD students may take this course for credit.
A course syllabus is posted here:
https://ims.utoronto.ca/wp-content/uploads/2014/04/IMS-syllabus-2017-REV-MSC1090H.pdf

Note: the Fall version of this course is now full but materials including lectures and recordings for students wanting to audit the course be posted on the following website:
https://ims.utoronto.ca/wp-content/uploads/2014/04/IMS-syllabus-2017-REV-MSC1090H.pdf

A similar course will be taught at UTSC in the Winter term (they are exploring online versions): 
http://utsc.utoronto.ca/gradpes/ees1137h-quantitative-applications-data-analysis  and MSC1090 may be taught at St.G. in the Winter term.

Other SciNet courses, which are 4-weeks long and that we can handle as last year are:

For students without experience at all in programming:
* "Introduction to Programming with Python"
New to programming? Learn the basics of programming using python in eight one-hour sessions over the course of four weeks. Sessions will consist of a mix of lectures and hands-on exercises.

* "Intro to Scientific Computing with Python"
Learn about research computing even with little programming experience. Covers programming in python, best practices and visualization. Some experience with python is required. The course will last 4 weeks with 2 lectures per week (mini/modular grad  course).

Additionally I'd suggest to refer more advanced students to our courses' website, where  they can find more courses on advanced topics, such as Machine Learning and Neural 
Molecular Genetics: MMG1012H (Y)
Students must take 2 course topics in order to complete this course. The mark in this course is the average of the two marks obtained in the topics taken. Note: all graduate students in our department must complete MMG1012 (i.e. two Course Topics) before the end of a student’s second year in the program. Courses from other departments cannot replace this course.  Topics include:
A Practical Course in Programming for Biologists; Background and Topics in Molecular Genetics, Functional Genomics, and Computational Biology

Statistics: STA4515H--Multiple Hypothesis Testing and its Applications Course 
Description: A central issue in many current big-data scientific studies is how to assess statistical significance while taking into account the inherent large-scale multiple hypothesis testing. This 6-week graduate course will first go over the fundamental elements of single and multiple hypothesis testing, then it will move on to more advanced topics such as incorporating prior information to improve power, specific applications to whole genome genetic association studies, as well as discussions of the fallacy of p-value and alternative measures of statistical evidence and significance. Both analytical and empirical arguments will be presented, and participating students are expected to write a research report on suggested or self-selected topics related to multiple hypothesis testing.

Statistics: STA2080H  Fundamentals of Statistical Genetics Course 
Description: Statistical analysis of genetic data is an important emerging research area with direct impact on population health. This course provides an introduction to the concepts and fundamentals of statistical genetics, including current research directions. The course includes lectures and hands-on experience with R programming and state-of-the-art statistical genetics software packages.

Public Health: Bayesian Statistics

Math Department: Math models 
Math is offering a join undergrad-grad course, taught by a new Assistant Professor, Professor Adam Stinchcombe. He taught in Michigan before coming to U of T; a draft syllabus is here <http://www.math.toronto.edu/mpugh/MAT482_Mathematical_Modelling.pdf>. The prerequisites are MAT223H1 and MAT244H1 with a recommendation of  a probability course. Note: if you are intesrested in taking this course, spreak to Helen Rodd about what the course code will be. 

Cell and Systems Biology offers some courses that EEB grad students have taken in previous years. For example, see this CSB webpage: http://csb.utoronto.ca/graduate-studies/current-students/courses/

If you wish to take a course offered by another department, please discuss it with your supervisor(s) and your supervisory committee.  If they agree that it would be useful to take the course, first see if you can sign up for the course on ACORN/ROSI  If not, you will need to fill out the 'Request to add/drop course(s) form: http://www.sgs.utoronto.ca/Documents/Add+Drop+Courses.pdf 

Some courses require the instructor's approval in addition to that of the coordinator/academic advisor of the host department.  Once it is approved by the host department and your supervisor, please bring or scan and email the form to the EEB Graduate Office (ESC 3046) so that the course enrollment form must be approved by EEB's Associate Chair of graduate students.

With the professor’s permission, students are welcome to sit in on undergraduate courses to enhance their background in specialized topics (e.g., vertebrate anatomy, community ecology, etc.). (note: we cannot offer specialized graduate courses that would have enrollments of less than 8-10 students).  Also, with the professor’s permission, students may audit (or take for credit) graduate courses, even after they have completed the course requirements for their degree.

For future years, please do consider proposing special topics courses to faculty for a course that would be offered the following year.

Unfortunately, the Core Course in Ecology, which was scheduled to be offered this year (it is offered in alternate years), cannot be offered this year because both professors are on leave.  We hope that one of the other courses listed above will be a good alternate for this year.

If you wish to take a course offered by another university in Ontario: please ask Helen Rodd for the details on the Ontario Visiting Graduate Student Agreement (the course must be approved by your committee, SGS, etc.).

EEB GRADUATE COURSES OFFERED IN 2018-19:

Core course in Ecology (syllabus for 2015-2016 version of the course will be available soon)

Other EEB Graduate courses that may be offered in 2018-2019:

Talk to your supervisor, other graduate students and potential instructors about potential topics (e.g. a new or a class book, a series of related papers, etc.) for EEB Special Topics courses.

Special Topics in Ecology and Evolution - Classics and Cutting Edge of Ecology and Evolution 

EEB1250 Spatial Statistics (1/4 course): Marie-Josee Fortin
EEB 1210 Advanced Statistics(1/4 course): Marie-Josee Fortin
Other courses: TBA