Centre for Mathematical Biology (CMB) July1, 2012 to June 30, 2013

Centre for Mathematical Biology (CMB) July1, 2012 to June 30, 2013

1. Overview

The Centre for Mathematical Biology has provided an excellent environment for attracting, developing and retaining outstanding researchers.

The purpose of the Centre for Mathematical Biology is to provide a campus-wide resource for interdisciplinary and multidisciplinary research and training in mathematical biology. The Centre bridges the gap between life scientists and mathematicians in solving problems of significance to Canadians. Its activities fall into three categories: (i) facilitation of multidisciplinary connections between life scientists and mathematicians, and between academics and government/industry; (ii) training of a new generation of researchers; and (iii) development of interdisciplinary mathematical biology, locally, nationally and internationally.

During 2012-2013, the Centre was home to5 undergraduates, 20 graduate students, 7 postdoctoral fellows, 2 research associates, 4 core faculty members and many affiliated faculty.

Again, constructive collaborations flourished with federal and provincial governments, Mathematics in Information Technology and Complex Systems (MITACS), NSERC networks, NGOs, industry, academic researchers within campus, and academic researchers worldwide.

The Centre was active in hosting 17 seminar speakers and 7 short-term visitors.

1. Scientific Activities & Infrastructure

There were 4 core investigators for the Centre, (Lewis, de Vries, Hillen, and Wang). (Also see Appendix A). Scientific activities at the Centre are defined as the activities of these core investigators.

(a)Current Major Multidisciplinary Research Collaborations

Projects with no Centre publications are typically in their first few years, with papers currently in the submission/review stage but the research is on-going. For simplicity of presentation, only the projects that have associated publications are shown.

Project / Senior Researchers / Centre Trainees¹ / Centre Publications / Funding Agencies
Dept / Campus / Off-Campus
Animal Movement Modelling / 3 / 2 / 4 / 3 / 2, 4, 6, 10, 12, 20, 26, 30, 37, 38 / NSERC Discovery & Accelerator, Alberta Innovates—Technology Futures, NSERC CGS, Banting
Biological Invasions / 2 / 1 / 6 / 3 / 7, 8, 9, 27, 28 / NSERC Discovery and Accelerator , University of Alberta, Department of Biological Sciences, the Canadian Aquatic Invasive Species Network (CAISN)
Cell Movement / 1 / 1 / 14, 15 / NSERC Discovery
Evolution of Cell Size and Body Size / 1 / 1 / 13 / NSERC Discovery
F1000 / 1 / 1 / 43 / N/A
Infectious Disease Modelling / 2 / 1 / 4 / 5 / 24, 25 / Alberta Prion Research
Institute, Alberta Innovation, NSERCDiscovery AcceleratorOxford Centre for Collaborative and Applied Mathematics
Instream Flow Needs: A Mechanistic Model-based Approach / 1 / 1 / 7 / 1 / 32, 33 / NSERC Discovery, Alberta Water Research Institute
Microbiology / 1 / 7 / 2 / 31 / NSERC Discovery
Mountain Pine Beetle Modelling / 2 / 4 / 2 / 1 / 11 / NSERC Discovery, Alberta Innovates Bio Solutions, Genome Alberta
Other / 3 / 4 / 2 / 5, 18, 36, 39, 40, 41, 42 / NSERC DiscoveryAccelerator, Oxford Centre for Collaborativeand AppliedMathematics
Models for Population Cycles / 1 / 2 / 3, / NSERC Discovery
Risk Assessment of Oil Sands / 2 / 1 / 1 / 16 / Alberta Environment, MITACS, NSERC Discovery & Accelerator
Mathematical Models of Cancer and Cancer Therapy / 2 / 3 / 2 / 1, 21, 34, 35 / NSERC Discovery
Sea Lice in Salmon / 2 / 7 / 1 / 17, 22, 23, 29 / NSERC Discovery, Accelerator & Vanier, MITACS, Alberta Innovates, Pacific Institute for Mathematical Sciences (PIMS)
Theory of Delay Differential Equations / 2 / 2 / 1 / 19 / NSERC Discovery
Totals² / 26 / 8 / 45 / 24 / 43

¹ Many of the projects involve additional trainees not at the Centre but these are not added here

²The units here are person times projects. In other words, individuals participating in more than one project are counted for each project they participate in.

(b)Educational Projects and Initiatives

PIMS International Graduate Training Centre (IGTC): This program continued to flourish under the auspices of the Pacific Institute for Math Sciences.

The ITGC in Mathematical Biology Annual Summit, held in Naramata, BC was attended by de Vries and Hillen. This year's annual summit celebrated graduate students and their research in mathematical biology at PIMS universities through three main scientific events:

• research talk and graduate-level workshop in interacting particle systems by Dr. Stephen M Krone, Mathematics Professor, University of Idaho

• research talks and posters by graduate students in mathematical biology
• professional development workshop by Thomas Hillen and Gerda de Vries: What do I do next? How to come up with new research project ideas

Immediately preceding the workshop there was a symposium in mathematical biology at the UBC Okanagan campus, featuring research talks by faculty.

Mathematical Biology Journal Club: Hillen and de Vries hosted a weekly seminar meeting at the Centre, to discuss CMB student’s work in progress, to meet with visitors and to read pertinent journal papers.

Dr. Hillen was supervisor to 5 graduate students and 3 undergraduate students while Dr. de Vries was supervisor to 3 graduate students, 2 undergraduate students and a visiting student from Universidad Simón Bolívar.

Wang Research Group:

Wang Research Group consists of 6 graduate students and2 postdoctoral fellows. Besides weekly individual meetings, they held regular group meetings to discuss several areas of mathematical biology as diverse as modeling stoichiometry-based ecological interactions, microbiology, infectious diseases, habitat destruction and biodiversity, risk assessment of oil sands pollution. Dr. Wang, his students and postdocs also had joint activities with other groups in the Centre.

Lewis Research Group:

The Lewis Research Group consists of 6 graduate students, 6 postdoctoral fellows and 2 research associates. Dr. Lewis and his lab members held weekly lab meetings to discuss their research and to touch base on Centre activities. Visitors to the Centre were invited to participate in lab meetings held during the time of their visit.

Graduate Summer Course on Mathematics Behind Biological Invasions

The course ran in the summer of 2013 and taught a group of international graduate students. Hillen and Lewis co-developed this course and Lewis was one of four principal lecturers. The theme was mathematical theory, techniques and insight applied to the process of biological invasions. This course was connected to Lewis’ Killam Research Fellowship (2012-14) of the same name. One outcome of the course was a new book, coauthored with the other lecturers.

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(b)Personnel

Faculty:

There were four core faculty members for the 2012/2013 year. They were: Gerda de Vries, Thomas Hillen, Mark Lewis and Hao Wang.

Support Staff:

Mark Duller remained the Centre’s part-time Computer Analyst andKimberley Wilke-Budinski provided part-time administrative support.

Graduate Students, Funding and Awards:

• Amanda Swan: MSc – continuing - (NSERC Alexander Graham Bell Canada Graduate Scholarship)

• Chaochao Jin:MSc – continuing - Mathematical inverse problem of infectious disease transmission

• Cody Nitschke – withdrew

• Cole Zmurchok: MSc– continuing - (Queen Elizabeth II Graduate Scholarship)
• Maryam Khajen Alijani:MSc – completed- Stochasticity in modelling biological systems

• Michael Bryniarski: MSc– continuing - Mathematical Ecology - (PIMS International Graduate Training Centre for Mathematical Biology, JM Mitchell recruitment scholarship)

• Nicholas Piazza: MSc – continuing - Infectious disease modelling with seasonal incidence, vaccination and multi-cell spatial spread

• Theresa Stocks: MSc - completed

• Wafa Veljee: MSc – continuing

• Xihui Lin: MSc – completed

• Andria Dawson: PhD – completed - Models for mixed wood forests - (Queen Elizabeth II Graduate Scholarship)

• Carlos Contreras: PhD – visiting student

• Diana White: PhD – continuing - Mathematical modelling of microtubule dynamics in human columnar epithelial cells

• Harshana Rajankaruna: PhD – continuing - Population viability models for invasive aquatic species

• Jonathan Martin: PhD – completed - Forest fire research

• Jude Kong: PhD – continuing

• Marie Auger-Methe: PhD – continuing - State –space models and the analysis movement by Arctic mammals - (Andrew Stewart Memorial Prize, Alberta Innovates-Health Solutions, Honorary Izaak Walton Killam Memorial Scholarship and the Steve and Elaine Antoniuk Graduate Scholarship)

• Silogini Thanarajah: PhD – completed - Mathematical models for ecological dynamics - (PIMS IGTC Fellowship in Math Biology)

• Stephanie Peacock: PhD – continuing - Modelling disease transmission from aquaculture to wild salmon – (Vanier Canada Graduate Scholarships, Alberta Innovates Graduate Student Scholarship, D. Alan Birdsall Memorial Scholarship, PIMS IGTC Fellowship in Math Biology (honorary))

• Ulrike Schlaegel: PhD – continuing - Modelling wolf movement and researching state-side models

(Alberta Innovates – Technology Futures iCORE Graduate Recruitment Scholarship)

Postdoctoral Researchers, Funding and Awards:

• Aditya Raghavan: PDF – continuing - Tree distribution and dynamics under variable environmental conditions

• Devin Goodsman; PDF – continuing - Mountain Pine Beetle dispersal Models – (Genome Alberta, Alberta Innovates Bio Solutions)

• Greg Breed: PDF – continuing - Models for Animal Movement - (Banting Postdoctoral Fellowship)

• Jimmy Garnier: PDF – completed - Effect of Climate change on genetic diversity – (NSERC Accelerator, French Department of Education and Research, France)

• Jonathan Potts: PDF – continuing - Animal movement models & models for territoriality – NSERC Accelerator, Killam)

• Olga Vasilyeva: PDF – completed - Analysis of River Dynamics – (Alberta Water Research Institute)

• Qihua Huang: PDF – continuing - Risk assessment of oil sands pollution on fish - (Alberta Environment Internship, MITACS, CAISN, Alberta Water Research Institute)

Research Associates/Assistants:

• Alex Potapov: Research Associate – continuing - Integrated systems for invasive species – (CAISN, Alberta Innovates Bio Solutions, Alberta Water Research Institute)

• Mario Pineda-Krch: Research Associate – completed - Collaborative research on genomics MPB – (Genome Alberta, Alberta Innovates Bio Solutions)

Undergraduate Students

• Andreas Buttenschoen: BSc – continuing (NSERC Undergraduate Student Research Award)
• Jeff Bachman: BSc - completed (NSERC Undergraduate Student Research Award)

• Paul Fritsch: BSc - completed
• Jeff Zielinski: BSc – completed

• Cole Zmurchok: BSc – completed

(e)Visitor/Seminar Program

The Centre held the PIMS Mathematical Biology Seminar Series each Monday of the Fall and Winter terms. Names of the speakers are listed below and include speakers from Alberta, across Canada, the US, Europe and the Middle East.

Visiting Students

• Karl Mokross (Louisiana State University) - June 30 – July 18, 2012
• Carlos Contreras, (Universidad Simón Bolívar, Departamento de Computo Científico y Estadística) August 2012 – December 2012
• Guillaume Bastille-Rousseau (Trent University) – November 12 – December 7, 2012

Short Term Visitors

• Dr. Frederic Hamelin (France) July 1 – July 22, 2012
• Dr. Péter K. Molnár, (USA) October 1- October 5, 2012
• Dr. Jeff Musgrave (Ottawa) October 14 – October 16, 2012
• Dr. Zoi Rapti – (USA) February 24 – February 27, 2013
• Dr. Mishtu Banerjee, (Calgary) April 7 – April 9, 2013
• Dr. Sergey Petrovskiy (UK) May 25 – June 14, 2013
• Dr. Alan Hastings (USA) May 26 – June 14, 2013

Visiting Speakers from Universities other than the University of Alberta

• Dr. Péter K. Molnár, Princeton University

Metabolic Approaches to Predicting Climate Change Impacts on Seasonal Host-Macroparasite Systems

• Carlos Contreras, Universidad Simón Bolívar, Departamento de Computo Científico y Estadística

Understanding the binding mechanism of histone H1 using model comparison criteria and FRAP experiments

• Jeff Musgrave – University of Ottawa

How dispersal in patchy landscapes affects persistence and spread

• Olga Vasilyeva – University of Ottawa/University of Alberta

Persistence and competition in advective environments

• Zoi Rapti – University of Illinois at Urbana-Champagne

Daphnia epidemics and the role of food resources, competitors and predators

• Mishtu Banerjee, PhD,Statistical Modelling Analyst Tesera Systems Inc., Calgary

One model to rule them all? A brief history of the diversity stability debate

Seminar Speakers from the University of Alberta

• Thomas Hillen

Mathematical modelling with fully anisotropic diffusion

• Violeta Kovacev-Nikolic

Persistent homology in analysis of point-cloud data

• Jimmy Garnier

The impact of long distance dispersal and Allee effect on the dynamics of range-expanding populations

• Stephanie Peacock

Models to management: sea lice transmission from farm to wild salmon

• Greg Breed

Analyzing citizen science data to detect community-wide climate driven population changes in Eastern North American butterflies

• Jonathan Potts

Territory formation from an individual-based movement-and-interaction model

• Qihua Huang

Mathematical risk assessment of contaminents on fish population dymanics

• Thomas Hillen/Jeff Zielinski

Merging-emerging systems can describe spatio-temporal patterning in a chemotaxismodel

• Travis Craddock

A role for homeostatic drive in the perpetuation of complex chronic illness

• Silogini Thanarajah

Modelling bacterial competition and bacteriophage in a petri dish

• Ulrike Schlaegel

Cognitive maps in animal movement models and consistency of movement models

• Aditya Raghavan

Testing the “strict homeostasis” assumption in stoichiometric producer-grazer models via homoclinic bifurcations

• Vakhtang Putkaradze

Graduate recruiting seminar: Geometry everywhere: sensors, renewable energy and high tech devices

1. Business Plan Implementation

(a)Space

The Centre occupies Central Academic Building (CAB) rooms 545A (visitor), 545B (director), 545C (research), 545 (computing), 549 (library/meeting room) and 551 (postdoc/research associate/computer support personnel).

(b)Governance

Director: Mark Lewis (Math/Stat Sciences and Biological Sciences)

Advisory Board Members: Gerda deVries (Math/Stat Sciences) Russ Greiner (Computing Science), Hao Wang (Math/Stat Sciences), Subhash Lele (Math/Stat Sciences), Jack Tuszynski (Cross Cancer Institute)

(c)Financial Summary July 1, 2012 to June 30, 2013

StartingBalance as of July 1, 2012 - $17,944.40

Balance Forward as of June 31, 2013 - $8,377.56

INCOME
Source / Anticipated Revenue / Total Revenue / Source / Expenditures
Math/Stat Sci / $0 / $0 / Admin Staff / $5,249.20
Science Faculty / $0 / $0 / Speakers/Hosting / $1,757.25
VP Research / $0 / $0 / Supplies / $2,560.39
TOTALS / $0 / $0 / TOTALS / $9,566.84

(d)Evaluation of the CMB According to Established Metrics

1)Multidisciplinary Research Projects

Number of multidisciplinary researchers
Involved in projects (in Dept., Campus,
And Other) / 06-07 / 07-08 / 08-09 / 09-10 / 10-11 / 11-12 / 12-13
Faculty from Math & Stat Sciences, UA / 18 / 22 / 30 / 39 / 40 / 31 / 26
Faculty from other depts., UA / 10 / 13 / 12 / 16 / 17 / 14 / 9
Faculty from other institutions / 41 / 81 / 78 / 63 / 86 / 65 / 46
Centre trainees (grad students, research
associates & postdocs) / 34 (20) / 38 (19) / 24¹ / 37¹ / 35¹ / 31¹ / 24¹
Total #’s involved in multidisciplinary
research / 103 / 154 / 144 / 155 / 178 / 141 / 105
Number and quality of papers arising from projects
These #’s include Centre trainees and
core faculty
Book Chapters / 7 / 7 / 3 / 0 / 3 / 2²
Journal Articles / 23 / 34 / 39 / 24 / 30 / 19 / 18
Total # of publications / 23 / 41 / 46 / 27 / 30 / 22 / 20
Research funding arising from the projects³
See also Formula for funding and PIMS IGTC Funding4 / $926,187 / $821,718 / $759,072 / $678,123 / $610,136 / $411,500 / $454,525

Notes:

¹2012-2013, 2011-2012, 2010-11, 2009-10 and 2008-09 numbers represent Centre trainees during 2008-09 and 2009-10 and 2010-11 2011-2012 only. Previous years include trainees who had previously completed their training at the Centre. Actual figures for 2006-07 and 2007-08 are now in brackets ( ).

²Book Chapters – does not include 3 books written during this time period.

³Yearly funding for the listed interdisciplinary research projects comes directly to the four core faculty based on FEC reporting.

4Formula for funding: (i) use FEC reporting amounts, (ii) exclude double counting any grants (i.e. grants that are shared by two faculty); (iii) exclude any amounts that don’t come to the U of Alberta.

4PIMS IGTC funding: funding from Pacific Institute for Mathematical Sciences to support the International Graduate Training Centre

2)Education Initiatives

a)Number of undergrad, grad students (MSc & PhD) and postdocs trained

06-07 / 07-08 / 08-09 / 09-10 / 10-11 / 11-12 / 12-13
High School Students / 1 / 0 / 0 / 2 / 2 / 0 / 0
Undergraduates / 4 / 2 / 5 / 7 / 6 / 8 / 5
Graduate Students / 12 / 11 / 14 / 21 / 21 / 19 / 20
Postdocs / 6 / 7 / 4 / 5 / 2 / 4 / 7
Research Associates / 2 / 1 / 2 / 2 / 2 / 2 / 2
Total students and postdocs / 25 / 21 / 25 / 37 / 33 / 33 / 34

b)Quality of training, awards and recognition of students, placements of students and postdocs

A major educational initiative is the International Graduate Training Centre (IGTC) in Mathematical Biology. This is allowing us to recruit and support more high quality students.

c)Awards, Fellowships & Graduates

06-07 / 07-08 / 08-09 / 09-10 / 10-11 / 11-12 / 12-13
Awards received by graduate students / 11 / 22 / 33 / 32 / 26 / 17 / 14
Number of graduating students / 2 / 3 / 3 / 1 / 5 / 4 / 6

3)Visitor Program

a)Number of visitors/seminar speakers

06-07 / 07-08 / 08-09 / 09-10 / 10-11 / 11-12 / 12-13
PIMS MathBio Seminar Speakers Worldwide / 16 / 18 / 15 / 13 / 14 / 3 / 6
PIMS MathBio Seminar Speakers from the U of Alberta / 7 / 7 / 12 / 13 / 12 / 11 / 13
Long and Short Term Visitors / 1 / 1 / 13 / 14 / 10 / 3 / 7
Total Number of Visitors / 24 / 26 / 40 / 40 / 36 / 17 / 26

Out of town visitors were scheduled to meet with students, postdocs and faculty to discuss mutual research topics.

4)Outreach

Dr. Lewis gave a public lecture at the University of Victoria on Mathematics of Planet Earth and a presentation to graduate students at the PIMS Young Researchers Conference at the University of Alberta. In May 2013, Dr. Lewis was a Distinguished Lecturer at a Mathematics of Planet Earth Summer SchoolentitledThe Mathematics BehindBiological Invasions, held at the University of Alberta.Dr. Lewis along with Dr. Hillen and postdoc, Jonathan Potts, organized this event.

The article in Ecological Applications - a collaborative effort with grad student Stephanie Peacock – garnered a lot of press coverage. Dr. Lewis and Stephanie worked with the UA press office plus there were articles nation-wide, including papers such as the Globe and Mail.

Dr. deVriesgave 2 lectures for high school students through the Centre for Global Education and 2 public lectures, the first in February 2013, for the Mathematics of Planet Earth and the Canadian Mathematical Society and the other in June 2013, for the Canadian Applied and Industrial Mathematics Society Annual Meeting. She also was a panel member and gave a presentation to high school students through the AIHS Heritage Youth Research Summer Program (HYRS).

Dr. Wang continues to actively recruit graduate students through his personal connections and his frequent visits to Chinese universities.

APPENDIX A

Major Stakeholders and terms of reference

Individual Researchers:

1)Core faculty during the 2011-12 period were;

• Gerda de Vries
• Thomas Hillen
• Mark Lewis
• Hao Wang

Core faculty use the Centre, typically, on a daily basis and run Centre activities. They, their students and postdocs, define the Centre and its initiatives. They have access to Centre facilities including; computing resources, library, and office space for postdocs and visitors.

2)Associated faculty in mathematical biology in Mathematical & Statistical Sciences;

• Herb Freedman
• Subhash Lele
• Michael Li

These faculty members use the Centre occasionally and typically interact with core faculty (above) on some of the Centre activities and research. Centre resources are available to the associated faculty on a request basis.