Luke W. Johnston
lwjohnst@gmail.com @lwjohnst @lwjohnst86 0000-0003-4169-2616 lwjohnst Luke W. Johnston Luke W. Johnston
Team leader, researcher, software and data architect, software and data developer, data science and coding teacher, open science advocate.
Education
Formal university education.
1 Sept 2013 to 14 Sept 2017 | University of Toronto, Toronto, Canada
Thesis title: Fatty acid composition in four serum lipid fractions and the pathogenesis of diabetes.
1 Sept 2011 to 30 Aug 2013 | University of Toronto, Toronto, Canada
Thesis title: Association of Leg Length with Metabolic Abnormalities Underlying Type 2 Diabetes Mellitus.
1 Sept 2005 to 30 Apr 2010 | University of Waterloo, Waterloo, Canada
Funding
Grants for larger projects that include salary for multiple people as well as funds for resources.
1 Sept 2025 to 31 Aug 2030 | NovoNordiskFonden, Aarhus, Denmark
Contributor to a funded grant from the NovoNordiskFonden Steno National Collaborative Programme. I will act as Work Package 1 lead, which aims to provide modern operational and management practices that incorporate software and data engineering, iterative project management, and collaborative workflows and tools. Amount: DKK ~25 million
1 Jan 2022 to 31 Dec 2027 | NovoNordiskFonden, Aarhus, Denmark
Grant (NNF21OC0069462) from the NNF Data Science Research Infrastructure Programme to develop an infrastructure for managing, sharing, and discovering data. NNF posted a brief description of it. Amount: DKK 14,977,580.
Awards
Awards and honors given to and/or for me (e.g., scholarships or funds for my own salary).
1 Dec 2022 | Danish Diabetes Academy, Denmark
Recognition for involvement in education and networking of researchers in Denmark. Amount: DKK 25,000
1 Dec 2019 to 31 Dec 2023 | Danish Diabetes Academy, Denmark
Nationally competitive ~3-year fellowship. Extended because of the pandemic and because of receiving a larger project grant. Amount: DKK 1.8 million
23 Nov 2017 | University of Toronto, Toronto, Canada
Recognition for the best research article published in 2016 by a graduate student in the Department of Nutritional Sciences.
16 May 2017 to 18 May 2017 | Aarhus University, Aarhus, Denmark
Participation in a workshop aimed at applying for the Marie Curie Fellowship, with travel expenses and accommodations paid.
25 Apr 2017 | University of Toronto, Toronto, Canada
For recognition of outstanding extra-curricular contributions to the faculty and the university as a whole. Contributions include creating a workshop series (offered in the Graduate Professional Skills program) to teach coding to graduate students, playing an instrumental role in starting a student group (UofTCoders) to allow for peer-level skill sharing of coding and programming for science and research, and for running short, twice-monthly coding sessions in the Department of Nutritional Sciences.
10 Mar 2017 to 11 Mar 2017 | Mozilla Science Lab, Montreal, Canada
Attendance to a workshop hosted by the Mozilla Science Lab to train on using open source and processes for research projects. Amount: USD 300
8 Jun 2015 | Banting and Best Diabetes Centre, University of Toronto, Toronto, Canada
For attendance to the American Diabetes Association 75rd Scientific Sessions. Amount: CAD 1000
1 Sept 2014 to 31 Aug 2017 | Canadian Diabetes Association, Toronto, Canada
Nationally competitive award. Amount: CAD 21000
1 Sept 2014 to 31 Aug 2015 | Banting and Best Diabetes Centre, Toronto, Canada
University-wide awards. Amount: CAD 3840
1 Sept 2014 to 31 Aug 2015 | University of Toronto, Toronto, Canada
University-wide awards. Amount: CAD 3000
1 Sept 2014 to 31 Aug 2015 | Government of Ontario, Toronto, Canada
Awarded, but declined for the CDA Doctoral Award. Amount: CAD 15000
28 Jun 2014 | International Society for the Study of Fatty Acids and Lipids, Stockholm, Sweden
Given out during the International Society for the Study of Fatty Acids and Lipids 2014 Biennial Congress
1 Jun 2014 | Banting and Best Diabetes Centre, Toronto, Canada
For attendance to the American Diabetes Association 74rd Scientific Sessions. Amount: CAD 1000
22 May 2014 | University of Toronto, Toronto, Canada
For attendance to the International Society for the Study of Fatty Acids and Lipids 2014 Biennial Congress. Amount: CAD 1120
22 Apr 2014 | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
For attendance to the International Society for the Study of Fatty Acids and Lipids 2014 Biennial Congress. Amount: CAD 200
1 Sept 2013 to 31 Aug 2014 | Government of Ontario, Toronto, Canada
Provincial-level graduate scholarship. Amount: CAD 15000
8 May 2013 | Banting and Best Diabetes Centre, Toronto, Canada
For attendance to the American Diabetes Association 73rd Scientific Sessions. Amount: CAD 1000
1 Sept 2012 to 31 Aug 2013 | Government of Ontario, Toronto, Canada
Provincial-level graduate scholarship. Amount: CAD 15000
Employment
Positions and places where I work or worked.
1 Jun 2022 to present | Department of Clinical Medicine, Aarhus University & Steno Diabetes Center Aarhus, Aarhus, Denmark
Working on a project building an open infrastructure for health data, funded by the NovoNordisk Foundation.
1 Dec 2019 to 31 May 2022 | Steno Diabetes Center Aarhus, Aarhus, Denmark
Working on a project funded by the Danish Diabetes Academy. Doing research in diabetes epidemiology, specifically on identifying: the metabolic mediation between early childhood biomarkers and adult diabetes status; developing causal structure learning methods; and, creating a framework (as text and as software) for conducting reproducible and open scientific research. Supervisor: Dr. Daniel Witte
1 Feb 2018 to 30 Nov 2019 | Department of Public Health, Aarhus University, Aarhus, Denmark
Doing research in diabetes epidemiology, specifically on identifying: Patterns of accelerometry-derived physical activity with metabolic status; the metabolic mediation between early childhood biomarkers and adult diabetes status; developing a simulation method for incorporating multiple epidemiological results into a single framework; and, assisting a PhD student’s social network analysis on the programming aspects of work. Supervisor: Dr. Daniel Witte
20 Sept 2017 to 31 Jan 2018 | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Finishing up PhD research projects, maintaining and developing a website for the PROMISE data dictionary and description and training new graduate students on data analysis using R. Supervisor: Dr. Anthony Hanley
1 Jan 2011 to 30 Jul 2011 | Propel Center for Population Health Impact, University of Waterloo, Waterloo, Canada
Collected air quality samples from Region of Waterloo-owned social housing. Analyzed the air quality data using MS Excel. Produced and tested a survey for Program Training and Consultation Centre on SurveyMonkey. Wrote three reports on data collected from the survey results. Organized and scheduled interviews and data collection dates for a study in the Waterloo Region evaluating the School Food and Beverage Policy PPM150. Managed a team of 4 researchers to collect survey and interview data from primary and secondary schools in the Waterloo Region. Managed the storing and organizing of data collected from the surveys and interviews. Supervisor: Karen Pieters, Dr. Ryan David Kennedy, and Dr. Rhona Hanning
1 Aug 2010 to 30 Aug 2010 | Health Psychology Lab, University of Waterloo, Waterloo, Canada
Analyzed data from previous cigarette smoking experiments done in 2008 using MS Excel. Conducted a smoke-free policy scan of YMCAs and YWCAs in Ontario and presented findings to the Tobacco-free Sports and Recreation Community of Practice. Supervisor: Dr. Ryan David Kennedy
1 Sept 2009 to 20 Dec 2009 | Child Health Evaluative Sciences, Hospital for Sick Children, Toronto, Canada
Analyzed data from the WHO and PLoS Medicine using MS Excel. Developed a method for interpreting fracture data from the National Ambulatory Care Reporting System using statistical probability equations. Supervisor: Dr. Andrew Howard
1 Jan 2009 to 30 Apr 2009 | Toronto Rehabilitation Institute, Toronto, Canada
Examined balance in clinical populations, including individuals with dementia, using pressure plates. Used EMG electrodes, VICON markers and other monitoring equipment to obverse and collect data from research participants. Analyzed data from various experiments and studies using LabView and MATLAB software. Evaluated the reliability of using Bluetooth technology in the foot switch device (industry gold standard) and analyzed the relationship with an accelerometer. Supervisor: Dr. Avril Mansfield and Dr. William McIlroy
1 Sept 2008 to 20 Dec 2008 | Health Psychology Lab, Waterloo, Canada
Used MS Excel and SPSS 17.0 to organize and analyze data from experiments and prepare the data for presentations at provincial and international tobacco control conferences. Independently conducted a phone survey of Ontario’s university campuses’ outdoor smoking policies and prepared a poster to be presented at a tobacco control conference. Supervisor: Ryan David Kennedy
1 May 2008 to 30 Aug 2008 | Health Psychology Lab, Waterloo, Canada
Managed 3 projects aimed at measuring tobacco smoke pollution in outdoor and quasi-outdoor environments. Organized and analyzed data using MS Excel and SPSS 17.0. Supervised and scheduled a team of 10 Research Assistants. Supervisor: Ryan David Kennedy
Certificates
Certificates of completion or participation in courses, workshops, or other training.
6 Aug 2020 | RStudio, Boston, USA
Certificate for completing an instructor training program.
21 Aug 2019 to 19 Dec 2019 | Aarhus University, Aarhus, Denmark
A teacher training programme for future and current instructors of university-level courses.
21 Feb 2018 to 11 Jun 2018 | Mozilla, Online
Training programme for those who want to or are currently leading open source projects.
9 Nov 2017 | School of Graduate Studies, University of Toronto, Toronto, Canada
Certificate of completing a program of courses and workshops offered to graduate students to develop their professional skills, such as project management, communication, and leadership.
23 Nov 2016 to 24 Nov 2016 | Mitacs, Toronto, Canada
An intensive course on learning the basics of project management.
15 Nov 2016 | Data Carpentry, Online
Certificate for completing an instructor training program required to teach Data Carpentry workshops.
1 Aug 2015 | University of Toronto, Toronto, Canada
Certificate of completing the university’s teacher training program for graduate students.
26 May 2015 | Software Carpentry, Online
Certificate for completing an instructor training program.
Package development
Creation of or contribution to software packages or software-related products.
28 Jul 2025 to present | Zenodo/GitHub
Co-creator. A template for making a Git repository that follows strongly opinionated practices for building and managing a data package. These practices include using Seedcase Python packages, such as Seedcase Sprout, and the Frictionless Data Package standard.
3 Jul 2025 to present | PyPI
Co-creator. Sprout is one component of the Seedcase Project framework that aims to take data created or collected for research studies and “grow” it in a structured way using modern data engineering best practices. Sprout is designed to organise, describe, and store data for effective discovery, management, and analysis.
26 Nov 2023 to present | GitHub
Co-creator. Sprout is a Python software package that is a component of the Seedcase framework that aims to take data created or collected for research studies and “grow” it in a structured way using modern data engineering best practices. Sprout is the backbone of the Seedcase family; this is where data is uploaded, described, and stored based on a relational database design.
20 Nov 2022 to present | GitHub
Co-creator. An R package that aims to make it easier and more explicit to classify type 1 and type 2 diabetes within a Danish register context.
10 Jul 2022 to present | GitHub
Creator. The goal of ukbAid is to help our research group at Steno Diabetes Center Aarhus (SDCA) that is working on the UK Biobank (UKB) on the research analysis platform (RAP). This package and the general workflow we are using will help us be as reproducible as possible, but without sharing any data that is not permitted.
8 Apr 2022 to present | CRAN
Creator. The ‘NetCoupler’ algorithm identifies potential direct effects of correlated, high-dimensional variables formed as a network with an external variable. The external variable may act as the dependent/response variable or as an independent/predictor variable to the network.
9 Mar 2022 to present | Denmark Statistics servers
Creator. The main goal of dstDataPrep is to convert all the SAS data files on Denmark Statistics servers for the Steno Aarhus DARTER Project into modern and faster formats like Parquet. It also helps researchers access and import these central data sources into the fast and modern analytic tool DuckDB.
9 Oct 2019 to present | CRAN
Contributor. Use ‘rmarkdown’ and ‘pagedown’ to generate HTML and PDF conference posters.
28 Nov 2017 to present | GitLab
Creator. The aim of this package is to run audits on datasets to check for errors or typos in values. For instance, with a column called MonthsPerYear, the values should be integers that go from 1 to 12. If there are violations to this pattern, the values need to be investigated at the raw data source. This is a companion package to the main PROMISE package.
18 Sept 2017 to present | GitLab
Creator. The goal of PROMISE.scrub is to provide functions that help with cleaning and preparing the PROMISE dataset for eventual use in analyses and research projects. There are several of these packages that all work to make it easier to handle the different needs of preparing the PROMISE dataset, at least from a data management point of view, to be trustworthy and of sufficient quality control.
18 Sept 2017 to present | GitLab
Creator. The goal of PROMISE.methods is to provide functions for creating the data dictionary and other functions for the dataset and method documentation. This is a companion package to the main PROMISE package.
29 Jul 2016 to present | CRAN
Creator. Mainly used to build tables that are commonly presented for bio-medical/health research, such as basic characteristic tables or descriptive statistics.
15 Jul 2016 to 10 Sept 2023 | CRAN
Creator. Use a consistent syntax to create data structures of common statistical techniques that can be continued in a pipe chain. Design the analysis, add settings and variables, construct the results, and polish the final structure. Rinse and repeat for any number of statistical techniques. Archived due to better packages that had been built since I first created this.
30 Apr 2016 to present | CRAN
Creator. Create a project directory structure, along with typical files for that project. This allows projects to be quickly and easily created, as well as for them to be standardized. Designed specifically with scientists in mind (mainly bio-medical researchers, but likely applies to other fields).
23 Nov 2014 to present | CRAN
Contributor. Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.
Data engineering and management
Activities involving building, designing, structuring, organizing, and managing data, databases, and data pipelines.
1 Jun 2025 to present | Steno Diabetes Center Aarhus, Aarhus, Denmark
Collaborator. The Seedcase Project team is collaborating with the ON-LiMiT study group to build, organise, structure, and help manage the data they will collect.
16 Nov 2016 to present | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Creator. I built, as well as occasionally maintain, the PROMISE cohort database. It originally had no organization or structure, with files across different computers and with different names. I applied data engineering practices to structure it into a pipeline that checks, validates, re-organizes, and FAIR-ifies the data. Setting it up as an (unpublished) R package made it easier to test, fix, validate, reuse, and share it with other researchers using PROMISE data.
Committees
Participation in committee, group, or council level activities.
7 Jan 2022 to present | Steno Diabetes Center Aarhus, Denmark
Contribute to managing the project applications, setting up new projects, discussing and doing administrative tasks, managing the Research Analysis Platform (RAP), maintaining the ukbAid package and website.
1 Jan 2020 to 6 Nov 2021 | Danish Diabetes Academy, Denmark
Brainstorm and decide on overall school theme, develop the challenge project material and output, find and invite speakers for sessions, as well as contributing to creating the podcast on the challenge material.
14 Jan 2016 to 31 Jan 2018 | University of Toronto & Mozilla Science Lab, Toronto, Canada
Responsible for managing the finances, identifying potential sources of funding and applying to them as applicable, reimbursing students for expenses, and buying the snacks for the coding sessions. Other communal duties include maintaining the GitHub repository and dealing with Issues and Pull Requests (via GitHub) that may arise.
1 Sept 2014 to 31 Aug 2017 | University of Toronto, Toronto, Canada
Responsible for the accounting of the NSGSA finances, reimbursing students for expenses, applying for the Graduate Student Union Head Grant to secure funding, and dealing with any finance related issues that may come up.
Outreach activities
Activities involving some type of outreach to a diverse audience, including the general public.
21 Nov 2024 | Danish Diabetes and Endocrinology Academy, Copenhagen, Denmark
Panel discussion many possible career paths of someone with a life science background.
24 Sept 2024 | Danish Diabetes and Endocrinology Academy, Denmark
Interviewed by the Danish Diabetes and Endocrinology Academy about my postdoctoral fellowship, my career path, and how I ended up working on health data engineering and software engineering.
3 Nov 2022 | Aarhus University, Aarhus, Denmark
Interviewed by an Aarhus University journalist about the importance of open science and the barriers to effective open science practices.
27 Oct 2022 | Danish Diabetes Academy, Denmark
Speaker on a podcast discussing how to move researchers more towards incorporating open science practices.
12 Sept 2022 to 14 Sept 2022 | Chalmers University of Technology, Gothenburg, Sweden
Developed the website for this conference with the videos of the talks and poster abstracts.
Supervision and mentoring
Acting as a formal (co-)supervisor to students and their projects or as a mentor to others.
1 Jun 2025 to 31 May 2026 | Danish Diabetes and Endocrinology Academy, Denmark
Acted as a mentor to a postdoctoral researcher working in Denmark. Through the program, mentors and mentees are matched and guided through the year-long mentoring programme with support from an expert.
1 Jun 2024 to 31 May 2025 | Danish Diabetes and Endocrinology Academy, Denmark
Acted as a mentor to a postdoctoral researcher working in Denmark. Through the program, mentors and mentees are matched and guided through the year-long mentoring programme with support from an expert. The pilot program was to test the feasibility and interest in a larger program that the Danish Diabetes and Endocrinology Academy might run in the future.
1 Mar 2023 to 3 Jun 2023 | Universitat Oberta de Catalunya, Barcelona, Spain
Supervised Núria in a (remote) Master’s certificate in Biostatistics and Bioinformatics while she was doing her PhD in Chalmers University of Technology Gothenburg, Sweden. Thesis title: Pipeline in R for creating multi-metabolite signatures of dietary adherence from observational data.
1 Sept 2017 to 31 Jan 2018 | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Co-supervised with Dr. Anthony Hanley. I trained Shahen in R and statistics, as well as assisted in guiding the research project and analysis. Project title was Metabolomic Profiling of the DASH Diet: Novel Insights for the Nutritional Epidemiology of Type 2 Diabetes Mellitus.
1 Sept 2014 to 30 Apr 2015 | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Co-supervised with Dr. Anthony Hanley for the Research Projects course (NFS394) in Nutritional Sciences. Supervision consisted of helping guide the development of the research question and teaching Windy coding in SAS and using statistical techniques to analyze the data. Project title was Validating a bioelectric impedance instrument against the gold standard dual-energy x-ray absorptiometry on measures of adiposity.
Teaching
Teaching activities, excluding curriculum development.
26 May 2025 to present | Steno Diabetes Center Aarhus, Denmark
Three hour workshop introducing GitHub to beginners, through the use of the GitHub web interface.
7 Dec 2022 to present | Danish Diabetes and Endocrinology Academy, Denmark
Three day workshop on using R for reproducible workflows and approaches to data processing to PhD students and postdoctoral researchers.
8 Sept 2020 to present | Danish Diabetes and Endocrinology Academy, Denmark
Three day workshop on using R for reproducible pipelines and collaboration of data analysis projects to PhD students and postdoctoral researchers.
22 Jun 2020 to present | Danish Diabetes and Endocrinology Academy, Denmark
Three day workshop on an introduction to using R for reproducible data analysis to PhD students and postdoctoral researchers.
22 Oct 2019 to 23 Oct 2019 | Aarhus University, Aarhus, Denmark
Coordinate and instruct a 2-day Software Carpentry workshop to any member of Aarhus University.
21 May 2019 to 19 Mar 2019 | German Institute of Human Nutrition Potsdam-Rehbrueke, Potsdam, Germany
Three day workshop teaching an introduction to using R for reproducible data analysis to PhD students and postdoctoral researchers.
4 Mar 2019 to 19 Mar 2019 | Danish Diabetes and Endocrinology Academy, Denmark
Four day workshop teaching an introduction to using R for reproducible data analysis to PhD students and postdoctoral researchers.
9 Jul 2018 to 13 Jul 2018 | TIB Leibniz Information Centre for Science and Technology and University
Library , Hannover, Germany
Taught and contributed to workshop material on building FAIR (findable, accessible, interoperable, and reusable) data and software.
1 Jun 2018 to 12 Jun 2020 | Aarhus University Community of Researchers Using Open Software, Aarhus, Denmark
Founded a group dedicated to skill sharing of data analysis in the statistical programming language R (and others). Organize and instruct several sessions on using R, in a participatory live coding format.
7 Sept 2017 to 21 Dec 2017 | Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
Created the curriculum (along with five other members). Taught three lectures, created and marked assignments. Supervisor: Dr. Martin Krkosek
7 Sept 2017 to 21 Dec 2017 | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Gave a lecture and created the assignment (see website). Marked the assignment. Supervisor: Dr. Valerie Tarasuk
8 May 2017 to 9 May 2017 | Software Carpentry, Toronto, Canada
Instructed the second day of the two-day workshop at Ryserson University on advanced uses of R.
3 Feb 2017 to 4 Feb 2017 | Software Carpentry, Toronto, Canada
Acted as helper to the instructors at a two-day workshop introducing computing to researchers and students at the University of Toronto. Duties were to answer any questions and fix any problems that novice learners encountered during the two day workshop.
19 Jan 2017 | Software Carpentry and UofTCoders, Toronto, Canada
Helped learners during the Git session of the two day workshop.
2 Jan 2017 to 28 Apr 2017 | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Marked assignments and exams. Supervisor: Dr. Debbie Gurfinkel
14 Sept 2016 | Software Carpentry, Toronto, Canada
Taught the first R session to novice learners at a two-day workshop on introducing computing to researchers and students at York University.
1 Sept 2016 to 21 Dec 2016 | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Marked exams. Developed and marked a short assignment. Answered any student questions. Supervisor: Dr. Carol Greenwood
27 Jul 2016 to 10 Aug 2016 | CUPE3902 Unit 5, Toronto, Canada
The UofTCoders members were hired by CUPE3902 Unit 5 to teach Python to post-doctoral fellows. As a core member of the UofTCoders, I acted as a helper to the instructors at the three-part workshop series introducing the Python programming language. Duties were to answer any questions and fix any problems that novice learners encountered during the Python sessions.
26 May 2016 to 12 Apr 2017 | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
I wanted to increase the computing capacity of my graduate department and to start to promote a culture of code-sharing and code reviews. Since how analyses are conducted and what the code is to create the scientific results is increasingly becoming more important, I wanted to start teaching students how to use R efficiently and productively. I’ve also set up a code review with my lab, so it was efficient for me to wrap these workshops up with the code reviews.
9 May 2016 to 10 May 2016 | Software Carpentry, Toronto, Canada
Taught the Git session to novice learners at a two-day workshop on introducing computing to researchers and students at the University of Toronto, as well as acted as helper during the Shell and Python sessions.
25 Apr 2016 to 26 Apr 2016 | Software Carpentry, Toronto, Canada
Acted as helper to the instructors at a two-day workshop introducing computing to researchers and students at the University of Toronto. Duties were to answer any questions and fix any problems that novice learners encountered during the R sessions.
1 Sept 2015 to 31 Dec 2015 | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Gave two lectures during the course and developed and marked the final (third) assignment. Supervisor: Dr. Sarah Orr
16 Jul 2015 to 17 Jul 2015 | Software Carpentry, Toronto, Canada
Coding workshop hosted at the Hospital for Sick Children, Toronto. I taught version control using Git and acted as helper for the Shell and R sessions. Supervisor: Tom Wright
11 Jun 2015 to 31 Jan 2018 | UofTCoders, University of Toronto, Toronto, Canada
Was involved in developing a PhD student group aimed at teaching and peer-sharing computing skills such as Git, R, Python, and many other computing programs.
29 Jan 2015 to 30 Jan 2015 | Software Carpentry, Toronto, Canada
Coding workshop hosted at the Hospital for Sick Children, Toronto. I provided technical support, worked through students’ problems and issues with them, and answered any questions. Supervisor: Tom Wright
30 Oct 2014 to 31 Oct 2014 | Software Carpentry, Toronto, Canada
Coding workshop hosted at the Gerstein Library, University of Toronto. I provided technical support, assisted students’ with problems and issues, and answered student questions. Supervisor: Dr. Greg Wilson
1 Oct 2014 to 23 Nov 2015 | Graduate Professional Skills Program, University of Toronto, Toronto, Canada
Taught three workshops on SAS and R. SAS workshops were co-instructed and co-developed with Dr. Daiva Nielsen. R workshops were co-instructed with Sarah Meister. We taught version control, beginner and advanced coding techniques, and how to structure research projects around the idea of reproducibility. Consistent with our mission statement, our material is publicly available online at https://github.com/codeasmanuscript.
1 Sept 2014 to 31 Dec 2014 | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Developed and lead tutorials for graduate students. Developed and marked the final exam. Answered any student questions. Supervisor: Dr. Carol Greenwood
1 Sept 2013 to 31 Dec 2013 | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Lead tutorials for undergraduate students. Developed and marked the midterm exam. Answered any student questions. Supervisor: Dr. Carol Greenwood
1 Jan 2013 to 30 Apr 2013 | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Answer student emails and questions. Mark midterm exam, assignment and final exam. Invigilate midterm and final exam. Supervisor: Dr. Elena Comelli
Educational resources
Educational resources that I’ve developed or contributed to.
1 Oct 2020 to present | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Reproducibility and open scientific practices are increasingly being requested or required of scientists and researchers, but training on these practices has not kept pace. This course intends to help bridge that gap and covers the fundamentals and workflow of data analysis in R. This repository contains the lesson, lecture, and assignment material for the course, including the website source files and other associated course administration files.
1 Oct 2020 to present | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
A 3-day course on how to clean, reorganize, and process larger and more complex data before it can be analyzed, for researchers, PhD students, and postdocs.
29 Jun 2020 to present | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Reproducibility and open scientific practices are increasingly being requested or required of scientists and researchers, but training on these practices has not kept pace. This 3-day course intends to help bridge that gap and covers the fundamentals and workflow of data analysis in R. This repository contains the lesson, lecture, and assignment material for the course, including the website source files and other associated course administration files.
29 Jun 2020 to present | Department of Nutritional Sciences, University of Toronto, Toronto, Canada
A 3-day workshop for researchers introducing modern and reproducible data analysis tools and workflows with R. Taught to PhD students and postdoc researchers.
17 Jun 2019 | GitHub
Interactive course material on how to analyze cohort datasets in R.
4 Mar 2019 to 19 Mar 2019 | GitHub
Material for a 4-day course taught for PhD and PostDocs from the Danish Diabetes Academy.
9 Jul 2018 to 13 Jul 2018 | TIB Leibniz Information Centre for Science & Technology and University Library, Hannover, Germany
Week long Carpentries-based workshop aimed at teaching FAIR principles for research data and for software management and development. Contributed to and taught the workshop material.
18 Dec 2017 to 6 Jun 2019 | TIB Leibniz Information Centre for Science & Technology and University Library, Hannover, Germany
Quantitative Methods in R for Biology is a course aimed at undergraduates at a third year level or above. The course covers statistics and data analysis for ecology and reproducible quantitative methods in R.
1 Sept 2017 to 22 Dec 2017 | Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
Pilot course to teach computational and quantitative analyses in R for ecology and evolutionary biology undergraduate students.
1 Oct 2014 to 23 Nov 2015 | School of Graduate Studies, University of Toronto, Toronto, Canada
Developed a multi-day workshop series on initially SAS with colleague Dr. Daiva Nielsen and later I developed a series on R. These workshops aimed to teach scientific coding skills to graduate students, such as using version control, structuring research projects, using reproducibility concepts, and “software development” concepts in a scientific coding context.
Journal articles
Academic outputs that lead to an article published in a journal. Some entries were also published as preprints and so have a duplicate entry in the Preprints section.
2024 | School of Graduate Studies, University of Toronto, Toronto, Canada
2024 | School of Graduate Studies, University of Toronto, Toronto, Canada
2024 | School of Graduate Studies, University of Toronto, Toronto, Canada
2022 | School of Graduate Studies, University of Toronto, Toronto, Canada
2022 | School of Graduate Studies, University of Toronto, Toronto, Canada
2021 | School of Graduate Studies, University of Toronto, Toronto, Canada
2021 | School of Graduate Studies, University of Toronto, Toronto, Canada
2020 | School of Graduate Studies, University of Toronto, Toronto, Canada
2020 | School of Graduate Studies, University of Toronto, Toronto, Canada
2019 | School of Graduate Studies, University of Toronto, Toronto, Canada
2019 | School of Graduate Studies, University of Toronto, Toronto, Canada
2019 | School of Graduate Studies, University of Toronto, Toronto, Canada
2019 | School of Graduate Studies, University of Toronto, Toronto, Canada
2019 | School of Graduate Studies, University of Toronto, Toronto, Canada
2018 | School of Graduate Studies, University of Toronto, Toronto, Canada
2017 | School of Graduate Studies, University of Toronto, Toronto, Canada
2016 | School of Graduate Studies, University of Toronto, Toronto, Canada
2013 | School of Graduate Studies, University of Toronto, Toronto, Canada
2010 | School of Graduate Studies, University of Toronto, Toronto, Canada
Books
Work that has been published in a book format.
6 Aug 2021 | School of Graduate Studies, University of Toronto, Toronto, Canada
ISBN: 367698323
Presentations
Work that I have contributed to or that I’ve lead that was presented at conferences, seminars, and other events, either online or in-person.
15 Oct 2024 | Danish Digitalization, Data Science and AI, Virtual
18 Nov 2021 | Life Science Trainers Talk Series “How I Teach Life Scientists…”, Virtual
5 Jul 2021 to 9 Jul 2021 | UseR! 2021 Conference, Virtual
5 Jul 2021 to 9 Jul 2021 | Annual UseR Conference, Virtual
20 May 2021 to 21 May 2021 | Annual Meeting of the Danish Epidemiological Society, Virtual
16 Dec 2020 | IARC Nutritional Methodology and Biostatistics Group, Virtual
21 Sept 2020 to 24 Sept 2020 | European Association for the Study of Diabetes Annual Meeting, Online
3 Nov 2019 to 7 Nov 2019 | ObesityWeek, Las Vegas, USA
7 Jun 2019 to 11 Jun 2019 | American Diabetes Association XX Scientific Sessions, San Francisco, US
11 May 2019 to 14 May 2019 | European Diabetes Epidemiology Group Annual Meeting, Mondorf-les-Bains, Luxembourg
1 Oct 2018 to 5 Oct 2018 | Annual Meeting of the European Association for the Study of Diabetes, Berlin, Germany
14 May 2018 to 16 May 2018 | European R User Meeting, Budapest, Hungary
21 Apr 2018 to 24 Apr 2018 | European Diabetes Epidemiology Group Annual Meeting, Helsingør, Denmark
21 Apr 2018 to 24 Apr 2018 | European Diabetes Epidemiology Group Meeting, Helsingør, Denmark
21 Apr 2018 to 24 Apr 2018 | European Diabetes Epidemiology Group Annual Meeting, Helsingør, Denmark
29 Oct 2017 to 2 Nov 2017 | ObesityWeek, Washington, DC, USA
20 Oct 2017 | 4th Annual BBDC-Joslin-UCPH Conference, Toronto, Canada
19 Jun 2017 to 22 Jun 2017 | 35th International Symposium on Diabetes and Nutrition, Skagen, Denmark
9 Jun 2017 to 13 Jun 2017 | American Diabetes Association 77th Scientific Sessions, San Diego, US
9 Jun 2017 to 13 Jun 2017 | American Diabetes Association 77th Scientific Sessions, San Diego, US
9 Jun 2017 to 13 Jun 2017 | American Diabetes Association 77th Scientific Sessions, San Diego, US
11 Mar 2017 | Working Open Workshop, Mozilla Science Lab, Montreal, Canada
29 Oct 2016 | Mozilla Festival, London, UK
10 Jun 2016 to 14 Jun 2016 | American Diabetes Association 76th Scientific Sessions, New Orleans
10 Jun 2016 to 14 Jun 2016 | American Diabetes Association 76th Scientific Sessions in New Orleans, New Orleans, US
10 Jun 2016 to 14 Jun 2016 | American Diabetes Association 76th Scientific Sessions in New Orleans, New Orleans, US
5 Dec 2015 | International Diabetes Epidemiology Group Scientific Meeting, Vancouver, Canada
30 Nov 2015 to 4 Dec 2015 | International Diabetes Federation World Diabetes Congress, Vancouver, Canada
9 Jun 2015 to 12 Jun 2015 | 33rd International Symposium on Diabetes & Nutrition, Toronto, Canada
5 Jun 2015 to 9 Jun 2015 | American Diabetes Association’s 75th Scientific Session, Boston, US
28 Jun 2014 to 2 Jul 2014 | Biennial Congress of the International Society for the Study of Fatty Acids and Lipids, Stockholm, Sweden
14 Jun 2014 to 17 Jun 2014 | American Diabetes Association’s 74th Scientific Sessions, San Francisco, US
21 Jun 2013 to 25 Jun 2013 | American Diabetes Association’s 73th Scientific Sessions, Chicago, US
2011 | 7th National Conference on Tobacco or Health, Making the Connection: Knowledge Transforming Health, Toronto, Canada
2011 | 17th Annual Meeting of the Society on Research on Nicotine and Tobacco, Toronto, Canada
21 Sept 2010 to 24 Sept 2010 | Safety 2010 World Conference, London, UK
17 Aug 2010 | Meeting of the Tobacco-free Sports and Recreation Community of Practice, Waterloo, Canada
8 Mar 2009 to 12 Mar 2009 | 14th World Conference on Tobacco or Health, Mumbai, India
10 Nov 2008 | Tobacco Control for the 21st Century: Challenges in Research and Evaluation, Toronto, Canada
10 Nov 2008 | Tobacco Control for the 21st Century: Challenges in Research and Evaluation, Toronto, Canada