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.
BSc in Kinesiology
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.
DP-Next: Sustainable Type 2 Diabetes Prevention for the 21st Century
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).
Research Education and Networking Award
1 Dec 2022
Danish Diabetes Academy, Denmark
Recognition for involvement in education and networking of researchers in Denmark. Amount: DKK 25,000
Danish Diabetes Academy Postdoctoral Fellowship
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
Michael C. Archer Research Excellence Award
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.
Marie Skłodowska-Curie Master Class and Travel Fund
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.
Gordon Cressy Student Leadership Award
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.
Working Open Workshop and Travel Scholarship
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
Trainee Travel Award
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
Doctoral Student Research Award
1 Sept 2014 to 31 Aug 2017
Canadian Diabetes Association, Toronto, Canada
Nationally competitive award. Amount: CAD 21000
Graduate Novo Nordisk Studentship
1 Sept 2014 to 31 Aug 2015
Banting and Best Diabetes Centre, Toronto, Canada
University-wide awards. Amount: CAD 3840
Margaret and Nicholas Fodor Fellowship
1 Sept 2014 to 31 Aug 2015
University of Toronto, Toronto, Canada
University-wide awards. Amount: CAD 3000
Ontario Graduate Scholarship
1 Sept 2014 to 31 Aug 2015
Government of Ontario, Toronto, Canada
Awarded, but declined for the CDA Doctoral Award. Amount: CAD 15000
New Investigator Award
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
Trainee Travel Award
1 Jun 2014
Banting and Best Diabetes Centre, Toronto, Canada
For attendance to the American Diabetes Association 74rd Scientific Sessions. Amount: CAD 1000
Conference Travel Grant
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
Alumni Travel Award
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
Ontario Graduate Scholarship
1 Sept 2013 to 31 Aug 2014
Government of Ontario, Toronto, Canada
Provincial-level graduate scholarship. Amount: CAD 15000
Trainee Travel Award
8 May 2013
Banting and Best Diabetes Centre, Toronto, Canada
For attendance to the American Diabetes Association 73rd Scientific Sessions. Amount: CAD 1000
Ontario Graduate Scholarship
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.
Team leader
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.
DDA postdoctoral researcher
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
Postdoctoral researcher
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.
- Assisting a PhD student’s social network analysis on the programming aspects of work.
Supervisor: Dr. Daniel Witte
Postdoctoral fellow
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
Research Assistant
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
Research Assistant
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
Research Assistant
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
Research Assistant
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
Research Assistant
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
Project Manager
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.
RStudio Instructor Training and Certification Program
6 Aug 2020
RStudio, Boston, USA
Certificate for completing an instructor training program.
Aarhus University Teachers Training Programme
21 Aug 2019 to 19 Dec 2019
Aarhus University, Aarhus, Denmark
A teacher training programme for future and current instructors of university-level courses.
Mozilla Open Project Leaders Training
21 Feb 2018 to 11 Jun 2018
Mozilla, Online
Training programme for those who want to or are currently leading open source projects.
Graduate Professional Skills
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.
Foundations of Project Management I
23 Nov 2016 to 24 Nov 2016
Mitacs, Toronto, Canada
An intensive course on learning the basics of project management.
Data Carpentry Instructor Training
15 Nov 2016
Data Carpentry, Online
Certificate for completing an instructor training program required to teach Data Carpentry workshops.
Advanced University Teaching Preparation
1 Aug 2015
University of Toronto, Toronto, Canada
Certificate of completing the university’s teacher training program for graduate students.
Software Carpentry Instructor Training
26 May 2015
Software Carpentry, Online
Certificate for completing an instructor training program.
Package development
Creation of or contribution to software packages.
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.
osdc: An Open-Source Diabetes Classifier for Danish Registers
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.
ukbAid: Aid Steno Researchers Who Work on the UKB RAP
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.
NetCoupler: Inference of Causal Links Between a Network and an External Variable
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.
dstDataPrep: Convert Denmark Statistics Data into Modern Formats
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.
posterdown: Generate PDF Conference Posters Using R Markdown
9 Oct 2019 to present
CRAN
Contributor. Use ‘rmarkdown’ and ‘pagedown’ to generate HTML and PDF conference posters.
PROMISE.audit: Identifies Unexpected Values in the PROMISE Datasets
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.
PROMISE.scrub: Scrub the PROMISE dataset
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.
PROMISE.methods: PROMISE Method Documentation and Data Dictionary Helpers
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.
carpenter: Build Common Tables of Summary Statistics for Reports
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.
mason: Build Data Structures for Common Statistical Analysis
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.
prodigenr: Research Project Directory Generator
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).
broom: Convert Statistical Objects into Tidy Tibbles
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.
PROMISE cohort data managed as an R package
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.
Scientific program organizing committee for the Danish Diabetes Academy Postdoctoral Winter School
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.
Treasurer for the UofT Coders council
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.
Treasurer for the Nutritional Sciences Graduate Student Association
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.
The Future is Transparent: Moving Towards Open Science
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
Acting as a formal (co-)supervisor to students and their projects.
Master’s student Núria Estanyol-Torres
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.
Master’s student Shahen Yashpal
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.
Bachelor student Windy Wang
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.
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.
Reproducible Research in R: An introductory workshop on modern data analyses and workflows
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.
Reproducible Quantitative Analyses and Workflows using R
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.
Reproducible Quantitative Methods: Data analysis workflow using R
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.
FAIR Data and Software workshop
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.
Peer-led, participatory live coding R training sessions
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.
Theoretical Ecology and Reproducible Quantitative Methods in R (EEB430)
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
Public Health Nutrition (NFS1201)
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
Software Carpentry workshops (R)
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.
Software Carpentry workshops (Python)
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.
Software Carpentry workshops (R)
19 Jan 2017
Software Carpentry and UofTCoders, Toronto, Canada
Helped learners during the Git session of the two day workshop.
Basic Human Nutrition (NFS284)
2 Jan 2017 to 28 Apr 2017
Department of Nutritional Sciences, University of Toronto, Toronto, Canada
Marked assignments and exams.
Supervisor: Dr. Debbie Gurfinkel
Software Carpentry workshops (R)
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.
Advanced Nutrition (NFS484-1484)
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
CUPE3902 Post-doc Python workshops
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.
Software Carpentry workshops (Python)
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.
Software Carpentry workshops (R)
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.
Public Health Nutrition (NFS1201)
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
Software Carpentry Workshop (R)
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
Peer-led, participatory live coding training sessions
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.
Software Carpentry Workshop (R)
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
Software Carpentry Workshop (Python)
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
Code as Manuscript: R and SAS coding workshops
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.
Advanced Nutrition (NFS484-1484)
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
Advanced Nutrition (NFS484-1484)
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
Nutritional Microbiology (NFS485)
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
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
A 3-day workshop for researchers introducing modern and reproducible data analysis tools and workflows with R. Taught to PhD students and postdoc researchers.
acdcourse: Analyzing Cohort Datasets with R
17 Jun 2019
GitHub
Interactive course material on how to analyze cohort datasets in R.
Reproducible Quantitative Methods: Data analysis workflow using R
4 Mar 2019 to 19 Mar 2019
Material for a 4-day course taught for PhD and PostDocs from the Danish Diabetes Academy.
FAIR Data and Software: A Carpentries-based workshop
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.
UofTCoders/rcourse: Quantitative Methods in R for Biology
18 Dec 2017 to 6 Jun 2019
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.
Theoretical Ecology and Reproducible Quantitative Methods in R (EEB430)
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.
Code as Manuscript: Data wrangling, visualization, and reproducibility in R
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
Urinary Vitamin D Binding Protein: A Marker of Kidney Tubular Dysfunction in Patients at Risk for Type 2 Diabetes
2024
Dihydroceramide- and ceramide-profiling provides insights into human cardiometabolic disease etiology
2022
Escaping irreproducible research practices and spreading awareness through education and (re-)training
2022
Metabolomic profiling of the {Dietary Approaches to Stop Hypertension} diet provides novel insights for the nutritional epidemiology of type 2 diabetes mellitus
2021
r-cubed: Guiding the overwhelmed scientist from random wrangling to Reproducible Research in R
2021
Next generation diabetes scientists shape global research culture
2020
Effect of familial diabetes status and age at diagnosis on type 2 diabetes risk: a nation-wide register-based study from Denmark
2020
A graduate student-led participatory live-coding quantitative methods course in R: Experiences on initiating, developing, and teaching
2019
The Distribution of Fatty Acid Biomarkers of Dairy Intake across Serum Lipid Fractions: The Prospective Metabolism and Islet Cell Evaluation (PROMISE) Cohort
2019
The macrophage activation marker soluble CD163 is longitudinally associated with insulin sensitivity and β-cell function
2019
Associations of Calcium from Food Sources versus Phosphate Binders with Serum Calcium and FGF23 in Hemodialysis Patients
2019
Determinants of longitudinal change in insulin clearance: the Prospective Metabolism and Islet Cell Evaluation cohort
2019
2018
Association of non-esterified fatty acid composition with insulin sensitivity and beta cell function in the Prospective Metabolism and Islet Cell Evaluation (PROMISE) cohort
2017
Longitudinal associations of phospholipid and cholesteryl ester fatty acids with disorders underlying diabetes.
2016
Short leg length, a marker of early childhood deprivation, is associated with metabolic disorders underlying type 2 diabetes mellitus: the PROMISE cohort study
2013
Low-income countries’ orthopaedic information needs: Challenges and opportunities
2010
Books
Work that has been published in a book format.
Research Software Engineering with Python
6 Aug 2021
ISBN: 0367698323
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.
How I Teach Life Scientists About Reproducibility and Data Analysis Using R
18 Nov 2021
Life Science Trainers Talk Series “How I Teach Life Scientists…”, Virtual
Presentation type: Oral
NetCoupler: Inferring causal pathways between high-dimensional metabolic data and external factors
5 Jul 2021 to 9 Jul 2021
UseR! 2021 Conference, Virtual
Presentation type: Oral
r-cubed: Guiding the overwhelmed scientist from random wrangling to Reproducible Research in R
5 Jul 2021 to 9 Jul 2021
Annual UseR Conference, Virtual
Presentation type: Contributed
NetCoupler: Inferring causal pathways between high-dimensional metabolic data and external factors
20 May 2021 to 21 May 2021
Annual Meeting of the Danish Epidemiological Society, Virtual
Presentation type: Oral
NetCoupler: Inferring causal pathways between high-dimensional metabolic data and external factors
16 Dec 2020
IARC Nutritional Methodology and Biostatistics Group, Virtual
Presentation type: Oral
The metabolic pathways between components of stature and HbA (1c): a causal structure learning approach in the UK Biobank
21 Sept 2020 to 24 Sept 2020
European Association for the Study of Diabetes Annual Meeting, Online
Presentation type: Oral poster
Adipose Tissue Insulin Resistance and Inflammation Are Independently Associated With Dysglycemia
3 Nov 2019 to 7 Nov 2019
ObesityWeek, Las Vegas, USA
Presentation type: Contributed
Metabolomic Profiling of the Dietary Approaches to Stop Hypertension (DASH) Diet: Novel Insights for the Nutritional Epidemiology of Type 2 Diabetes Mellitus (T2DM)
7 Jun 2019 to 11 Jun 2019
American Diabetes Association XX Scientific Sessions, San Francisco, US
Presentation type: Contributed
A data-driven approach at characterizing heterogeneity in neuropathy assessments
11 May 2019 to 14 May 2019
European Diabetes Epidemiology Group Annual Meeting, Mondorf-les-Bains, Luxembourg
Presentation type: Oral poster
Leg length, a marker of early childhood conditions, associates with specific clusters of serum fatty acids
1 Oct 2018 to 5 Oct 2018
Annual Meeting of the European Association for the Study of Diabetes, Berlin, Germany
Presentation type: Oral poster
An R toolkit to simplify and automate an open scientific workflow
14 May 2018 to 16 May 2018
European R User Meeting, Budapest, Hungary
Presentation type: Oral
21 Apr 2018 to 24 Apr 2018
European Diabetes Epidemiology Group Annual Meeting, Helsingør, Denmark
Presentation type: Oral poster
Longitudinal Associations of Soluble CD163 with Insulin Sensitivity and Beta-Cell Function: The Prospective Metabolism and Islet Cell Evaluation (PROMISE) Cohort
21 Apr 2018 to 24 Apr 2018
European Diabetes Epidemiology Group Meeting, Helsingør, Denmark
Presentation type: Contributed
Combining dietary and biomarker data to evaluate associations of dairy intake with risk of type 2 diabetes (T2DM): The PROspective Metabolism and ISlet cell Evaluation (PROMISE) cohort
21 Apr 2018 to 24 Apr 2018
European Diabetes Epidemiology Group Annual Meeting, Helsingør, Denmark
Presentation type: Contributed
Determinants of Longitudinal Change in sCD163, a Biomarker of Adipose Tissue Macrophage Activation
29 Oct 2017 to 2 Nov 2017
ObesityWeek, Washington, DC, USA
Presentation type: Contributed
Longitudinal Associations of Soluble CD163 with Insulin Sensitivity and Beta-Cell Function: The Prospective Metabolism and Islet Cell Evaluation (PROMISE) Cohort
20 Oct 2017
4th Annual BBDC-Joslin-UCPH Conference, Toronto, Canada
Presentation type: Contributed
Serum Fatty Acids Derived from Dairy Consumption Are Associated with Longitudinal Changes in Insulin Sensitivity and Beta-cell Function: The Prospective Metabolism and Islet Cell Evaluation (PROMISE) Cohort
19 Jun 2017 to 22 Jun 2017
35th International Symposium on Diabetes and Nutrition, Skagen, Denmark
Presentation type: Contributed
Urinary Vitamin D Binding Protein as a Potential Biomarker for Nephropathy in Subjects at Risk for Type 2 Diabetes: The Prospective Metabolism and Islet Cell Evaluation (PROMISE) Cohort Study
9 Jun 2017 to 13 Jun 2017
American Diabetes Association 77th Scientific Sessions, San Diego, US
Presentation type: Contributed
Fatty Acids Produced by De Novo Lipogenesis (DNL) of Refined Carbohydrates are Associated with Worsening of Metabolic Syndrome (MetS) Components: The Prospective Metabolism and Islet Cell Evaluation (PROMISE) Cohort
9 Jun 2017 to 13 Jun 2017
American Diabetes Association 77th Scientific Sessions, San Diego, US
Presentation type: Poster
Longitudinal Associations of Soluble CD163 with Insulin Sensitivity and Beta-Cell Function: The Prospective Metabolism and Islet Cell Evaluation (PROMISE) Cohort
9 Jun 2017 to 13 Jun 2017
American Diabetes Association 77th Scientific Sessions, San Diego, US
Presentation type: Contributed
Community Building Panel Discussion
11 Mar 2017
Working Open Workshop, Mozilla Science Lab, Montreal, Canada
Presentation type: Panel
Study Groups - Crossing the Boundaries of Discipline
29 Oct 2016
Mozilla Festival, London, UK
Presentation type: Contributed
Triglyceride Fatty Acid (TGFA) Composition Longitudinally Associates with Changes in Insulin Sensitivity (IS) and Beta-Cell Function Over 6-yrs in the Prospective Metabolism and Islet Cell Evaluation (PROMISE) Cohort
10 Jun 2016 to 14 Jun 2016
American Diabetes Association 76th Scientific Sessions, New Orleans
Presentation type: Poster
Serum Fatty Acids Derived from Dairy Consumption Are Associated with Insulin Sensitivity and Beta-cell Function: The PROspective Metabolism and ISlet Cell Evaluation (PROMISE) Cohort
10 Jun 2016 to 14 Jun 2016
American Diabetes Association 76th Scientific Sessions in New Orleans, New Orleans, US
Presentation type: Contributed
Multivariate Determinants of Reduced Insulin Clearance in Prospective Metabolism and Islet Cell Evaluation (PROMISE) Cohort
10 Jun 2016 to 14 Jun 2016
American Diabetes Association 76th Scientific Sessions in New Orleans, New Orleans, US
Presentation type: Contributed
5 Dec 2015
International Diabetes Epidemiology Group Scientific Meeting, Vancouver, Canada
Presentation type: Oral
30 Nov 2015 to 4 Dec 2015
International Diabetes Federation World Diabetes Congress, Vancouver, Canada
Presentation type: Poster
Serum Non-Esterified Fatty Acid (NEFA) Concentrations are Associated with Longitudinal Progression of Beta-Cell Dysfunction: Prospective Metabolism and Islet Cell Evaluation (PROMISE) Cohort
9 Jun 2015 to 12 Jun 2015
33rd International Symposium on Diabetes & Nutrition, Toronto, Canada
Presentation type: Oral
Serum Non-Esterified Fatty Acid (NEFA) Concentration is Associated with Longitudinal Progression of Beta-Cell Dysfunction: Prospective Metabolism and Islet Cell Evaluation (PROMISE) Cohort
5 Jun 2015 to 9 Jun 2015
American Diabetes Association’s 75th Scientific Session, Boston, US
Presentation type: Oral poster
28 Jun 2014 to 2 Jul 2014
Biennial Congress of the International Society for the Study of Fatty Acids and Lipids, Stockholm, Sweden
Presentation type: Oral
14 Jun 2014 to 17 Jun 2014
American Diabetes Association’s 74th Scientific Sessions, San Francisco, US
Presentation type: Poster
21 Jun 2013 to 25 Jun 2013
American Diabetes Association’s 73th Scientific Sessions, Chicago, US
Presentation type: Poster
Secondhand Smoke in Common Spaces of Public Housing – Findings from Waterloo Region
2011
7th National Conference on Tobacco or Health, Making the Connection: Knowledge Transforming Health, Toronto, Canada
Presentation type: Contributed
An Environmental Scan of Tobacco-free Policies of YMCA & YWCA Locations in Ontario, Canada
2011
17th Annual Meeting of the Society on Research on Nicotine and Tobacco, Toronto, Canada
Presentation type: Contributed
Probability of Multiple Fractures in Childhood Session
21 Sept 2010 to 24 Sept 2010
Safety 2010 World Conference, London, UK
Presentation type: Contributed
Report of the Smoke-free Policy Scan of YMCAs and YWCAs in Ontario
17 Aug 2010
Meeting of the Tobacco-free Sports and Recreation Community of Practice, Waterloo, Canada
Presentation type: Oral
Experimental Evaluation of Outdoor and Adjacent Indoor Tobacco Smoke Pollution in Doorways
8 Mar 2009 to 12 Mar 2009
14th World Conference on Tobacco or Health, Mumbai, India
Presentation type: Contributed
An Environmental Scan of Tobacco Control Policies on University Campuses in Ontario
10 Nov 2008
Tobacco Control for the 21st Century: Challenges in Research and Evaluation, Toronto, Canada
Presentation type: Contributed
Experimental Evaluation of Tobacco Control Policies in Outdoor Environments
10 Nov 2008
Tobacco Control for the 21st Century: Challenges in Research and Evaluation, Toronto, Canada
Presentation type: Contributed