The DSI Research Software Development Office supports researchers to build new tools or to refine existing software tools to improve usability and robustness and enhance existing functionality.
Only open-source projects are considered for support so that we can disseminate research software beyond the research space in which it is created.
For further information and timelines see Research Software Development Program.
Chronic Disease Population Risk Tool (CDPoRT)
Prof. Laura Rosella (Dalla Lana School of Public Health, University of Toronto) developed an RShiny app that enables non-coding users to upload data and view analysis results via a web portal. The app’s focus is on the Chronic Disease Population Risk Tool (CDPoRT), which utilizes population-level health system data to predict future chronic disease burden based on individual characteristics. The tool provides data-driven support, guiding resource allocation and improving public health planning.
To enhance accessibility and usability, Prof. Rosella sought research software support to create a new web interface for the existing algorithm. The DSI Research Software Development played a crucial role in designing the new web interface, developing new code, creating associated documentation, and performing prototyping. Their collaborative efforts ensure that the tool is easily accessible online, allowing researchers and decision-makers to benefit from the data-driven insights provided by the CDPoRT.
GtiHub can be viewed here (currently private pending release)
Prof. Benjamin Haibe-Kains (University Health Network) looked to build upon ORCESTRA, a cloud-based platform to provide an automated and streamlined data processing pipeline submission process to accelerate the pipeline integration process, thus greatly expanding the catalog of the curated data Biomedical objects. This data is used in cancer research have been used to, among many, to identify biomarkers of drug and radiation response, as well as potential toxicities.
The DSI Research Software Development team consulted on the software architecture and recommend potential enhancements so that the software can be extended to a multitude of data types. The team is also working on enhancing data security, conducting a thorough review of the existing architecture within the data processing layer to identify areas for improvement, and considering the reengineering of the pipeline submission feature with a potential migration to the cloud environment.
GtiHub can be viewed here
Dr. Angeliki Veroniki (Unity Health Toronto) aimed to develop a user-friendly web interface called Rank-Heat Plot R Shiny tool. This tool allows health researchers to upload spreadsheets containing medical treatment results and visualize and compare outcomes easily. It particularly addresses the challenges faced by health researchers, especially in data interpretation, when utilizing network meta-analysis (NMA) that combines evidence from multiple randomized trials to compare various treatments.
The DSI Research Software development team created the R Shiny interface for the Rank-Heat Plot tool. They updated existing R code as necessary and collaborated with lab members to deploy the application on an on-premise servers or in the cloud, depending on requirements. The tool can now empower clinicians, guideline developers, and policy makers to make well-informed decisions regarding drug coverage, provide recommendation and discuss optimal treatment options with patients across different outcomes.
Prof. Bo Wang (Laboratory Medicine & Pathobiology, Temerty Faculty of Medicine, University of Toronto) developed scGPT, a GPU-powered tool that empowers non-technical users to conduct RNA-seq analysis. It leverages a pre-trained machine learning model and enables tasks like gene expression profiling, differential gene expression analysis, clustering, and more.
Temporary development site can be viewed here
Prof. Ewan Dunbar (Department of French, Faculty of Arts & Science, University of Toronto) recently introduced a prototype web interface. This interface serves as a platform for speech researchers to conveniently upload their audio files and access downloadable speech features essential for speech processing tasks. The software holds significant value for both experimental and clinical speech researchers, aiding them in their respective endeavors.
To bring this prototype to life, the DSI Research Software Development team took charge of developing the required code and documentation for implementing the new tool. Their expertise and efforts were instrumental in transforming the concept into a functional and user-friendly web interface.
Dr. Gregory Schwarz (University Health Network) had a vision to deploy a set of tools for clustering and visualizing single-cell data. To bring this vision to life, the DSI Research Software Development team developed an app as a reimplemented version of an existing static visualization algorithm. The team was responsible for code development and documentation to ensure the tool’s functionality and usability.
One notable component of TooManyCells is its custom-made visualization feature. The DSI Research Software Development team designed this component, which presents cell relationships as a tree. Through the utilization of TooManyCells, it has become possible to identify rare cancer cells that contribute to disease progression, thus addressing an important need in the field. As a result of their efforts, an article describing the tool has been submitted for publication.
Widget-enabled Jupyter notebook enabling non-technical users to run existing algorithms easily.
Researcher: Leo Chou, UofT
DSI Software development office: Code, deployment.
GEMINI Web Portal
A new web portal that will allow physicians to log in and view the reports assigned to them. There is also a backend and admin portal from which the Gemini team will be assigning reports and managing the portal
Researcher: Amol Verma, Unity Health Toronto
DSI Software development office: Implementation end to end including deployment.
An open-source dynamics package which is a collection of numerical integrators and tools to enable dynamical simulations of bodies such as stars, planets, asteroids, and comets
Researcher: Hanno Rein, University of Toronto Scarborough
DSI Software development office: Bug fixes and enhancements. Containerizing the application and implementing the visualization widget
RLEA Sample Tracker
Developing a new database app for sample images, sample metadata, and analysis results.
Researcher: Monica Ramsey, UTM
DSI Software development office: Code, documentation, deployment.
Gender differences in co-authorship networks
Study of men’s and women’s positioning in global scientific collaboration networks. Data analysis project using Elsevier’s Scopus database. Topic is gender within context of research collaboration networks.
Researcher: Megan Frederickson, UofT
DSI Software development office: Consulting, data transformation.
A web application that helps international and domestic university students to develop academic language competencies and foster cross-cultural knowledge exchange through a digital platform.
Researcher: Eunice Jang, UofT, OISE
DSI Software development office: Prototyping, code and architecture review.
Livres d’heures: textes et langue
Digital humanities. Goal is a searchable database of TEI-coded medieval manuscripts.
Researcher: Dorothea Kullman, UofT
DSI Software development office: Consulting (GitHub, TEI, project structure).
The University of Toronto provides resources for data infrastructure. You can view a complete set of resources at the Centre for Research Innovation & Support Digital Research Infrastructure Portal