Supporting the Advancement of Essential Oncology Software for Research within Princess Margaret

CDI recognizes that software is critical to modern scientific research, advancing medical discoveries while providing a framework for reproducibility and transparency.

However, many of these software solutions do not have dedicated funding for maintenance, let alone for growth and maximizing their potential for transformational impact. In a targeted effort to advance the use of essential oncology software for research, CDI launched an open call to fund and provide expertise to software-centered projects that are essential to biomedical research.

The open call resulted in the selection of three Princess Margaretdeveloped software projects for the 2022-2023 funding round: cBioPortal developed by the Dr. Trevor Pugh Lab; the Computational & Bench Scientist Ecosystem (CoBE) developed by the Dr. Mathieu Lupien Lab; and XevaDB developed by the Dr. Benjamin Haibe-Kains Lab.

Key Highlights

cBioPortal, developed by the Pugh Lab, is an open-source software platform that links clinical and genomic data from patients with cancer across the country. This software enables clinical and research teams to easily access genomic data, integrate clinical and genomic data, and analyze the data at both the patient and cohort levels.

Computational & Bench Scientist Ecosystem (CoBE), developed by the Lupien Lab, is a web portal recommendation engine that allows scientists to quickly find or contribute software tools and bioinformatics pipelines that address analytical needs from genomics data. CoBE packages software pipelines as fully reproducible code capsules that provide consistent, preloaded environments, allowing users to quickly run any software pipeline in the CoBE database with their own data. CoBE empowers users to share the capsules used in their own publications, ensuring reproducibility of their work.

XevaDB, developed by the BHK Lab, is a database with an intuitive web interface that allows clinicians and researchers to easily access patientderived xenografts of drug response and genomic profiles. XevaDB allows for concurrent visualizations of drug response and associated molecular data such as mutation, copy number alterations, and gene expressions.