Essential Oncology Software for Research

Meet the 2022-2023 Selected Software’s


A software tool to link clinical and genomic data from patients with cancer across the country

cBioPortal is an open-source software platform that enables clinical and research to easily access and use genomic data, integrate clinical and genomic data, and analyze and visualize the data at both patient and cohort levels.

The Pugh Lab operates and is one of the NIH-funded developers of the platform. is a local instance of the cBioportal software hosted at University Health Network, Princess Margaret Cancer Centre, which CDI will support.

Pugh Lab, 2022

Visit the software application here:


Computational & Bench Scientist Ecosystem (CoBE)

Aiming to transition CoBE from its current beta phase into a production-level software product. Key focuses include improving the user experience in anticipation of an increasing user base in 2023

CoBE is a web portal recommendation engine allowing scientists to rapidly find or contribute software tools and bioinformatic pipelines that address the most pressing analytical needs from genomics data. CoBE addresses the distinct needs of two types of users, the “bench scientists” and the “computational scientists”.

CoBE packages software pipelines as fully reproducible code capsules that provide consistent pre-loaded 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 in their work.

Lupien Lab, 2022

Visit the software application here:


Increasing the value of XevaDB in the Princess Margaret community by expanding the database with added patient samples and ensuring that data is easily accessible to clinicians and researchers

With the rise of in vivo cancer models derived from patient tumors, multiple pharmacogenomic studies used patient-derived xenografts (PDX) to investigate the relationship between molecular features and drug response. However, the experimental designs used to generate these datasets lack a standard format to store both the metadata and multimodal genomic and pharmacological profiles

To address this issue, the team developed XevaDB, a database of PDX drug response and genomic profiles with an intuitive web interface. XevaDB allows for concurrent visualizations of drug response and associated molecular data such as mutation, copy number alterations, and gene expressions.

The BHK Lab, 2022

Visit the software application here:

Thank you to everyone who applied for CDI’s Essential Oncology Software for Research, 2022-2023 period. Miss this cycle? We encourage you to apply next year!

Program Details

We are excited to announce an open call to support Essential Oncology Software for Research.

CDI recognizes that software is critical to modern scientific research, advancing medical discoveries while providing a framework for reproducibility and transparency. Princess Margaret (PM) Research and Clinical labs have developed software packages, libraries, and applications that have become essential tools for research.

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 bolster the use of PM-developed software for research, CDI is seeking applications for software-centered projects requiring support that are essential to biomedical research within PM.


  • The software solution must be in active use
  • Developed and/or maintained by groups within PM
  • Have already demonstrated impact and show need and/or potential for continued improvement and growth

Key dates

  • May 1, 2022 – Applications open
  • Jun 1, 2022 – Applications close
  • Jul 1, 2022 – Earliest notification of decision (subject to change)
  • Aug 1, 2022 – Earliest start date (subject to change)
  • Mar 31, 2023 – End of program


CDI is looking to support three (3) applications with CDI funds to be used towards up to 30% FTE of a software developer. Funding support will be from Aug 1, 2022 to Mar 31, 2023 with the possibility for renewal for another year dependent on deliverables, performance and budget allocation.


Selected software teams will be asked to present their work 2-3 times during the funding period to the CDI team and keep documentation of changes being made to the software. Teams will also be asked to complete a close-out report in March 2023 showing their progress and impact on users.

Application process

The application window for the 2022-2023 cycle is now closed. We encourage you to come back and apply next year!

Applications will be reviewed by the CDI team based on the following criteria:

  1. Alignment with CDI program (for more detail, please visit the home page)
  2. Demonstrated active use and the potential for broad impact across research programs/labs
  3. Developed and/or maintained by PM Research and/or Clinical labs
  4. Potential for continued improvement and growth, i.e., scalable architecture and development roadmap

Testimonials from 2021 teams

The CDI team was pleasant, welcoming, and accommodating. We appreciated the team’s ongoing support and feedback for both our project and others. – Segway, 2021

The CDI team is very collaborative and helped in providing the required resources and help to get started with the Keycloak ​Integration for user authorization and authentication. – PharmacoDB, 2021

It was a positive experience working with CDI team members. We would like to convey thanks to our CDI team member Mickey. Additionally, thanks to our project manager Sophia for keeping track of our project updates as well as Tran and Benjamin for coordinating the project. –, 2021

Contact us

If you have any questions, you can reach us here at