August 3, 2018

Open source in open science: Accelerating cancer research (Part 2)

Part 2 of Open source software

Find part 1 here: Open source in open science: Accelerating cancer research


OICR researchers have contributed to major open source projects available to the global research community in order to accelerate cancer research. Click the link below to read about more of OICR’s open source software projects.

Continue reading – Open source in open science: Accelerating cancer research (Part 2)

August 1, 2018

Open source in open science: Accelerating cancer research (Part 1)

Open source

In the effort to bring better disease prevention and treatment to patients faster, cancer researchers are thinking more creatively about ways to conduct high-quality scientific research. Concerns about the quality, efficiency and reproducibility of research have motivated the open science movement – the growing trend of making data, methods, software and research more accessible to the greater scientific community.

Open source software (OSS), a major component of open science, enables research groups to reduce redundant efforts in software engineering by sharing software code and methods. In addition to improving efficiency, OSS promotes high-quality research by enabling collaboration, and helps make research easier to reproduce by making it more transparent.

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May 23, 2018

OICR’s Cancer Genome Collaboratory wins 2018 OpenStack Superuser award for contributions to the cancer research community

Vincent Ferretti's lab at work.

Based on popular vote and review by the Superuser Editorial Advisory Board, OICR’s Cancer Genome Collaboratory team has won the 2018 OpenStack Vancouver Summit Superuser Award. The Award recognizes OICR’s use of OpenStack, an open-source software platform for cloud computing, to enable cancer research worldwide. Previous winners of the Superuser Award include AT&T, CERN and Comcast.

“We’re proud to be recognized by the greater research community that we support,” Vincent Ferretti, Director and Senior Principal Investigator, Genome Informatics at OICR, says. “OpenStack has helped us contribute to the cancer research community in Ontario, across Canada and internationally.”

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November 2, 2017

Novel approach yields four robust biomarkers for breast cancer drug response

Dr. Benjamin Haibe-Kains and Zhaleh Safikhani pose for a photo

Biomarkers that can help predict a patient’s response to a given drug are central to testing new therapies in clinical trials as well as selecting which drugs to use in the clinic. Some of the biomarkers in use today rely on the overall expression of a given gene to predict if a drug will be of benefit. While these types of biomarkers have aided cancer research and treatment, a group led by Dr. Benjamin Haibe-Kains recently published research that is ushering in a new class of biomarkers – those based on gene isoforms (the different expression of the same gene within an individual). This work opens the door to more precise biomarkers.

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October 4, 2017

New software uses machine learning to identify mutations in tumours without reference tissue samples 

DNA sequence

One of the main steps in analyzing cancer genomic data is to find somatic mutations, which are non-hereditary changes in DNA that may give rise to cancer. To identify these mutations, researchers will often sequence the genome of a patient’s tumour as well as the genome of their normal tissue and compare the results. But what if normal tissue samples aren’t available?

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February 13, 2017

International collaboration cooks up powerful new software: MISO

LIMS system

Keeping track of samples and organizing their associated data is a crucial part of the research process. Like many labs around the world, those at OICR were using a commercially available Laboratory Information Management System (LIMS) to perform this task. However, the researchers using it found that this tool placed far too many constraints on their work. So what did they do? They built their own in partnership with the Earlham Institute (EI) in the U.K. This collaboration has resulted in powerful, flexible and open source software called MISO (Managing Information for Sequencing Operations).

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October 18, 2016

Reactome releases 10,000th annotated human protein, a major milestone that will benefit research community

Reactome - Graphic announcing the 10,000th human protein annotated

Open source tools like Wikipedia and Google Maps help us get things done faster in our daily lives. In the same way, researchers rely on a variety of open source tools to help them make discoveries faster. Reactome (www.reactome.org) is one such tool. Researchers use it because it relates human genes, proteins and other biomolecules to the biological pathways and processes in which they participate, helping to facilitate new cancer research breakthroughs. Earlier this month Reactome reached a major milestone when it released its 10,000th annotated human protein to the research community. We spoke to OICR’s Dr. Robin Haw, who is Project Manager and Outreach Coordinator at Reactome, about the history of the project, the importance of this particular milestone and where the project is headed next.

Continue reading – Reactome releases 10,000th annotated human protein, a major milestone that will benefit research community