January 9, 2017

Pan-Canadian research team uncovers ‘signature’ to reduce overtreatment of prostate cancer

Dr. Paul Boutros

A team of researchers and clinician-scientists from across Canada have discovered a signature of 41 mutations that are common in prostate cancer and will help to prevent patients with non-aggressive disease from being overtreated. Dr. Paul Boutros, a Principal Investigator in OICR’s Informatics and Bio-computing Program and Co-Lead of the Canadian Prostate Cancer Genome Network (CPC-GENE), answered a few questions about how the signature was developed and its potential impact on patients.

Continue reading – Pan-Canadian research team uncovers ‘signature’ to reduce overtreatment of prostate cancer

October 26, 2016

TorBUG continues tonight with speaker Dr. Laura Hug from the University of Waterloo

Torbug - Lecture illustration

The Toronto Bioinformatics User Group (TorBUG) continues this evening with another session of leading-edge bioinformatics topics and speakers. TorBUG sessions encourage learning, sharing and networking with colleagues in bioinformatics. Anyone who is interested is welcome to attend.

Continue reading – TorBUG continues tonight with speaker Dr. Laura Hug from the University of Waterloo

October 25, 2016

From our Annual Report: Constructing the cloud

Illustration showing clouds

OICR’s reputation as leader in managing and analyzing big data has grown over the past year as the Institute has worked with private and public partners to bring more genomic and health data to the cloud.

Continue reading – From our Annual Report: Constructing the cloud

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

September 15, 2016

Dr. Paul Bourtos talks genomics and prostate cancer research

Dr. Paul Boutros, Principal Investigator in Informatics and Bio-computing at OICR, spoke to our partners at Prostate Cancer Canada/Movember Canada about the role of genomics and informatics in prostate cancer research. Boutros also spoke about the CPC-GENE project – the largest study of prostate cancer genomics in the world.

September 15, 2016

Canadian government makes big investment in big data research

OICR's server room

On September 13 the Government of Canada, through Genome Canada, made a $4 million investment in Canadian big data research to help improve real world challenges such as infectious disease outbreaks, managing food crops and combating cancer.

Of the 16 projects funded across Canada, three are based at OICR. Led by OICR Principal Investigators Drs. Paul Boutros, Vincent Ferretti, Jared Simpson and Lincoln Stein (Stein is also OICR’s Interim Scientific Director and leader of the Institute’s Informatics and Biocomputing Program), the projects are developing ways to make genomics and health data more manageable, securely accessible and easily understood. Together these projects will help to facilitate cancer research and assist in the adoption of more precision medicine. As well, they have applications in other fields of genomics research beyond cancer, such as agriculture and energy.

Continue reading – Canadian government makes big investment in big data research

August 23, 2016

OICR Software Engineering Club August session now online

A talk given for the Ontario Institute for Cancer Research’s Software Engineering Club on PGMLab (Probabilistic Graphical Model Lab) and developing web applications for Celery. Javascript web technologies such as React, Redux, Immutable.js, ECMAScript 6 (ES6) are discussed. Python technologies such as Klein and Celery for asynchronous task queueing are also discussed.

August 9, 2016

OICR’s Software Engineering Club goes global

SEC-Image

Software powers an increasingly large portion of our lives, from the phones in our hands to the computers we work at to the cars we drive. The engineering expertise behind all these tools has, unsurprisingly, become a hot commodity.

In cancer research software engineering is particularly important because the efficiencies and improvements that software engineers can find in fields such as data management can help researchers collaborate, work faster and take on more difficult challenges.

Continue reading – OICR’s Software Engineering Club goes global

July 8, 2016

Bioinformatics.ca is keeping Canadian bioinformaticians at the top of their game

A bioinformatics.ca class.

Since 1999, the Canadian Bioinformatics Workshop series has been training the next generation of Canadian bioinformaticians and helping current bioinformaticians keep their skills up to date. This year’s series is well underway with a summer session of classes in Toronto and Vancouver recently wrapped and another session set to launch in the fall. The bioinformatics.ca workshop series is funded by registration fees paid by participants, led by OICR’s Francis Ouellette and facilitated by staff at OICR, including Ann Meyer, Manager, Knowledge and Research Exchange. We spoke to Ann about the series, why it is necessary and what the next steps for bioinformatics.ca will be.

Continue reading – Bioinformatics.ca is keeping Canadian bioinformaticians at the top of their game

June 28, 2016

OICR’s Dr. Clare Jeon discusses how the discovery of protein signatures could lead to cheaper, easier diagnostic tests for prostate cancer

Dr. Clare JeonResearchers at the Ontario Institute for Cancer Research, University Health Network and Eastern Virginia Medical School, in a paper published today in the journal Nature Communications, have identified protein signatures in urine that can accurately diagnose aggressive prostate cancer. The signatures could be used to develop a test for prostate cancer that uses a patient’s urine sample to determine whether he has prostate cancer and another test that could identify how aggressive the disease is. This would help to replace more invasive tests such as PSA test and biopsy, which also have high rates of over-diagnosis and in many cases lead to over-treatment.

Continue reading – OICR’s Dr. Clare Jeon discusses how the discovery of protein signatures could lead to cheaper, easier diagnostic tests for prostate cancer

June 16, 2016

OICR-developed software helping track Zika in Brazil

Field Laboratory tracking Zika
Photo: University of Birmingham

Scientists from the University of Birmingham in the U.K. have established a mobile DNA sequencing lab in Brazil to help that country track the spread of the Zika virus. The lab, based inside a minibus, is travelling through the areas of Brazil that have been most affected. A central part of the technology they are using is the small, USB-powered MinION genome sequencer. OICR’s Dr. Jared Simpson, an Investigator in the Informatics and Bio-computing Program, developed the software used to sequence samples on the device.

Read the news release: Mobile laboratories help track Zika spread across Brazil

Related: Tracking Ebola with portable sequencers: Could this technology be the key monitoring the spread of Zika?

June 14, 2016

Extreme Streams: The What, How and Why of Observables

Observables are great for building UIs and RxJS is an amazing implementation of them. Despite the library’s awesome power, it’s relatively underutilized mostly due to it being “hard”. This talk gives a high level overview of “what” observables are, “how” you use them, and “why” they are useful, through a basic implementation and a real world example (searching reddit for cute animals).