Ontario Institute for Cancer Research



, Ontario


Job Type:


Degree Level Required:

Bachelor's, Masters

355 days ago Apply now

Position:                     Bioinformatician II
Location:                    MaRS Centre, Toronto
Department:               Genome Sequence Informatics

Reports To:                Senior Manager
Salary:                        Commensurate with level of experience
Hours:                        35 hours/week

Job Type:                   Hybrid
Status:                        Full-time, Permanent

OICR is seeking an experienced and passionate Bioinformatician to join the Genome Sequence Informatics (GSI) team at OICR. The Bioinformatician functions in a junior to intermediate technical role that requires an individual with proven skills in both biology and computing, and who is dedicated to supporting a multi-disciplinary team of scientists, laboratory technicians, and informatics professionals.

GSI is part of the Genomics program at OICR ( and supports the sequencing teams that manage both clinical and research projects. GSI designs applications to streamline and automate analysis, control the data lifecycle, and create useful and dynamic reports at scale. We ensure that data flows smoothly, securely and correctly from the lab through to the clinicians and researchers who use it. We use languages and software tools like Java, Python, Perl, Javascript, OpenStack, Open Grid Engine, Univa, MySQL and PostgreSQL.

The main areas covered by GSI are:

  • Lab tracking: Develop the open source MISO LIMS ( augmented by other applications.
  • Pipeline/Data management: Develop and run workflow systems like Vidarr ( and Cromwell ( to automate and streamline data analysis, tracking, and workflow management.
  • Data release: Delivery of sequencing and analysis, archiving of data for long term storage and deposition of data to public archives.
  • Reporting: Maintain of a suite of specialized reports for quality control, forecasting, and lab operations, and to accompany data delivery.
  • Analysis: Development of analysis workflows to run in our pipeline system, and development of tools supporting analysis tracking and data management. Conducting project-specific analysis on sequencing data with an emphasis on cancer genomics, both for internal research projects and for collaborators.
  • Cancer Genome Interpretation: Analyze and interpret genomic data using accredited pipelines and processes for clinical purposes.

The Production Bioinformatician’s primary responsibilities are with the Analysis team, working with leading-edge sequencing data and using high-throughput production pipelines to support internal and external projects and collaborators.

The responsibilities include:

  • Performing initial stage analysis on next-generation sequencing data; transforming data from sequence to information meaningful for biologists.
  • Ensuring that data is managed efficiently, securely, and without loss or corruption through its lifecycle.
  • Providing bioinformatics support and training to end-users (research laboratory staff, remotely located collaborative users).
  • Responsibility for researching, planning, implementing, and testing bioinformatics software tools that meet the analysis needs for specific collaborative projects.
  • Development and support of protocols and workflows for standard analysis tasks.
  • Continuous interaction with the production development team to ensure that the NG sequencing software pipeline is consistently, reliably, efficiently and correctly processing data.
  • Interaction with collaborative research groups to explain next-generation sequencing capabilities and limitations, advise on experimental design, and present findings tools, techniques.
  • Work with 3rd party software vendors to characterize and resolve problems with production software systems.
  • Responsibility for documenting and communicating pipeline processes and building the team knowledge base.


  • Bachelor’s or master’s degree in related discipline with demonstrated experience in the skill set, or equivalent education or work experience required.
  • Advanced skills in Linux shell programming environment.
  • Proficiency with some Linux based scripting language (Python, Perl, etc.) required.
  • Competence with general purpose software development languages such as C, C++, Java preferred.
  • Experience with statistical and graphical software packages (R, Matlab) and associated bioinformatics libraries.
  • Must have excellent communications and interpersonal skills.
  • Willingness to be accessible and respond to production pipeline issues outside of normal working hours.
  • Experience supporting a high availability production software environment.
  • Experience providing end-user software support, diagnosing and resolving end-user issues.
  • Experience working in a multidisciplinary team environment.
  • Experience working with data from the Illumina, Nanopore or other sequencing platforms is highly desirable.
Additional Information:

New employees who may be required to work at OICR offices are required to be fully vaccinated for COVID-19 subject to the duty to accommodate on the basis of protected grounds pursuant to the Ontario Human Rights Code.

Fully vaccinated is defined as having received all of the required doses of a Health Canada approved vaccine and having received the final dose at least 14 days before your employment start date. 

As described above, the requirement to be fully vaccinated is subject to the Ontario Human Rights Code. If the candidate is unable to receive the COVID-19 vaccine for a reason protected by the Code, requests for accommodation from the vaccine policy will be assessed on a case-by-case basis.  

To learn more about working at OICR, visit our career page.

OICR is a collaborative, not-for-profit research institute accelerating the development of new cancer research discoveries for patients around the world while maximizing the economic benefit of this research for the people of Ontario. We are dedicated professionals who bring expertise to each of our roles. We are looking for individuals who share our values of excellence, innovation, collaboration, impact, responsibility and community.

Launched in December 2005, OICR is an independent institute funded by the Government of Ontario through the Ministry of Colleges and Universities.

For more information about OICR, please visit the website at

CLOSING DATE:       Until Filled

OICR is committed to fostering a climate of equity, diversity, inclusion, and accessibility. This commitment is central to, and mutually supportive of, our research excellence mandate. We welcome and respect the diversity of all members of our community and we support an inclusive culture for all. We welcome all applicants, and encourage applications from racialized persons, Indigenous Peoples, women, persons with disabilities, LGBTQ2S persons, and others who may contribute to furthering a diversity of ideas within our community. OICR is committed to fair assessment of a candidate’s abilities, and consideration for diversity of thought, method, and experience. Providing an accessible workplace and recruitment process is important to us, as described in our Accessibility Plan (  Should you require accommodation during any stage in the recruitment process, please complete the form at the bottom of page received related to accommodation will be handled confidentially.  

The Ontario Institute for Cancer Research thanks all applicants. However, only those under consideration will be contacted.

Resume Format: If you elect to apply, you will need a text or HTML version of your resume so that you can cut and paste it into the application box provided. Before you submit the completed application, you will be asked to attach one or two files to your application. Please attach your resume as a .pdf or .doc file.


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