Jobs

Join “The Laboratory for RNA-Based Lifeforms” in University of Toronto’s Donnelly Centre. Together with Dr. Artem Babaian the work will develop the state of the art for the detection and sequence analysis of RNA viruses and virus-like agents.

(Micro)Biology is undergoing a paradigm shift in our understanding of Earth’s genetic diversity. This is being driven by the widespread adoption and exponential drop in cost of DNA/RNA sequencing, with 100+ petabytes of public sequence data available today, and growing. Our lab aims to pioneer a new-generation of computational analysis techniques optimized for exabase/exabyte-scale datasets.

Recently we’ve developed an AWS-cloud backed computing architecture, Serratus (https://github.com/ababaian/serratus), which has enabled us process 5.7 million datasets (10.2 petabases) in only 11 days. This analysis revealed 130,000+ novel RNA viruses across the world, where only 15,000 were previously known in public databases. Learn more in our first Nature paper, or watch our HCLS21 talk.

Position: Software Developer III
Site: MaRS Centre, Toronto
Department: Genome Informatics
Reports To: Director, Genome Informatics and Principal Investigator
Salary: Commensurate with level of experience
Hours: 35 hours/week
Status: Full-time, Permanent

We are growing! With new projects and lots of exciting technologies, the Ontario Institute for Cancer Research (OICR) is looking for a passionate and talented Software Architect to join the Genome Informatics team to continue building cutting edge tools and infrastructures used by researchers around the globe to fight cancer.

Our open source applications handle vast amounts of data (2+ PB) and run on large compute environments. Designed and implemented by our in-house developers, we maintain a diverse set of tools and projects, from complex ETL systems to modern user interfaces. The Genome Informatics team has worked on a variety of projects including:

• ICGC-DCC (github, application) – Our most mature and well known project is a submission system comprised of an ETL pipeline and data portal coordinating cancer research on 86 projects with participants from all over the world. With ICGC-ARGO ICGC is entering a new phase with an engaging and complex set of software engineering challenges ahead of us, such as providing researchers with access to 100’s of billions of genetic variants.
• ICGC-ARGO (github, application) – The next generation and evolution of the original ICGC-DCC, this platform aims to uniformly analyze specimens from 100,000 donors with high quality clinical data in order to address outstanding questions that are vital to the quest to defeat cancer.
• Cancer Genome Collaboratory (github, website) – A compute and storage cloud operated by the team which is progressively enhanced with more tools to assist researchers running analysis pipelines.

• VirusSeq Data Portal for COVID-19 (github,application) – The goal of the CanCOGeN VirusSeq project is to sequence up to 150,000 viral samples from Canadians testing positive for COVID-19 and make the sequences and associated non-personal contextual data available for research and exploration in an open-source and open-access data portal

• Human Cancer Models Initiative (HCMI) Catalog (github, application) – A searchable catalog of cancer models.

As part of the Genome Informatics team, the successful candidate will be joining some of the above-mentioned projects, but also be contributing to Overture.bio (github, website), our suite of open-source components for big data genomic science in the cloud.

We are looking for a passionate Software Developer/Architect to join our agile development team. In this role, you will serve as a technical guiding force for multiple ongoing projects as well as be responsible for spearheading and championing technical innovation. This would be an ideal position for a solid software developer who is looking to transition towards a software architect role.

New employees who may be required to work on-site 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.

Position: Software Developer I
Site: MaRS Centre, Toronto
Department: Genome Sequence Informatics
Reports To: Manager, Infrastructure & Software Development
Salary: Commensurate with level of experience
Hours: 35 hours/week
Status: Full-time, Permanent

We are looking for a passionate software developer to join the Genome Sequence Informatics (GSI) team!

GSI designs applications to streamline and automate analysis for the Genomics program (https://genomics.oicr.on.ca), controls the data life cycle, and creates useful and dynamic reports at scale. We ensure data flows smoothly, securely, and correctly from the lab through to the clinicians and researchers who use it. Our primary languages are Java, R, Python, Javascript, MySQL, PostgreSQL, and MongoDB and we use technologies like Docker, OpenStack, Prometheus.IO, Loki, Promtail, and Univa Grid Engine, and are expanding into Cloud environments like Microsoft Azure. Many of GSI’s software projects are open-source and available on GitHub: https://github.com/oicr-gsi/ and https://github.com/miso-lims.

GSI has three sub-teams:

• Infrastructure: Includes laboratory tracking, pipeline and data management, and reporting. This team develops the open source MISO LIMS (https://miso-lims.github.io) and associated applications, workflow systems like Vidarr and Cromwell (https://cromwell.readthedocs.io) to automate and streamline data analysis, tracking, and workflow management, and maintains a suite of specialized reports for quality control, forecasting, and lab operations.
• Analysis: Bioinformatics analysis and data release. Develops the analysis techniques and pipelines used by OICR Genomics for alignment, de novo assembly, variant detection, quantification of tumour heterogeneity and purity, RNAseq analysis, variant significance prediction, structural variant calling, immune detection, cfMeDIP, and others. This team also archives data for long-term storage and releases data to collaborators and public archives.
• Cancer Genome Interpretation: Validates pipelines for accreditation, analyzes and interprets genomic data using accredited pipelines and processes, and drafts reports for clinical cases.

Software developers in GSI are enthusiastic and autonomous. As part of the team, you will be involved in all aspects of development of new applications for high-impact cancer research and clinical reporting, as well as monitoring, diagnosing, and pushing fixes to improve stability and performance of existing applications. You will develop and improve our production system within a research environment.

New employees who may be required to work on-site 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.

Job Reference No. RP_R00008_Birol Lab_2022_09_08

Summary

The Genome Sciences Centre (GSC) is a leading international organization for genomics and bioinformatics research. Our mandate is to advance knowledge in those areas, and to realize the social and economic benefits of genomics research. The Research Programmer analyzes large-scale genomics data and provides support for research projects in the Bioinformatics Technology Lab (BTL) / Genome Sciences Centre – BC Cancer through developing software, data models, analysis pipelines, and documentation. The successful candidate will work independently in a multidisciplinary environment, and participate as a project team member on specific genome research projects to develop / test code and help analyze large volumes of genomics data.

The successful applicant will be part of a team of research scientists working in a dynamic environment to primarily develop and apply data analysis algorithms and protocols to analyze genome data. You will be contributing to advancing science, cancer and genome research locally and worldwide.

The Ontario Institute for Cancer Research (OICR) is seeking a full-stack Software Developer I to join a team developing leading edge opensource applications for analyzing genomic data in cloud compute environments. The applications will be used by researchers around the world to process and interpret vast amounts of cancer genomic data and to apply this understanding to new paradigms for diagnosing and treating cancer.

The project you will work on, Dockstore (https://dockstore.org) is an open source project aimed at providing a scientific tool repository and framework for launching large-scale, cloud-based genomics analysis. Dockstore combines the Docker software container system with portable, standard-compliant workflow descriptions, to create software packages that describe their inputs, outputs, and parameterization, and can easily be combined to form higher-level workflows. This work is closely tied to, and drives adoption of international standards created as part of the Global Alliance for Genomics and Health (GA4GH)..

The MaRS Centre has a mandatory COVID-19 vaccination policy in place that requires proof of full COVID-19 vaccination or proof of a medical exemption issued pursuant to the Government of Ontario guidelines.  Accordingly, as a condition of employment, new employees who may be required to work on-site 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.

Learn more about working at OICR here.

The role will focus on a series of aims derived from a long term (American) National Institutes of Health U24 grant to operate a production Dockstore ecosystem while developing features to improve its robustness and security. You will have the opportunity to be exposed to a large set of technologies, including compute clouds, container virtualization systems, and genomic workflow technologies. In addition, there will be opportunities to improve your Java back-end and Javascript front-end development skills. As part of our development team you will be working closely with internal and external stakeholders to create an infrastructure that will have a potentially significant impact on society. In addition, you will be working closely with our collaborators at UCSC (University of California Santa Cruz, which forms part of our software development team).

Other responsibilities of the role include researching and designing new features to process new workflow languages and/or services in the Dockstore ecosystem, and supporting the integration of Dockstore into a variety of third party open source and commercial products. We will provide opportunities to conduct outreach and training.