Jobs

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. CBDBDev_P01067_HSA123442_BioApps_2022_03_03

Canada’s Michael Smith Genome Sciences Centre (GSC) is a state-of-the-art, large scale, high throughput, clinically accredited genomics and bioinformatics facility. If you have a computer science degree and experience in database programming and design—along with an interest in research science and motivation to contribute to efforts toward improving the lives of cancer patients—consider joining our team at the GSC!

The GSC’s Computational Biologist provides database planning, development and maintenance to support our core sequence pipelines. Duties include analysis, dissemination, as well as storage management and compression, of over 5Pb of internally generated sequencing data.

The position is anchored within a team of exceptional scientists, computational biologists and programmers, which collaborate directly on the development of robust, cost efficient, and competitive processes for new targeted and precision medicine analytical pipelines. By working within the GSCs bioinformatics facility, you will develop close relationships with world-renown computational and genome science technologists, cancer researchers and medical scientists; have access to one of the most robust computational and next generation genome sequencing technology facilities in Canada, all while living in one of the most beautiful, diverse and eclectic cities in the world. Your work will help to save lives and contribute to a world free from the fear of cancer.

This is an opportunity to work with highly motivated colleagues in a science-oriented, creative and dynamic environment. We offer a competitive salary, excellent benefits and significant career development opportunities. Apply now!

Phenomic (https://phenomic.ai/) is a seed stage company using machine learning (ML), deep learning and bioinformatic approaches to identify new targets to disrupt tumor stroma, with an initial focus on cancer associated fibroblasts (CAFs). The main rationale behind this focus lies in the fact that stromal signatures are associated with poor response to current immunotherapy drugs in several indications including pancreatic, colorectal, lung, breast and other cancer types. As part of the company products, we are building single cell RNA-seq and spatial transcriptomic (scRNA) analysis tools for published and proprietary human and mouse stromal cell datasets. Our tools incorporate ML and bioinformatic methods to understand current targets of interest and identify new ones.

We are looking for a co-op computational biologist/bioinformatician to join the development of our ML and bioinformatic tools.

• 3+ years of Python and Bash scripting
• Writing Snakemake or similar pipelines
• HPC computing
• Contribute code with team members using git
• Bioinformatics
• Human Clinical Genomics
• OMIM, Gnomad, ClinVar, HGMD, and other databases
• Handling and exploring VCF files
• High level communication, documentation, organizational, and time-management skills