- Ontario Institute for Cancer Research
- Toronto, ON, Canada
- Job Type:
- Degree Level Required:
- Apply Now
The Ontario Institute for Cancer Research (OICR) is seeking a talented Bioinformatician to join the Data Curation and Bioinformatics team under the Data Coordination Centre (DCC) of the International Cancer Genome Consortium (ICGC) Accelerating Research in Genomic Oncology (ARGO) (https://icgc-argo.org/). To ensure the success of reaching ARGO’s ambitious goal of uniformly analyzing the genomes of more than 100,000 participants and linking these data to high-quality clinical information, the Software Engineering group led by Dr. Yung is tasked to build robust and scalable solutions used by the DCC and Regional Data Processing Centres (RDPCs) for data management and analysis. The candidate will join our efforts by contributing to developing bioinformatics analytic pipelines, exploring and integrating open source data resources, supporting external collaborators including ARGO members and cancer researchers, and internal team members such as business analysts and software engineers.
We are looking for a talented individual with a passion for bioinformatics in computational cancer genomics. If you are passionate about the field and want to become part of a team building cutting-edge solutions from the ground up, just get in touch.
- Develop scalable, portable and reproducible computational workflows to perform uniform analyses;
- Develop technical plan and implement tools for data quality control, validation and reporting;
- Perform routine workflow execution, monitoring and debugging for ARGO RDPC in the Collaboratory OpenStack environment;
- Perform benchmarking tests to evaluate different solutions and suggest optimizations;
- Develop fully automated workflows for routine data handling processes, such as data transfer from EGA to ICGC data repository;
- Participate code review collaboratively with peers to improve code quality;
- Explore public biological databases and open source bioinformatics tools, suggest integration approaches and build prototype to evaluate/fine-tune integration plan;
- Interact with business analysts to assist the translation of bioinformatics needs into software functional requirements and specifications;
- Provide technical support to ICGC ARGO program members resolving data submission issues and other ARGO RDPC members to ensure smooth data processing;
- Provide helpdesk support for external users with wide range of requests including data accessibility, data download and portal functionality etc;
- Contribute to preparing and maintaining documentation for user guides, SOPs and data processing pipelines;
- Maintain and update ARGO dictionary and metadata schemas to enhance data validation, and support for new data types and data elements;
- Other assigned scripting and data handling tasks.
- Undergraduate degree or higher in bioinformatics, genomics, computational biology or computer sciences with significant bioinformatics experience;
- Extensive programming experience with Python or other languages, preferably in large-scale projects;
- Experience with bioinformatics resources, databases, tools and common standard formats;
- Working experience in analyzing large genomics datasets (raw sequencing data, gene expression, germline and somatic mutational events, copy number variants, methylation, etc.);
- Knowledge of software development best practices, eg, modular design with clean decoupling, source code version control, unit test, continuous integration etc;
- Knowledge of or experience using existing scientific workflow systems, such as CWL / WDL / Nextflow / Snakemake etc is an asset;
- Experience with user support is an asset;
- An interest in cancer research and knowledge of cancer genomics and biology/genetics;
- Experience in designing relational database schema and good knowledge of big data No-SQL solutions (e.g. Elasticsearch, MongoDB) is an asset;
- Be highly self-motivated and detail-oriented;
- Strong verbal and written communication skills.