Senior Application Specialist, CanDIG

Institution/Company:
University Health Network
Location:
Toronto, ON, Canada
Job Type:
  • Staff
Degree Level Required:
Bachelor's
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Senior Application Specialist, CanDIG

Genomics and health data volumes are exploding. These rapidly expanding pools of data have the possibility of making entirely new types of health research and clinical decision-making possible, but only if the consented data is available for researchers to analyze, and for clinicians to study while protecting participants’ privacy.

CanDIG (https://distributedgenomics.ca) is a national project connecting Canada’s health research data, making the data available for federated analyses while respecting institutional and provincial needs to protect their data and their patients privacy.

As a driver project for the Global Alliance for Genomics and Health (https://ga4gh.org), we are part of an international community of peers tackling these problems together, often for the first time. Combining modern tools in novel ways, we are tackling the particular problems of genomics and health data (i.e. massive, complex, data sets of many quite different data types) all with very strict privacy needs.

After an initial prototyping phase, CanDIG is moving in to production and developing a scalable, API-driven backend for genomic and clinical/phenotypic data for its sites. As this is developed, we will be building privacy preserving federated analyses methods on top of that foundation.

All of our work is open source, and we collaborate widely with teams across Canada and internationally. Our team brings together experts from a variety of disciplines including biology, bioinformatics, genomics, high performance computing, data architecture, and software development.

We are looking for a passionate candidate to jump right into hands-on operations and testing of current and future versions of the CanDIG stack, working jointly with our development team to create and run solutions facilitating project operation both internal and production environments. This role requires a strong level of autonomy and understanding of your domain of expertise.

Responsibilities:

• Design and implement solutions for deployment, monitoring, alerting, backups;
• Perform System administration (Linux) and operations;
• Perform Daily monitoring, administration, and troubleshooting of HPC systems;
• Support end users in a scientific research environment;
• Deploy and maintain bioinformatics tools on a distributed file system;
• Design and implement those solutions with minimal supervision, independently seeking input from relevant teammates or collaborators the constraints/requirements and proposing design decisions based on that input
• Own the health and operation of internal and production environment operation;
• Work with other sites across the country on designing and implementing best-practices for operations and monitoring;
• Contribute to technical documentation;
• Troubleshoot issues - correctness or performance - on any layer of the technology stack (db, application, software);
• Participate with development team and help automate test deployment and moving test deployments into production;
• Respectfully review other teammates’ infrastructure code, and incorporating respectful code reviews into your own work;
• Work with health research projects to help them ingest data;
• (Optional) eventually represent CanDIG at collaboration and standards-setting meetings

Qualifications:

Qualifications:

• Excellent communication and teamwork skills;
• Demonstrated ability to work both independently and in a team
• Demonstrated ability to collaborate with external partners
• Demonstrated ability to build and ship tools that others can build upon
• Willingness to learn what is needed for the task at hand
• Willingness to improve the team’s tools and processes
• Extensive experience with Linux operating systems and automation (e.g. bash, scripting);
• Proficiency with cluster schedulers such as SGE, Slurm, Torque, etc.
• Experience deploying and operating software in a team environment, including understanding of modern development lifecycles;
• Practical experience with version control tools (such as git and GitHub);
• Experience with virtualization technologies;
• Experience in documenting and writing tests for infrastructure code, and using CI/CD pipelines with those tests
• Enough experience in Python to be able to read and understand infrastructure or glue code written idiomatically in that language
• Strong collaboration skills to work with internal team members and external collaborators.
• Ability to manage time between multiple priorities

If you have experience with or are interested in learning any of these that would be great:

• Monitoring of web applications
• Familiarity with authorization of web applications;
• Experience handling genomics or clinical data
• OpenID Connect knowledge
• HL7/FHIR data model for clinical/phenotypic data
• Experience with 12-factor app or microservice architectures
• Docker compose, Terraform, Ansible or similar for deployment
• Experience working in a distributed team
• Privacy-oriented mindset or experience
• Experience with bioinformatics or health data
• Demonstrated experience writing code relevant to backend services
• Experience with database modeling and designing
• OpenID Connect knowledge
• HL7/FHIR data model for clinical/phenotypic data
• Experience with 12-factor app or microservice architectures
• Docker compose, Terraform, Ansible or similar for deployment
• Experience working in a distributed team
• Privacy-oriented mindset or experience
• Experience with bioinformatics or health data
• Demonstrated experience writing code relevant to backend services
• Experience with database modeling and designing