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HTS Bioinf - Bioinf Group roles

This document describes the different roles and responsibilities in the bioinformatics group.

Bioinformatics coordinator

Responsible for overall coordination of work in the group.

  • Develop a vision for the bioinformatics group and translate this into concrete projects
  • Recruit competent staff matching the needs of the group
  • Maintain overview of current and future activities, and communicate these to the group
  • Manage/supervise most major projects
  • Understand requirements, create overall plans and draft specifications
  • Assign resources
  • Follow up against goals
  • Conduct regular group meetings and one-on-one meetings with individuals in the group
  • Communicate with management
  • Bi-weekly coordination meetings with GDx unit leader
  • Monthly coordination meetings with SLD section leader and GDx unit leader
  • Participate in external projects work requiring broad overview
  • Manage external collaborations and develop relationships in the field
  • Research partners
  • Other hospitals, Norbioinf, NACG, GA4GH, etc.

Required competencies:

  • Broad overview of bioinformatics field, technologies, methods
  • Articulation and communication of vision
  • Good overall understanding of diagnostic process and role/opportunity for bioinformatics
  • General overview of the infrastructure, understanding of pipelines and variant interpretation processes
  • Project/process management (e.g. creating a work breakdown structure, overall issue management)
  • Structure/progress/quality control tracking with relevant tools
  • Knowledge of staff skills/interests and schedules
  • At home in OUS (knowledge of how it works, including how to promote/improve/use existing resources)
  • Proactive communication (for external parties & management)

Head of engineering

Responsible for creating and implementing best practice engineering vision and strategy, coaching the development team collectively and individually.

  • Oversee product development and delivery (top-level and day-to-day)
  • Define project strategy, help the group translating the stakeholder needs into requirements and technical architecture, and ultimately to products
  • Follow up work, provide guidance to the engineering team on best practices, code review, system architecture, etc., and improve development processes
  • Establish and maintain quality standards (tests, documentation, etc.)
  • Closely follow industry benchmarks and own the process of knowledge sharing
  • Define and develop the technology stack and software architecture
  • Participate in recruitment
  • Set up and support the engineering team, identify the team's needs for development and training, help them become better engineers

Required competencies:

  • Experience in operating and influencing at a strategic level
  • Knowledge and deep technical understanding of software development industry and processes
  • Leadership and management skills with the ability to optimise team performance and development

Production coordinator

Responsible for ensuring smooth production.

  • Ensure enough people are trained for production
  • Plan the production shifts and staffing (including vacation)
  • Ensure proper transfer of production duty
  • Coordinate incoming issues related to production, between the lab and the bioinformaticians
  • Be a contact person for the lab, participate often in lab standups
  • Keep track of upcoming production volume, storage space for production data, Dragen license and downtime on production infrastructure
  • Continuously identify and suggest improvements to production routines

Required competencies:

  • Deep knowledge of production procedures lab system and variant calling pipelines
  • General understanding of ELLA (e.g. generate new passwords for users, delete analysis, etc.)
  • Ability to do quick investigations (locate the logs and communicate to relevant people)
  • Good knowledge of the technology of the system
  • Knowledge of where is what; from sequencer to ELLA, how the pipelines and infrastructure are organized (configs, paths..)
  • Well-connected in the group and with lab staff
  • Understanding of the sequencing process (helpful but not required)

Production duty responsible

The detailed responsibilities of this rotating role are described in other documents, but the main ones are:

  • Run and monitor production pipelines
  • Update annotation data according to "HTS Bioinf - Update Databases"
  • Provide necessary quality and performance data when validating new versions of software or instruments

Required competencies:

  • See procedure for "Training for running pipeline"
  • Competence on pipeline and ELLA production
  • Diagnostic workflow
  • Location of logs
  • How to start and stop production
  • How to update annotation data

Production automation engineer

Responsible for ensuring smooth running and support for future development of production systems.

  • Identify opportunities for automation and develop solutions that scale production
  • Maintain the fully-automated production pipeline
  • Be main knowledge person of LIMS and lab systems

Required competencies:

  • Automation and monitoring
  • Systems integration
  • Deep knowledge of Clarity LIMS (workflow, protocol, step, etc.) and Clarity API (used for automation)
  • General understanding of the lab processes
  • Knowledge of NSC IT infrastructure

Release coordinator

Responsible for coordination of pipeline repositories releases.

  • Plan and prepare releases (parts of this work can be delegated to others)
  • Content of a specific release (issue grooming with respect to releases)
  • Versioning and tags
  • Release schedule and date
  • Deployment to production
  • Ensure CI tests run in a production-like staging environment before release
  • Communicate releases to all stakeholders
  • Ensure affected documentation is updated
  • Work with SK to improve the release process and the related paperwork ("Endringskontroll" etc.)
  • Ensure the procedures are followed for updates to production systems
  • Train others to increase redundancy

Required competencies:

  • Deep knowledge of production procedures and pipelines, the technology of the system (esp. infrastructure, interdependencies, databases, credentials needed) and version control
  • Deep knowledge of CI pipelines and staging/production infrastructure/environment
  • Trigger the various CI tests
  • Create release artifacts (vcpipe, reference data and singularity images)
  • Deploy the new pipeline and restart the services
  • Documentation writing skill
  • Ability to fill an "Endringskontroll"

System administrator

Responsible for the continuous functioning of the infrastructure.

  • Maintain and develop the infrastructure used for development and testing
  • Development servers
  • Cloud services (Gitlab, DigitalOcean, Slack, AWS)
  • Maintain production infrastructure
  • Diagnostic part of NSC
  • p22 in TSD (currently delegated to Tony)
  • General system administration of physical and virtual systems (VMs)
  • Install and maintain hardware
  • Keep systems patched and up to date
  • Monitor the system capacity (storage, compute)
  • User administration
  • Keep main file system directories clean

Required competencies:

  • System administration of Linux-based systems
  • Red Hat and package management: yum / dnf, rpm
  • Ubuntu
  • Virtualization software like VMWare and Docker/Singularity containers
  • Hardware
  • RAID arrays, LLVM / LVM - software RAID / partition management
  • Networks
  • Deep knowledge of local infrastructure
  • Operational knowledge of pipelines ecosystem
  • Programming (advanced and versatile Bash, Perl, Python)


Maintain, improve and implement new features in pipelines, and/or ELLA and other internal tools.

  • Implement new features/modules
  • Refactor existing code
  • Write good documentation
  • Follow development practices of the group. See "Development and review" procedure.
  • Create and update tests
  • CI/CD, unit testing, end-to-end / E2E testing
  • Investigate and solve bugs in production (conduct investigations)
  • Ensure that third-party software not directly related to variant calling but used in production systems is patched and up to date (operating system, Docker, Nextflow, programming languages and core libraries (JavaScript, Perl, Python, shells, scripts), in-house source code updates in Gitlab)

Required competencies:

  • vcpipe and bioinformatic analysis focus
  • Bash, Nextflow, Python, additional as needed
  • ELLA and full-stack focus
  • Backend: Python, Bash
    • Frameworks: FastAPI, Flask, Pydantic, Pytest, SQLAlchemy, Supervisor
  • Frontend: JavaScript, HTML, CSS/SCSS
    • Frameworks: CerebralJS, AngularJS
  • Technologies / platforms
  • Container systems: Docker, Singularity
  • VCS / version control system: git
  • Make
  • CI/CD automated testing / artifacts (Gitlab CI in particular)
  • Databases: PostgreSQL, SQLite3
  • Deep knowledge of systems architecture (of respective part or related tech)
  • Knowledge of bioinformatics (depends on the task - basic to very good)
  • Knowledge of data formats and standards (e.g FASTQ, BAM, BED, GFF, VCF)

Product manager (ELLA)

Manage and coordinate development and maintenance of ELLA.

  • Understand and create issues based on user needs
  • Align stakeholders around the vision of the product
  • Manage development plan (prioritize, assign and follow up issues; based on user needs, department goals and development capacity)
  • Provide user training and support, maintain user manuals
  • Manage and coordinate user testing and documentation for new releases

Required competencies:

  • Very good understanding of the domain (genetic diagnostics) and diagnostic workflows
  • Basic knowledge of our tech in systems with focus on possibilities and interconnections
  • Good overview of personnel resources
  • Ability to manage a software development project
  • Experience with testing and usability
  • Good communication and interpersonal skills

System owner / Tech lead

Responsible for a larger software system or specific repositories.

  • Keep repository and documentation clean, healthy and up to date
  • Coordinate releases together with release coordinator
  • Decide if/when owner must approve an MR
  • Keep CI tests comprehensive and green
  • Overview issues, although not responsible for them
  • Ensure redundancy in system know-how
  • Ensure that third-party software is patched and up to date. Follow development and initiate work to apply updates when necessary

Verification and Validation Responsible

Oversee verification and validation and write relevant documentation when changes are done in the unit. Relevant changes could be in IT systems, bioinformatic pipelines, infrastructure and methods.

Required competencies:

A 'Kompetanseplan' in 'Kompetanserportalen' describes the training required for the role.

Responsible role holders

Role Role holder Deputy
Bioinformatics coordinator Tony Håndstad
Head of engineering Georgios Gozadinos
Production coordinator Ying Sheng Yvan Strahm
Production automation engineer Xuyang Yuan Erik Severinsen
Release coordinator automation Xuyang Yuan Production duty responsible
Release coordinator variant calling Erik Severinsen Production duty responsible
Release coordinator annotation Ksenia Lavrichenko Production duty responsible
Release coordinator interpretation Øyvind Evju Developer ELLA
System administrator Erik Severinsen
Product manager ELLA Morten Cristoph Eike Øyvind Evju
Verification and Validation Erik Severinsen Ying in training

System owners

System System owner Deputy
Lab automation Xuyang Yuan Erik Severinsen
Variant calling Ying Sheng Sjur Urdson Gjerald
Annotation Ksenia Lavrichenko Francesco Bettella
Interpretation Øyvind Evju Georgios Gozadinos
Data sharing Tony Håndstad Francisco Luis Hernandez Sanches
Documentation Tony Håndstad Ksenia Lavrichenko

Other relevant documents