Ledig stilling på Universitetet i Oslo

Blindern og Urbygningen (Foto: Wikimedia og Colourbox)
Blindern og Urbygningen (Foto: Wikimedia og Colourbox)

Position in scientific computing infrastructure

Deadline: 10.05.2021

Universitetet i Oslo

The University of Oslo is Norway’s oldest and highest ranked educational and research institution, with 28 000 students and 7000 employees. With its broad range of academic disciplines and internationally recognised research communities, UiO is an important contributor to society.

Centre for Molecular Medicine Norway (NCMM) was established in 2008 and is the Norwegian node in the Nordic EMBL Partnership for Molecular Medicine. NCMM is a joint venture between the University of Oslo, Health Region South-East and the Research Council of Norway. NCMM has altogether 11 research groups. The overall objective of NCMM is to conduct cutting edge research in molecular medicine and biotechnology. NCMM focuses on precision medicine and systems technologies with expertise in computational biology, genome medicine, as well as chemical and structural biology.

About the position

A 3-year full-time position is aimed at those who want to work at the intersection of information technology, precision medicine, and computational biology research at the Centre for Molecular Medicine Norway (NCMM), University of Oslo. The main tasks of this position are the development and maintenance of the scientific computing infrastructure and scientific computing support at NCMM.

The position entails development and maintenance of the NCMM local high-performance computing (HPC) and data storage infrastructure. Furthermore, the successful candidate will provide support to NCMM scientists to utilize the USIT HPC facilities and the Services for Sensitive Data (TSD) in collaboration with the Department for Research Services at USIT. NCMM also collaborates with the Norwegian Elixir node. The position includes advanced IT-based research support at NCMM, up to a level of installing data analysis pipelines, setting up specialized databases, moving pipelines between infrastructures (such as different HPC and cloud-computing platforms), and organizing large scale storage and advanced front-ends to visualize research results and make them publicly available. Participation in writing the IT sections of research grants is expected, as is taking part in the planning and procurement of research eInfrastructure for NCMM. The position does not cover basic IT support (e.g. login, laptop operations), but requires coordination between the basic IT services and scientific computing services at NCMM.

The NCMM IT team includes three other employees and the infrastructure currently consists of approximately 150 desktop and scientific instrument computers, 12 Linux servers that serve a growing number of virtual machines for HPC and Life Science based applications, one Petabyte of server storage capacity, two gigabit grade Ethernet wired networks (lab production and academic network), as well as relevant printing and WiFi (Eduroam) facilities. The IT infrastructure serves over one hundred local scientists, as well as external scientific collaborators.

The Department for Research Infrastructure is located in the Division of IT in Research. USIT is responsible for the operations, development and user support for IT solutions and services at the University of Oslo (UiO). USIT is one of Norway’s largest public IT environments with 200+ employees. USIT works with a broad range of future oriented technologies across a large set of interesting problems.

More information

Detailed work description

The selected candidate will be, solely or as part of the IT team, responsible for:

  • Participating in capacity planning to ensure that the NCMM IT infrastructure can accommodate the scientific computing requirements of the scientists.
  • Hardware/software installation
  • Information security according to UiO policies (technical measures, policies)
  • Deployment of scientific computing software from source code or binary forms on a number of high-performance computing Linux servers. The deployment often involves efficiently automating the software deployment process.
  • Maintenance and adaptation of complex software pipelines (in Perl, Python and C/C++) that contain an increasing number of software dependencies to function properly.
  • Documenting the scientific computing environment both in terms of the number/type of applications, their versions with the goal to make the IT infrastructure easier to use by the NCMM scientists.
  • Interacting both with the Life Science and IT personnel. Frequent interaction with the NCMM life scientists is required in order to obtain a good understanding of their scientific domain and help them use the facilities in the most efficient manner.
  • Participating in the NCMM IT committee.

Qualification requirements

  • Bachelor’s degree in Computer Science or a combination of Computer Science/ Bioinformatics. Documented alternative experience can replace this formal requirement. A Master’s or PhD degree within the field will be an advantage.
  • At least 3 years of documented previous experience in hardware/software installation for scientific computing environment.
  • At least 3 years of documented previous exposure in an international R&D environment.
  • Good knowledge of Python 2.x/3.x, C/C++ and Perl (5.x/6.x) programming. Ability to install from source and troubleshoot scientific computing packages on Linux and Windows servers.
  • Good knowledge of Bash shell scripting.
  • Good knowledge of version control (svn/git), gdb, and other scripting language debugging tools is needed.
  • Knowledge of containers (eg, Docker, Singularity) for scientific computing infrastructures.
  • Knowledge of Cfengine Ansible and DevOps methodologies for configuration management and pipeline deployment automation
  • Good knowledge of SQL and the MariaDB/MySQL/Postgres RDBMS environments is important.
  • Intermediate knowledge of Linux server (RHEL, CentOS) administration: yum package management, web server and LVM administration, qemu/kvm virtualization, ability to use kickstart to automate Linux workstation and server deployments, NFS server administration.
  • Intermediate knowledge of network management.
  • Ability to communicate with non-technical users and help life scientists to use complex infrastructures.
  • Good interpersonal skills and command of the English language are essential.
  • Good time management skills and ability to work under pressure to meet deadlines.

Preferred additional skills

  • Knowledge of SLURM and exposure to supercomputing queue/ batch system environments to assist scientists to use National and European supercomputing facilities will be an advantage.
  • Exposure to genomics, transcriptomics, chemoinformatics and/or structural biology (in particular CryoEM) scientific applications is considered an advantage.

We offer

  • The position is for three years and posted as a “senior engineer” (SKO 1181) or an “head engineer” (SKO 1087), and the hired person will get a position according to the experience and qualifications held. For a senior engineer there is a much higher expectation to the ability to perform major tasks independently, and also the possibility to lead smaller projects. The salary level will be for SKO 1181 within the start range of 618 600 NOK to 744 60 NOK, while SKO 1087 will have a range of 575 600 NOK to 630 500 NOK.
  • Attractive welfare benefits and a generous pension agreement, in addition to Oslo’s family-friendly environment with its rich opportunities for culture and outdoor activities

How to apply

The application must include:

  • Cover letter statement of motivation
  • CV (summarizing education, positions and academic work)
  • Copies of educational certificates (academic transcripts only)
  • Documentation of English proficiency (if applicable)
  • List of reference persons: 2-3 references (name, relation to candidate, e-mail and phone number)

The application with attachments must be delivered in our recruiting system.

Formal regulations

Interviews with the best qualified candidates will be arranged.

According to the Norwegian Freedom of Information Act (Offentleglova) information about the applicant may be included in the public applicant list, also in cases where the applicant has requested non-disclosure.

Inclusion and diversity are a strength. The University of Oslo has a personnel policy objective of achieving a

balanced gender composition. We also want to have employees with diverse expertise, combinations of subjects, life experience and perspectives. We will make adjustments for employees who require this.

If there are qualified applicants with special needs, gaps in their CVs or immigrant backgrounds, we will invite at least one applicant in each of these groups to an interview.

Contact information

For more information about the position, please contact the NCMM Director Janna Saarela

For questions relating to the administrative aspects of the application, please contact Nina Modahl.

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