IT specialist in Cryogenic electron microscopy core facility

Job offer

IOCB Prague is a world-leading scientific institution dedicated to chemical and biological research. At IOCB, there is a strong emphasis on the translation of results from basic research into applications.

The cryogenic electron microscopy (cryo-EM) core facility studies 3D structure of proteins and their complexes using single particle analysis (SPA). The cryo-EM core facility thus closely cooperates with the IOCB groups in the field of structural biology and biochemistry. The team provides expertise in the field of SPA sample preparation and characterization, and SPA data collection and analysis. IOCB hosts state-of-the-art cryo-EM instrumentation for ultrahigh-resolution SPA analysis for the purposes of medicinal chemistry. In collaboration with the high-performance computing group (HPCg), we provide an environment for cryo-EM data processing and analysis at the local parallel computing cluster (400 CPU nodes, 87 GPU nodes, ~3 PBs of storage space and 1 PB of scratches).

The successful candidate will be a key and valued member of the cryo-EM core facility and will closely collaborate with both the HPCg and the IOCB IT department (ITS). The candidate’s main duty will be to deploy, configure, test, and maintain cryo-EM related software on the local hardware. The deployment strategies will be designed in collaboration with HPCg and ITS. The candidate will then be responsible for the administration and monitoring of the installed cryo-EM software. The candidate will help to develop local cryo-EM pipelines towards automation. The candidate will be in charge of writing and updating documentation of the cryo-EM software environment. Additionally, the candidate will be attending operational meetings, providing statistics and metrics for the running cryo-EM software, and presenting and reporting on developments.

The candidate will be in close contact with the local scientific users, including helping new users to familiarize themselves with the software environment, and discussing changes and updates to the cryo-EM software environment to adapt it to the needs of the scientists.

The candidate will benefit from a stimulating environment with top-tier research scientists, from access to edge computing hardware, from training and experience on HPC infrastructures, and from the possibility to improve their knowledge in the HPC ecosystem. This all in a flexible and motivating environment in our worldwide recognized research institution.

Responsibilities:

• Installation, configuration, testing, and maintenance of cryo-EM related software (CryoSPARC, RELION, SBGrid, Globus data transfer, EMhub, individual cryo-EM software packages, etc.)
• Cryo-EM software administration and monitoring
• Preparation and updating of software documentation
• Adaptation of the cryo-EM related software environment to better fit the requirements of our scientists.
• Proactively improving the Cryo-EM software environment

Required:

• Advanced level Linux (Our current distribution is Rocky 9)
• Advanced level on installation of software (package managers, compilation from sources, minor patching)
• Knowledge in HPC infrastructures (including compilers, MPI, HPC tools), training will be provided with the specifics of our cluster
• Ability to maintain and support complex research software
• Scripting/programming in bash and Python programming languages
• Capacity to communicate and interact with end users
• Fluency in technical English, written and oral

Desirable:

• Experience in one or more of the following: Spack, EasyBuild, CMake, OpenMPI, Ansible, NextFlow
• Experience in scientific computing support
• Experience with infrastructure automation/monitoring tools (e.g., Ansible, Pika)
• A methodical and accurate approach to work with attention to detail and a willingness to adapt, continuously learn, and innovate

We offer:

• Competitive financial remuneration
• Support in training
• 5 weeks of vacation plus 4 personal leave days
• Health insurance and full benefits package incl. contribution to supplementary pension insurance and contribution to sports/culture/leisure time, meal subsidy
• Meals subsidy
• Financial support for parents with small children
• State-of-the-art instrumentation portfolio

Additional information:

• Full-time employment contract
• Fixed-term contract initially for 1 year with anticipated extension
• The position is available immediately

How to apply:

• The application should consist of a cover letter (max. one page) describing your motivation, interests and experience, a curriculum vitae, and contact information of at least two references.
• Applications will be reviewed and considered until the position is filled.