High Performance Computing (HPC) specialist

High Performance Computing (HPC) specialist

Published Deadline Location
15 Sep 12 Oct Nijmegen

Job description

Radboudumc aims to be leading in personalized healthcare. The department of genetics in Nijmegen (in collaboration with the department of clinical genetics in Maastricht UMC) offers comprehensive DNA testing for thousands of patients with various medical conditions, on a yearly basis. The department is well known for applying cutting-edge technologies to continuously improve patient diagnostics and research into rare and common diseases. The DNA data that are generated are typically large and complex and therefore have high compute and storage demands. Several high-performance compute (HPC) clusters are currently being used for storage and analysis of these datasets.

The HPC environment at the Department of Genetics currently has a 6 petabyte storage cluster that is connected to 52 compute nodes, and is the central analysis platform for all genetic data. Among others this cluster enables the timely analysis for urgent genetic diagnostics and as such is absolutely essential for patient healthcare. In addition, the HPC environment is central to many translational research projects that investigate the utility of novel genetics technologies for implementation in patient diagnostics. For example, the HPC is one of central analysis nodes for the European Solve-Rare Diseases project. As such, there are high demands on the HPC environment in terms of performance and availability. An additional, smaller HPC environment is available at the MaastrichtUMC and serves as a backup system for the HPC in Nijmegen.

The department of internal medicine has recently acquired a cloud-based Linux environment that runs open source bioinformatics software, like R, BWA-MEM, GATK4, IMPUTE2, STAR, MACS2, QIIME2, PLINK etc. The researchers work on big datasets generated using clinical trials and patient cohorts which include whole genome sequencing, transcriptome, microbiome, epigenome, metabolic and phenotypic data. This platform will be crucial not only to centralize, process and analyze the raw data but also to share safely (sensitive data and has to be managed (FAIR), with security and privacy (GDPR) regulations) the processed data with collaborators outside the institute, country and continent. The final size will be somewhere around 150 to 200 TB which has to be completely accessible on reasonable terms and for longer periods.

Maintenance and management of these HPC systems requires general Linux and network knowledge, but also specific expertise on HPC hardware and software relevant for HPC computation and storage of large amounts of data. Besides the operational management both departments are looking for technical expertise for the development of long-term HPC infrastructure strategies that fit the needs of both departments.

Tasks and responsibilities:
Performing and monitoring of maintenance of the HPC systems and other relevant compute systems:
  • User support: account maintenance, software installations, (OS) updates and upgrades, technical support for users.
  • Management of the process of hardware maintenance monitoring, which are outsourced to external parties.
  • Technical troubleshooting and performance monitoring.
  • Management and creation of documentation for the use and maintenance of the HPCs.
  • Consulting on SLAs en contracts related to HPCs.
  • Translating requirements from biomedical users into technical hardware/software solutions.
  • Consulting and support with technical designs for future HPC infrastructure.
  • Help with organization and coordination of the above-mentioned tasks.
  • Communication and coordination with the hospital ICT department and HPC suppliers.

Specifications

Radboud University Medical Center (Radboudumc)

Requirements

We are looking for a enthusiastic new colleague with:
  • Extensive knowledge of Linux/Unix based operating systems.
  • Knowledge and experience with HPCs and HPC networks.
  • Knowledge and experience with HPCs middleware for monitoring and maintenance of HPCs.
  • Knowledge and experience with HPC hardware.
  • Affinity with distributed computing and storage solutions.
  • Applied university/university level education in an ICT related area, or equivalent.
  • Able to communicate with HPC users as well as management.
  • Preferably organizational experience at operational and tactical level.
  • Preferably experience with DevOps.

Conditions of employment

Fixed-term contract: 1 year with a possible extension.

Working at Radboud university medical center means that you are ahead of the curve and working together on the healthcare of the future. But there is more. Our secondary terms of employment are impressive. These are fully tailored to you thanks to our Employment Conditions Selection Model. At Radboud university medical center, you will be given trust, and you will take the responsibility to handle everything together. We provide annual courses, both professional and personal.
  • In addition to your monthly salary and an annual vacation allowance of 8%, you will receive an end-of-year bonus of 8.3%.
  • If you work irregular hours, you will receive an allowance.
  • As a full-time employee (36 hours per week), you are entitled to approximately 168 vacation hours (over 23 days) per year.
  • Radboud university medical center pays 70% of the pension premium. You pay the rest of the premium with your gross salary.
  • You get a discount on health insurance as well: you can take advantage of two group health insurance plans. UMC Zorgverzekering and CZ collectief.
In addition to our terms of employment, we also offer employees various other attractive facilities, such as childcare and sports facilities. Want to learn more? Take a look at the CAO UMC.

Employer

Radboudumc

The department of Genetics performs polyclinical treatment and diagnostics of heritable diseases and is one of the largest department in genetics in Europe. Research groups in the department of genetics perform high impact research on the genetics of heritable disorders such as cancer, deafness, blindness, intellectual disabilities and developmental disorders.

The division of Genome Diagnostics aims to be a frontrunner genetic testing. Therefore, they use novel data-intensive genetic technologies in order to offer the best possible diagnostics for patients. These data-intensive techniques require the development of dedicated software, automation and data management. An international team of 18 bioinformaticians and ICT developers is responsible for development, maintenance and support for these analyses at a quality level that is required for use in patient care. As HPC specialist you will play an essential role in this and are expected to pro-actively identify areas for possible improvements.

Department of internal medicine
The scientific research of the department of Internal Medicine complements basic science with translational and clinical research. As a department we are focused on the patient groups of infectious diseases, vascular damage, mitochondrial disorders and rare cancers. This department is one of the frontrunners with unique capabilities in conducting large-scale multi-omics studies both in population-based as well as patient cohorts.These studies are extremely crucial to identify therapeutic targets, which will then be followed up by clinical trials to evaluate the beneficial effects in patients.

To carry out these integrative studies, along with clinicians and biologists, a team of 8 bioinformaticians are involved in data analyses and management. As HPC specialist you will play an essential role in supporting these researchers in conducting these analyses as well as in data storage and management.

Radboudumc
Radboud university medical center is a university medical center for patient care, scientific research, and education in Nijmegen. Radboud university medical center strives to be at the forefront of shaping the healthcare of the future. We do this in a person-centered and innovative way, and in close collaboration with our network. We want to have a significant impact on healthcare. We want to improve with each passing day, continuously working towards better healthcare, research, and education. And gaining a better understanding of how diseases arise and how we can prevent, treat, and cure them, day in and day out. This way, every patient always receives the best healthcare, now and in the future. Because that is why we do what we do.

Read more about our strategy and what working at Radboud university medical center means. Our colleagues would be happy to tell you about it. #weareradboudumc

Additional information

All additional information about the vacancy can be obtained from Dr. Christian Gilissen, head of bioinformatics, department of genetics via +31 24 366 89 40 or from Dr. Vinod Kumar, PI, department of internal medicine.

Specifications

  • IT
  • Health
  • max. 36 hours per week
  • €2911—€4615 per month
  • University graduate
  • 145105-P786113-1

Employer

Radboud University Medical Center (Radboudumc)

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Location

Geert Grooteplein-Zuid 10, 6525 GA, Nijmegen

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Application procedure

All additional information about the vacancy can be obtained from Dr. Christian Gilissen, head of bioinformatics, department of genetics via +31 24 366 89 40 or from Dr. Vinod Kumar, PI, department of internal medicine.

Application procedure

Application procedure

All additional information about the vacancy can be obtained from Dr. Christian Gilissen, head of bioinformatics, department of genetics via +31 24 366 89 40 or from Dr. Vinod Kumar, PI, department of internal medicine.

Make sure to apply no later than 12 Oct 2021 23:59 (Europe/Amsterdam).