Research Software Engineer – Kemmeren Group

The Kemmeren group is looking for an enthusiastic, highly motivated research software engineer who excels in a stimulating, multi-disciplinary research environment and can play a central role in improving operational stability and scalability of our data analyses platforms.

Tasks and responsibilities

The candidate will play a significant role in further development of our existing genomics infrastructure by implementing best practices and improving technical designs to ensure platform stability at higher scalability. You will work in close collaboration with the computational PhDs and post-docs, as well as with bioinformaticians and IT-staff in the Kemmeren group and other entities in the organization we interact with.

Specific tasks include:

  • Solve complex problems at scale in teams, where you are the expert on software architecture best practices and technical designs.
  • Advisory role in technical decisions to improve research software engineering, sustainable development and operational stability.
  • Participate in research software lifecycle phases: refining requirements, (re-)designing solutions, improving interfaces, integrating with existing architectures.
  • Build scalable, highly available, and flexible omics data management system components using high-performance programming frameworks that support cloud technology.
  • Redesign and implement database schemas using SQL and optimize queries for improved performance and scalability.

Profile

We expect a highly motivated, pro-active candidate with a bachelor or master degree in software engineering or computer science with experience or a proven interest in research software development. Experience in the field of genomics/bioinformatics is desirable. Excellent technical and programming skills in Java or other modern programming language is required and knowledge of Linux, Bash, R and cloud environments is highly preferred. A good understanding of relational database engines like PostgreSQL and code development fundamentals, including object-oriented design, data structures and algorithm design are required. The candidate should have good communication skills in Dutch and English and be a flexible team player in a dynamic and diverse research environment.

Our job offer

We offer a fulltime position (36 hours a week). You will initially be appointed for the duration of one year, with a possible extension. You will be working in a very stimulating and cross-disciplinary research environment, combining cutting-edge research with state-of-the-art information technology platforms and compute environments. Your gross monthly salary will depend on experience and background, with a maximum of €5.473,- per month (scale 55 or 60 depending on qualifications and expertise), with 8,33% gross monthly salary holiday allowance and 8,33% end-of-year bonus. The Princess Máxima Center operates according to the collective labour agreement ‘cao algemene ziekenhuizen’.

Organisation

The Princess Máxima Center for Pediatric Oncology is a research hospital concentrating healthcare, research and education of pediatric cancer in a single location in Utrecht. The institute aims to provide the highest level of care for all children with cancer and has the ambition to cure all children of cancer and improve quality of life. The center brings together the best possible care and scientific research, creating a unique interdisciplinary institute for pediatric oncology in Europe.

The candidate will be part of the Big Data Core at the Princess Máxima Center. This unit is responsible for performing and developing bioinformatic data analyses regarding our institute-wide biobanking and clinical genomics activities. The Big Data Core is at the forefront of using next-generation sequencing technologies in research including exome sequencing (WES), whole-genome sequencing (WGS) and RNA-seq based analyses for all patients as well as DNA methylation-based classification of brain tumors. We have extensive experience with implementing novel technologies in a mixed diagnostic and research setting as well as coordinating bioinformatics infrastructures such as High-Performance and Cloud computing, workflow management systems, data sharing and collaboration facilities.

Project

In the coming years, the Máxima will continue to invest in the biobank as part of its strategic theme. The focus here is on understanding the genetic basis of childhood cancers and relevance for clinical care as well as how differences in genetic make-up impact quality of life. We aim to collect DNA data and clinical data for at least 2,500 childhood cancer patients and make these accessible in the cloud for international collaboration. By combining this data with data from our international partners within the Innovative Therapies for Children with Cancer (ITCC) Big Data consortium and other international cancer centers, we expect to analyze approximately 7,500 to 10,000 childhood cancers. Combining these data across multiple centers not only aids in understanding and treating common childhood cancers but will in particular increase our knowledge and treatment options for very rare cancer types. Since data on childhood cancers is distributed over different childhood cancer centers worldwide, providing standardized and harmonized analyses is extremely challenging. This is however essential to compare childhood cancers and reach the same conclusion, regardless of the software and infrastructure used. Within this larger theme, we are looking for a candidate who can help us improve the design and implementation of our existing analysis and data sharing platforms so that we can scale up to our international ambitions while maintaining operational sustainability and scalability.

Contact

Are you our new colleague? We are looking forward to meeting you! You can apply directly by clicking on the orange button on this page. This vacancy will close on February 25th 2024. For more information about this position, or to arrange an informal chat, please contact Dr. Patrick Kemmeren. Patrick will be happy to tell you more!

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