Software Engineer

The Department of Medical Epidemiology and Biostatistics (MEB) is among the largest departments of epidemiology in Europe with special focus on increasing our knowledge of the aetiology of different diseases. Our department consists of researchers, doctoral students, biostatisticians, data collectors and database administrators as well as administrative personnel, in total some 250 staff. The department is situated at campus Solna. Further information can be found at ki.se/meb

Research Group

The research group of Cancer Genomics at MEB is headed by professor Henrik Grönberg and has a translational focus, with the goal to pursue clinically relevant research questions.

The group is currently conducting large studies in prostate cancer where genomic profiling is used to address tumor grading, prognostication at diagnosis and optimizing treatment in the metastatic setting. The research group is currently responsible for targeted sequencing in a clinical trial, where the tumor profile is used for randomization of colorectal cancer patients. During Q1 2018, the division will also enable live profiling of circulating tumor DNA in metastatic prostate cancer in a clinical trial setting. The Cancer Genomics group is part of a larger research environment with 20-25 persons focused on different aspects of prostate cancer.

Duties

The candidate software engineer will work within a core team consisting of four lab engineers, two bioinformaticians and one cancer researcher (Johan Lindberg) with a supervisory role. The bioinformaticians include one MSc performing routine data analysis and one experienced PhD developing data analysis pipelines in a high performance computing environment. The team works in close collaboration with Clinical Genomics, ScilifeLab Stockholm and is partly located at SciLifeLab. Clinical Genomics hosts a larger team of 10 bioinformaticians, working primarily with sequencing data from various diseases in translational projects.

The candidate will work alongside current informatics staff to engineer new analysis tools, and to improve the computational analysis pipeline. Typical tasks include:

- Software engineering of computational pipelines
- Adapting existing bioinformatics tools to function within pipelines
- Implementing novel cancer genome analysis tools

Entry requirements

- Minimum bachelor's degree in computer science, software engineering, or equivalent
- Sound knowledge of computer science and software engineering fundamentals
- Experience in Python programming
- Experience with Linux command-line programming / Bash
- Knowledge of basic statistics (statistical tests, distributions, probabilities)
- Curiosity and willingness to learn the scientific topic

Bases of assessment

The following attributes and skills will provide an advantage in the assessment:

- Experience with high performance computing (e.g. use of SLURM)
- Experience in R programming
- Experience in front-end development
- Experience with databases (Relational/NoSQL)
- Experience with Perl programming
- Experience with Python programming
- Formal training in genomics / fundamentals of molecular biology

Application process
The application is to be submitted on the MyNetwork recruitment system.

At Karolinska Institutet a 6-month trial period is required for all permanent appointments.

Karolinska Institutet is one of the world’s leading medical universities. Its vision is to significantly contribute to the improvement of human health. Karolinska Institutet accounts for the single largest share of all academic medical research conducted in Sweden and offers the country’s broadest range of education in medicine and health sciences. The Nobel Assembly at Karolinska Institutet selects the Nobel laureates in Physiology or Medicine.
Pursuant to the regulations of the Swedish National Archives, applications are kept on file for two years after the appointment has gained legal force. The regulations do not apply to attachments that have been printed or otherwise published.
Karolinska Institutet strives to provide a workplace that has approximately the same number of women and men, is free of discrimination and offers equal opportunity to everyone.

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