Job: Genomics IT technician/cloud engineer/workflow developer (m/f/d), Digital Health Centre, Berlin Institute of Health/Charite, Germany
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8 weeks ago by
naveed.ishaque0 wrote:

The eilslabs (http://www.eilslabs.de) has recently moved Berlin, where Prof. Roland Eils has established the Digital Health Centre on the Berlin Institute of Health in Berlin.

We are looking to rebuild our team of international computational technicians, engineers and researchers. We are hiring a number of technicians at various levels of entry to assist scientific research, build cloud infrastructure, support international efforts for standardising cancer genome analysis etc. Here we advertise technical positions, but we are also looking for researcher staff.

Official application link: https://www.charite.de/service/stellenangebot/angebot/detailinfo/cc04_bih_0719_1_3_bioinformatics_workflow_developer_mf/

Salary: Based on Öffentlichen Dienst VKA E11/E12/E13. Final figure dependant on experience. Current range of E13 is €47.9k-€71.1k.

Deadline: 17th April 2019

Duration: 3 years, with possible extension. The position is a full time position (39 hours). Part time may also be possible.

Location: Central Berlin, Germany

Who we are

The Digital Health Centre, headed by Prof. Roland Eils, conducts innovative healthcare research with a strong focus on computational methods including application and development of big-data analytical methods, artificial intelligence and deep learning. We hare leaders in international projects (Human Cell Atlas, International Cancer Genome Consortium) and European life science networks (de.NBI, ELIXIR, European Open Science Cloud). We have state-of-the-art computational resources including in-house HPC, cloud, GPGPU (2 x Nvidia DGX1) and FPGA technology. You will develop and apply portable and standardized data analysis workflows for large scale deployment on local infrastructure, and both nationally and internationally. Initially you will play a central role in updating existing cancer ‘omics workflows, followed by development of novel workflows, e.g. for regulator genomics, single cell ‘omics and liquid biopsy of numerous disease entities.

Responsibilities

The research group of Roland Eils provides a dynamic, challenging, and rewarding research environment with the support of excellent technically staff. Your responsibilities are primarily to to work closely with research bioinformaticians and other bioinformatics workflow developers, while paying attention to career development and community engagement including but not limited to the following:

  • Closely collaborate with research scientist on big data projects to implement and deploy workflows
  • Closely collaborate with other bioinformatics developers on workflow implementation and deployment
  • Standardise and improve all aspects of existing and new workflows
  • Converting existing analysis pipelines to workflow languages (i.e. CWL)
  • Achieving compliance to existing standards (e.g. Global Alliance for Genomics and Health)
  • Identify and implement use of established nomenclature and ontology databases (e.g. HGVS, HGNC, uberon)
  • provide virtualized workflows to de.NBI and other collaborative infrastructures (e.g. ELIXIR, European Open Science Cloud)
  • Updating established cancer 'omics and other workflows, e.g. conforming to new international standards (GA4GH etc) and new genome or database releases
  • Implementation of novel workflows, e.g. for regulator genomics, single cell ‘omics and liquid biopsy of numerous disease entities.

Qualifications

  • A qualification in computer science, biotechnology, cancer genomics, or similar: PhD (senior technician), Masters/diploma degree (technician) or Bachelors degree or "Ausbildung" (junior technician)
  • Experience with linux based HPC or cloud environments
  • Excellent programming proficiency especially in Java, Javascript, Python, R, Julia, WebAssembly, Groovy, bash or similar
  • Experience in designing and implementing data analysis pipelines
  • Experience with a workflow management system (e.g., Galaxy, Snakemake, Nextflow, Cromwell, Funnel)
  • Experience with reproducible development using code repositories (e.g. git, SVN) and environment management (conda, bioconda, virtualenvs)
  • Demonstrated ability to conduct well documented and reproducible analyses of high throughput data
  • Experience interacting with IT and research specialists in an academic environment
  • Fluent in English (written and spoken)

Qualifications – desirable

  • Experience working in life science research
  • Awareness of community standards driven by GA4GH and other driver projects (e.g. Human Cell Atlas, IHEC, ICGC)
  • Experience in designing and implementing data analysis pipelines for next generation sequencing or image analysis
  • Grasp of CWL, WDL or other workflow languages
  • Experience with containers and virtualisation (e.g. Docker, Singularity, OpenStack)
  • Experience with build automation (e.g. Gradle, Bazel, Dolt, Make)
  • Prior experience in working with single cell ‘omics data, liquid biopsies, or 'omics data

Contact email: Please direct all enquires via the official email link. Informal enquiries should be sent to naveed.ishaque@charite.de

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