1-3 Bioinformatics workflow developer (m/f)

Employer
Charité – Universitätsmedizin Berlin
Location
10117, Berlin (DE)
Salary
E13
Posted
April 05 2019
Ref
CC04-BIH-07.19
Discipline
Health Sciences
Position Type
Full Time
Organization Type
Academia
Job Type
Other

DIE CHARITÉ – UNIVERSITÄTSMEDIZIN BERLIN
is a joint medical faculty, which serves both Freie Universität Berlin and Humboldt Universität zu Berlin. As one of the largest university hospitals in Europe with an important history, it plays a leading role in research, teaching and clinical care. The Charité university hospital has also made a name for itself as a modern business with certifications in the medical, clinical and management fields.

1-3 Bioinformatics workflow developer (m/f)

Berlin Institute of Health
Charité Campus Mitte

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.

Your area of responsibility
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.

Your profile

  • A PhD in computer science, biotechnology, cancer genomics, or similar OR relevant Masters degree with 2+ years working in life science research
  • Experience with linux based HPC or cloud environments
  • Excellent programming proficiency especially in Java, Javascript, Python, R, Julia or bash
  • Experience in designing and implementing data analysis pipelines for next generation sequencing or image analysis
  • Experience with a workflow management system (e.g., Galaxy, Snakemake, Nextflow, Cromwell, Funnel)
  • Awareness of community standards driven by GA4GH and other driver projects (e.g. Human Cell Atlas, IHEC, ICGC)
  • 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

  • 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 cancer genomics data

Ref. No.
CC04-BIH-07.19

Start
Immediately

Length of employment
3 years

Working Time
39 hrs/Week

Pay Scale
E13

Acc. to collective agreement TVöD VKA-K

Employees are grouped into pay scales according to their qualifications and personal requirements. You can find our collective bargaining agreements (Tarifverträge) here: https://www.charite.de/en/careers/

Please send your application quoting the reference numer until 17.04.2019 to:

Charité - Universitätsmedizin Berlin
naveed.ishaque@charite.de

Please only send documents electronically

For further information please contact Mr. Naveed Ishaque, naveed.ishaque@charite.de +49 (0)30 450 543096

DIE CHARITÉ – UNIVERSITÄTSMEDIZIN BERLIN
trifft ihre Personalentscheidungen nach Eignung, Befähigung und fachlicher Leistung. Gleich­zeitig wird eine Erhöhung des Anteils von Frauen in Führungs­positionen angestrebt und dies bei gleich­wertiger Qualifikation im Rahmen der rechtlichen Möglich­keiten berück­sichtigt. Ebenso ausdrück­lich erwünscht sind Bewerbungen von Menschen mit Migrations­hintergrund. Schwer­behinderte Bewerbe­rinnen und Bewerber werden bei gleicher Quali­fika­tion bevorzugt. Ein poli­zei­liches Führungs­zeugnis, gege­benen­falls ein erweitertes Führungs­zeugnis, ist vorzulegen. Eventuell anfallende Reise­kosten können nicht erstattet werden.

Data protection notice: Charité points out that personal data is stored and processed as part of the application process in different areas of Charité (e.g. faculty, staff committee, human resources department). Furthermore, the data may be transferred or processed within the group as well as in locations outside the group (e.g. authorities) to protect legitimate interests. By applying, you agree to our data protection regulations and terms of use, which you can find here.

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