Freie Universität Berlin - Fachbereich Mathematik und Informatik - Institut für Informatik AG Algorithmische Bioinformatik
Scientific Researcher (m/f/d) (subject to authorization)
limited to 30.06.2024
Entgeltgruppe 13 TV-L FU
reference code: FONDA-WiMi-2020
We are offering a PhD position in the research field FONDA (DFG-SFB): https://fonda.hu-berlin.de. - Within the DFG-SFB-project A2 (see description on the given website) the PhD student will mainly work on developing cost models for the adaptation of DAWs according to DADE patterns, adapting algorithmic components in the SeqAn library (www.seqan.de) and developing (reference based) compression techniques. A possible title for a PhD thesis would be “Making algorithmic components for sequence analysis amenable for self-configuring, genomic data analysis workflows”. The PhD student will investigate how to generalize algorithmic components for sequence analysis to make them easily adaptable for varying data access patterns and computational infrastructure. Based on the cost models she/he will also investigate which components should be chosen to optimize performance. Given the variety of sequence analysis components, the PhD student will choose a smaller set of suitable components for generalization, which also involves choosing between different algorithms that perform better in a given setting of data access pattern and computational infrastructure. Those components are then employed in a metagenomics workflow. The position is subject to the grant of funding by DFG.
MSc or Diploma in Computer Science or Bioinformatics
good general programming skills
excellent C++ skills
familiarity with bioinformatics sequence analysis
knowledge of workflow engines like Nextflow and Snakemake
How to apply:
All applications quoting the reference code should be directed preferably electronically in one PDF-file to: Prof. Dr. Knut Reinert: email@example.com
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Freie Universität Berlin
Fachbereich Mathematik und Informatik
Institut für Informatik
AG Algorithmische Bioinformatik
Herrn Prof. Dr. Knut Reinert
14195 Berlin (Dahlem)
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Freie Universität Berlin is an equal opportunity employer.