Jörgen Brandt

Personal information

Jörgen Brandt studied Information Technology and Networked Systems at HTW Berlin and Computer Science at Technische Universität Berlin with a focus on intelligent systems.

Since 2013 he is a member of the group for Knowledge Management in Bioinformatics at Humboldt University with scalable workflow languages as his primary research focus.

Jörgen Brandt is funded by the EU project BiobankCloud.


  • Research interests

    In many scientific areas, e.g., bioinformatics, the increase of data volume as well as workflow complexity necessitates workflow languages taylored towards parallelism and software integration.

    While data-parallel dataflow systems like Hadoop, Spark, or Flink can scale to a large number of nodes, scientific worklfow systems like KNIME or Galaxy integrate arbitrary software, including command line tools or libraries with R or Python interfaces.

    How general can a workflow language that focuses on parallelism and integration be? Can it host conditionals, compound data structures, and unbouned iteration? How should such workflows be composed from smaller parts?

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  • projects

    Open source projects

    Cuneiform is a workflow specification language which makes it easy to integrate heterogeneous tools and libraries and exploit data parallelism. Users do not have to create heavy-weight wrappers for establised tools or to reimplement them. Instead, they apply their existing software to partitioned data. Using the Hi-WAY application master Cuneiform can be executed on Hadoop YARN which makes it suitable for large scale data analysis.

    Cuneiform comes in the form of a functional programming language with a Foreign Function Interface (FFI) that lets users create functions in any suitable scripting language and apply these functions in a uniform way.

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  • publications

    Publications

    Brandt, J., Bux, M. and Leser, U. (2015). Cuneiform: A Functional Language for Large Scale Scientific Data Analysis. Algorithms and Systems for MapReduce and Beyond (BeyondMR2015). Brussels, Belgium.

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Programming Languages

  • Erlang
  • Java
  • C/C++
  • Matlab/Octave
  • Common Lisp
  • Python
  • R

Association and funding

BiobankCloud - Your PaaS for Biobanking

SOAMED

Humboldt-Universität zu Berlin