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Welcome to the Software Project Scientific Computing WS 2014/15


Registration: Prior registration in either Campus Management OR KVV des Fachbereichs is required.
If you have problems registering, contact katja.geiger[at]
Kickoff meeting: Friday 17.10.2014 at 10:00 in R126 of Arnimallee 6; further schedule to be discussed at first meeting


Lecturer: Frank Noé, Christoph Wehmeyer
Language: English
SWS:4 ; LP/Credits: 10
Students: MSc Mathematics or Computer Science
Requirements: see below


Date Time Location Lecturer
Fridays 10:00 Arnimallee 6, R126 (1st floor) Noé or Wehmeyer
Meeting schedule to be discussed at first meeting


Up to 10 master students of computer science and mathematics will collaborate on a software development project from the realm of scientific computing. We will specify the desired features and behavior of the software to be developed depending on the size and composition of the group - a typical project will include generation and analysis of numerical/simulation data as well as data management and storage. To meet the different backgrounds of mathematicians and computer scientists, the project will include aspects of both numerics (such as simulation aspects) as well as pure informatics (such as data processing, database design and development, software architecture design).
We will meet once a week to discuss progress and problems. Students will self-organize (with our assistance) in terms of dividing work and presenting results.


  • All students are required to have basic training in programming, be familiar with at least one of the languages (python, C, C++, Java). Matlab is not sufficient.
  • For computer science students, this module is a "Softwareprojekt", and they have to fulfill the corresponding requirements.
  • For mathematics students this module is a "Forschungsprojekt". Mathematics students should have gone through Coma I, II and Numerics I.

Scientific Background

A software development project will be selected that is relevant for applications in molecular dynamics or the simulation of cellular processes, i.e. biophysics / scientific computing in the life sciences. Knowledge in these areas is helpful but not necessary.

Software Aspects

  • Programming languages: The API is requested to be in Python. The underlying library can be developed in Python, C/C++ or Java (to be decided by the project group). If a web interface is available, additional languages might be involved, such as PHP.
  • Students will practice continuous integration, software design and git repository usage.
  • Community software tools such as github or gitlab will be used for software planning, development and issue management.
  • Open source software development for the scientific community

Credit Requirements

  • Active participation (documented by contributions / commits to code and development and regular participation / presentation in weekly meetings)
  • Final presentation of results and contributions
  • Submission of a written report


Name Consultation Hour Mail
Frank Noé appointment by email. Arnimallee 6, R213 frank.noe[at]
Christoph Wehmeyer Tue 14-15h. Arnimallee 6, R212a christoph.wehmeyer[at]

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