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Heidelberg University
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Open Call project, 2021Systems biology parameter estimation GUI

Total developer time: 2 months

Contact person: Dr. Sven Sahle, Bioquant, COS

Outline

The group has developed a user friendly tool for editing and simulating spatio-temporal models based on PDEs in systems biology: Spatial Model Editor.

They have also implemented ad-hoc scripts to perform parameter estimation by comparing simulations to measured fluorescence imaging data. The performance, maintainability and packaging of these scripts was improved in a previous small scale SSC development project (Systems biology simulation).

The goal of this project is to extend this functionality to more general use cases, and integrate it into the user-friendly graphical user interface.

SSC Role

  • Refactor and expand existing Python implementation
  • Prototype the user interface in close collaboration with research group and users of existing software
  • Integrate this functionality into the C++/Qt GUI code

Results

  • Parameter fitting implemented in latest 1.3.0 release

  • Show full screen mode

    Parameter optimization

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