Collaborative Research Center 1456

Open Source Software

Members of the CRC already use and actively contribute to the following Open Source projects as part of their research

Current projects:

  • Berkeley Advanced Reconstruction Toolbox for computational MRI (M. Uecker, main author) [Zenodo]
  • Netgen/NGSolve high performance finite element library (C. Lehrenfeld) [Homepage]
  • ProxToolbox nonlinear optimization toolbox (R. Luke, main author) [Homepage]
  • GROMACS molecular dynamics project (H. Grubmüller and B. L. de Groot) [Homepage]
  • Transport R package for optimal transport (B. Schmitzer) [Homepage]
  • Otinference R package for inference for optimal transport (A. Munk) [Homepage]
  • MultiScaleOT numerical optimal transport library (B. Schmitzer, main author) [Github]
  • regpy Python package for inverse problems (T. Hohage, C. Lehrenfeld, C. Rügge, M.Uecker) [Github]
  • HoloTomoToolbox Matlab toolbox for holographic tomography (T. Salditt) [Github]
  • Snip - Digital Labbook (M. Osterhoff) [Gitlab]
  • NeuralPredictors, a library for predicting neuronal responses (F. Sinz) [Github]
  • A library for computing Most Exciting Images for neurons (F. Sinz) [Github]
  • NNFabrik a library for automating large scale model training for neuroscience and beyond (F. Sinz) [Github]
  • ART-MOKE: Simulation and Analysis Tools for Angle-Resolved Transverse Magneto-Optical Kerr Effect Spectroscopy (M. Jansen) [Dataverse]
  • De novo Structural Ensemble Determination from Single Molecule X-ray Scattering using a Bayesian Approach (H. Grubmüller) [Gitlab]
  • Linearized optimal transport toolbox for Python (B. Schmitzer) [Gitlab]
  • MultiMatch package for colocalization analysis of chain-like structures (G. Nies) [Gitlab]
  • SimSpec (A. Kehl, H. Wiechers, M. Bennati and Y. Pokern) [Dataverse]
  • Sensorium Competition for benchmarking predictive models of the brain (A. Ecker, F. Sinz) [Homepage, Github]
  • MuSink (G. Mordant, T. Staudt) [Gitlab]

Former projects:

  • DataJoint framework for scientific databases and data pipelines (A. Ecker) [Homepage]
  • FDRSeg R package for estimation of step functions (H. Li, main author) [Homepage]