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Software

• Software-Entwicklungen am  Weierstraß-Institute Berlin (WIAS)
• Software-Entwicklungen am Zuse-Institut Berlin (ZIB)
• Software-Entwicklungen der Arbeitsgruppe 'Mathematical Geometry Processing 'an der Freien Universität Berlin
• Software-Entwicklungen der Arbeitsgruppe 'Numerische Mathematik'an der Technischen Universität Berlin

Life Science

• Software Kurzbeschreibung (engl.) Trägereinrichtung
• DUNE Set of C++ libraries for grid-based numerical methods for partial differential equations. Provides extreme flexibility without compromising on efficiency. Runs on all relevant platforms, including large supercomputers. Available under an open-source license.
  [Sander, Gräser, Kornhuber] [A17, A2, C17, F6] FU Berlin, with Universities of Heidelberg, Freiburg, Münster, Warwick, Stuttgart, RWTH Aachen and HPC- Simulation-Software & Services, Heidelberg
• Kaskade 7 Flexible finite element toolbox based on Dune for heterogeneous systems of elliptic and parabolic PDEs and optimization problems. Includes a variety of elements, solvers, and interfaces to third- party libraries. Freely available for academic purposes.
  [Weiser, Schiela?] [A17, F9, A22] ZIB and TU Berlin
• ERDA (Edge Refinement and Data Assessment) Parameter analysis of biological network models in the logical modeling framework of R. Thomas. The parameter space of discrete models of regulatory networks defined by underlying interaction graphs is investigated and pruned using constraint-based methods, in particular, utilizing time se- ries data. Consistency of modeling assumptions and experimental observations can be rigorously checked. [Bockmayr, Siebert] [A18] FU Berlin
• FFCA (Feasibility-based Flux Coupling Analysis)
  
  F2C2 (Fast Flux Coupling Calculator) Flux coupling analysis in constraint-based models of genome-scale metabolic networks. FFCA is based on a large number of feasibility checks for linear programs. F2C2 is a refined version with improved preprocessing and a significant reduction in the number of linear programs that have to be considered.
  [Bockmayr, Siebert] [A18] FU Berlin
• BioPARKIN BioPARKIN is a software package for parameter identification in systems biology modelling. It is based on the solver LIMEX for differential-algebraic equations and the Gauss-Newton method NLSCON for nonlinear least-squares problems. BioPARKIN combines a stand-alone library written in C++ for the numerical tasks with an easy-to-use graphical user interface. The use of the SBML file format ensures compatibility with other systems biology tools. The software is available for Windows, Mac OS X, and Linux (using Python and Qt) and can de downloaded at github.
  [Röblitz] [A18] ZIB
• EMMA (Emma’s Markov Model Algorithms) Software package for the generation, validation and analysis of Markov state models from molec- ular dynamics simulation data. Published in: M. Senne, B. Trendelkamp-Schroer, A.S.J.S. Mey, C. Schütte and F. Noé: “EMMA – A software package for Markov model building and analysis”. J. Chem. Theory Comput. 8 . pp. 2223–2238 (2012).
  [Noé, Schütte] [A19] FU Berlin and ZIB
• ZIBMolPY The core of the ZIBMolPy package is an implementation of the efficient, adaptive sampling al- gorithm ZIBgridfree, designed for molecular conformation dynamics. Publication: M. Weber, Dis- sertation, FU Berlin. Meshless Methods in Conformation Dynamics, Verlag Dr. Hut, 2006, ISBN 3-89963-307-5.
  [Weber] [A19] ZIB
• SHERLOCK Software Environment for Mass Spectrometry-based Cancer Diagnosis
  [Schütte, Conrad] [A19] UNDER NDA FU
• BigDFT BigDFT is a DFT massively parallel electronic structure code (GPL license) using a wavelet basis set. Wavelets form a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation). GTH or HGH pseudopotentials are used to remove the core electrons. Thanks to our Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with the proper boundary conditions.
  [Schneider] [A20] TU Berlin, In cooperation with CEA France and Univ. Basel

Networks

• Software Kurzbeschreibung (engl.) Trägereinrichtung
• LPP Experimental system to compute optimal line systems in public transport for entire cities, including advanced features such as direct connection optimization and operational constraints. The system has a VISUM interface.
  [Grötschel, Borndörfer] [B15] ZIB
• ZET Software for evacuation simulation and analysis. Features include an editing system to transport building plans into a mathematical model, an cellular automaton based evacuation simulation with a 3D visualisation and analysis module, as well as network flow over time algorithms for optimization.
  [Skutella] [B18] TU Berlin
• SCIP Optimization Suite SCIP is currently one of the fastest non-commercial mixed integer programming (MIP) solvers. It is also a framework for constraint integer programming and branch-cut-and-price. It allows total control of the solution process and the access of detailed information down to the guts of the solver.
  [Grötschel, Koch] [B20, (D17, G1)] ZIB
• VR-OPT High-performance optimization tool for the computation of strategic passenger train rotations for a standard week including advanced features such as rotation regularity and an integrated micro-model for train composition (type, sequence, and orientation).
  [Grötschel, Borndörfer] [B22] ZIB

Production

• Software Kurzbeschreibung (engl.) Trägereinrichtung
• WIAS-HiTNIHS The software WIAS-HiTNIHS constitutes a tool for both stationary and transient simulations of heat transport in axis-symmetric technical systems that are subject to intense heating by induction or resistance heating. The simulator accounts for heat transfer by radiation through cavities, and it allows for changes in the material parameters due to the rising temperature, e.g. employing temperature-dependent laws of thermal and electrical conductivity. Moreover, one can compute so-called traveling magnetic fields and resulting Lorentz forces acting on conducting liquids.
  [Klein-O] [C9] WIAS
• WIAS-SharP The goal of this software was the development and implementation of a numerical method to describe the evolution of temperature and phase volume fractions during laser and electron beam hardening in workpieces with arbitrary geometry. The results lead to the development of the software WIAS-SHarP, which is based on the FE/FV-toolbox pdelib and already successfully used in industry.
  [Weiss, Hömberg] [C11] WIAS
• SOFTubes - Shape Optimization for Flows in Tubes SOFTubes is based on OpenFOAM and STAR-CCM+ with the objective of optimizing the shape of tubes subject to geometric constraints. The underlying state equation is the stationary Navier-Stokes system. Particular objectives of interest are uniform outflow and/or minimization of the total pressure loss. The optimization method is shape gradient based and works without parametrization of the geometry.
  [Hintermüller] [C11, C28, C31] HU Berlin, in cooperation with BMW Motoren GmbH and MathTec
• DUNE Set of C++ libraries for grid-based numerical methods for partial differential equations. Provides extreme flexibility without compromising on efficiency. Runs on all relevant platforms, including large supercomputers. Available under an open-source license.
  [Sander, Gräser, Kornhuber?] [A17, A2, C17, F6] FU Berlin, with Universities of Heidelberg, Freiburg, Münster, Warwick, Stuttgart, RWTH Aachen and HPC-Simulation-Software & Services, Heidelberg
• NLEVP NLEVP: A collection of nonlinear eigenvalue problems.
  [T. Betcke, N. J. Higham, V. Mehrmann, C. Schröder, F. Tisseur] [C29] TU Berlin
• STCSSP STCSSP: A FORTRAN 77 routine to compute a structured staircase form for a (skew-)symmetric/(skew-)symmetric pencil.
  [T. Brüll and V. Mehrmann] [C29] TU Berlin
• GEOMS GEOMS: A software package for the numerical integration of general model equations of multibody systems.
  [A. Steinbrecher] [C29] TU Berlin
• GESDA GESDA: A Software Package for the Numerical Solution of General Switched Differential- Algebraic Equations
  [L. Scholz] [C29] TU Berlin
• GENDA A Fortran77 software package for the numerical solution of General Nonlinear Differential-Algebraic equations (DAEs) of arbitrary index. Institut für Mathematik, Technische Universität Berlin (Lena Scholz), preprint number 730-02. 2002: http://www3.math.tu-berlin.de/preprints/abstracts/Report-730-2002.rdf.html
  [Kunkel, Mehrmann, Seufer] [C4] TU Berlin
• SolveDAE A MATLAB package for the numerical solution of General Nonlinear Differential-Algebraic equations,
  [P. Kunkel, V. Mehrmann, S. Seidel] [C29] TU Berlin
• BIRA Solution of large sparse quadratic eigenvalue problems featuring user specified region for eigenvalues, robust block-Arnoldi-method, implicit restarting, reliable Householder-orthogonalization, several levels of parallelism (multiple shifts), portable FORTRAN implementation; commercially used in the software CONCEPT by SFE Berlin GmbH.
  [Mehrmann] [C29] TU Berlin
• KryPy KryPy is a Python (versions 2 and 3) module for Krylov subspace methods for the solution of linear algebraic systems. This includes enhanced versions of CG, MINRES and GMRES as well as methods for the efficient solution of sequences of linear systems.
  [Liesen] [C29] TU Berlin
• PyNosh Python framework for nonlinear Schrödinger equations
  [Liesen] [C29] TU Berlin

Electronic & Photonic Devices

• Software Kurzbeschreibung (engl.) Trägereinrichtung
• ILUPACK Multilevel ILU preconditioners for general real and complex matrices as well as real and complex symmetric (Hermitian) positive definite systems. TU Berlin
• LDSL-tool LDSL-tool (Longitudinal Dynamics in Semiconductor Lasers) is a tool for the simulation and analysis of the nonlinear longitudinal dynamics in multisection semiconductor lasers and different coupled laser devices. It is based on Traveling Wave (PDE) equations describing propagation of optical fields along longitudinal direction of the laser which are nonlinearly coupled with the ordinary differential equations for carrier densities and polarization functions. The software tool is used to investigate and design laser devices that exhibit various nonlinear effects such as self-pulsations, chaos, hysteresis, mode switching, excitability, mutual synchronization, and frequency entrainment by an external modulated optical or electrical signal.
  [Radziunas, Recke, Wolfrum] [D8] WIAS
• SCIP Optimization Suite SCIP is currently one of the fastest non-commercial mixed integer programming (MIP) solvers. It is also a framework for constraint integer programming and branch-cut-and-price. It allows total control of the solution process and the access of detailed information down to the guts of the solver.
  [Grötschel, Koch] [B20, (D17, G1)] ZIB
• Contributions to pythonocc Development of a CAD /Meshing software specifically tailored for the construction and discretization of complex 3D nano-photonic device geometries. The software is based on the PythonOCC CAD/CAM/CAE development framework (which relies on the Opencascade CAD kernel). Developed extensions to the PythonOCC Framework have been submitted.
  [Schmidt-F] [D23] ZIB
• CONCEPTS Flexible and highly accurate finite element and boundary element library for static, time-harmonic and time-dependent equations in 2D and 3D with applications in electromagnetics, acoustics, optics, structural mechanics, ...
  [Schmidt-K] [D26] TU Berlin in cooperation with ETH Zurich and INRIA Bordeaux South-Ouest

Visualization

• Software Kurzbeschreibung (engl.) Trägereinrichtung
• Amira
  ZIBAmira Amira is a 3D software platform for visualizing, analyzing, and understanding spatial and spatiotemporal data coming from many types of sources. It is used in life sciences, physical sciences, material sciences, environmental sciences and engineering. A core feature is the reconstruction of geometries from image data. The software is commercially distributed by the Visualization Sciences Group (an FEI Company). ZIBAmira is an extended version of Amira. It is used as platform in many research projects at ZIB, including the Matheon F2 project, and provided to research partners of ZIB in various application domains.
  [Hege] [F2] ZIB
• LDDMM-Lib LDDMM-Lib is a stand-alone library that provides flexible shape matching based on adaptive finite-element methodology from the open source library libMesh. It has an interface to the ZIBAmira software.
  [Hege] [F2] ZIB
• SSM-Lib SSM-Lib is a library that is part of ZIBAmira and an extension to Amira. It provides a variety of functions for model-based segmentation and reconstruction from image or shape data. At its core are statistical shape and intensity models.
  [Hege] [F2] ZIB
• QuadCover 3D surface parameterization
  [Polthier] [F4, F6] FU Berlin
• DUNE Set of C++ libraries for grid-based numerical methods for partial differential equations. Provides extreme flexibility without compromising on efficiency. Runs on all relevant platforms, including large supercomputers. Available under an open-source license.
  [Sander, Gräser, Kornhuber?] [A17, A2, C17, F6] FU Berlin, with Universities of Heidelberg, Freiburg, Münster, Warwick, Stuttgart, RWTH Aachen and HPC-Simulation-Software & Services, Heidelberg
• Kaskade 7 Flexible finite element toolbox based on Dune for heterogeneous systems of elliptic and parabolic PDEs and optimization problems. Includes a variety of elements, solvers, and interfaces to third-party libraries. Freely available for academic purposes.
  [Weiser, Schiela] [A17, F9, A22] ZIB and TU Berlin
• R-package fmri http://cran.r-project.org/web/packages/fmri/ and http://www.nitrc.org/ Analysis of single subject fMRI experiments. The package implements model and signal detection or FDR. Detected signals can be visualized in several forms.
  [Polzehl] [F10] WIAS
• R-package dti http://cran.r-project.org/web/packages/dti/ and http://www.nitrc.org/ Analysis of diffusion-weighted imaging. The package enables the whole analysis chain for dMRI experiments, from accessing medical image data to modeling, adaptive smoothing, fiber tracking and 2D and 3D visualization. Models include the tensor model, Q-Ball imaging, positive definite EAP and ODF estimation, Kurtosis imaging and tensor mixture models. Adaptive smoothing is implemented on functional data in $R^3$ and on the original data in R3 times S2.
  [Polzehl] [F10] WIAS
• R-package adimpro Package for image manipulation. Used in packages fmri and dti to produce camera ready output for publications.
  [Polzehl] [F10] WIAS
• Aws4SPM Plug-in for adaptive smoothing of fMRI time series for the SPM8 Software
  [Polzehl] [F10] WIAS
• POAS4SPM
  (to be released at http://www.fil.ion.ucl.ac.uk/~smoham/) Part of the ACID toolbox for SPM. Implements adaptive smoothing of dMRI data in R3 times S2
  [Polzehl] [F10] WIAS, in cooperation with UCL
• Aws plug-in for Brainvoyager
  (under development) Adaptive segmentation for fMRI experiments. Plugin for Brainvoyager QX (http://www.brainvoyager.com/)
  [Polzehl] [F10] WIAS
• jReality 3D scene graph implemented in Java. Suitable for developing interactive mathematical experiments that run equally in multi-screen virtual reality environments and on desktops. Available under a BSD license.
  [Pinkall] [F12] TU Berlin