Archive for the 'freeware' Category; python mac OSX, windows; open source software modeling environment and pde solver

CompuCell is an open source software modeling environment and pde solver. It is largely used for cellular modeling (foams, tissues, etc.), however, efforts are being made to include fluid simulation capabilities. Created in collaboration between groups at IU and Notre Dame, CompuCell provides an easy user interface for complex cellular modeling.

Integration with SBW

We have conducted a preliminary integration of CompuCell3D with Systems Biology Workbench (SBW) to link to subcellular models. As a result users can select the level of detail in their models while working within a single integrated framework.

see :


Source Code and ChangeLog

SVN Repository

To download from our repository, use your favorite svn client and download from:

Known Issues and Requirements

  • Python 2.5
  • Ubuntu users must install python-qt4
  • ———
  • Python and MAC OSX

    Python comes pre-installed on Mac OS X, but due to Apple’s release cycle, it’s often one or even two years old. The overwhelming recommendation of the « MacPython » community is to upgrade your Python by downloading and installing a newer version from the Python standard release page.

    If you are using Mac OS X 10.5, see the Leopard wiki page for detailed information.

    If you’re just curious…

    You don’t have to download anything. You can run a Python interpreter by double-clicking on Applications / Utilities / Terminal (here’s a picture), then typing « python » into the window that opens up.

    You’ll see a prompt that looks like this:

    Python 2.3.5 (#1, Mar 20 2005, 20:38:20)
    [GCC 3.3 20030304 (Apple Computer, Inc. build 1809)] on darwin
    Type "help", "copyright", "credits" or "license" for more information.

    (On Mac OS X 10.3 (Panther), it will say « Python 2.3.0 », an older version.)Try typing « 2 + 2 » and hit « Enter »:

    >>> 2 + 2

    You’ve just evaluated your first Python expression. It’s a simple environment, but good enough to work through the Python tutorial.By the way, if you download the recommended upgrade mentioned at the top of this page, the « IDLE » development environment will make working through the tutorial a bit easier.

  • ParaView is an application framework as well as a turn-key application; Modeling software OpenFOAM and ParaView ; mesh processing: generation, manipulation, conversion

    ParaView is an open source, multi-platform data analysis and visualization application. It has a client-server architecture to facilitate remote visualization of datasets

    It is an application built on top of the Visualization Tool Kit (VTK) libraries.

    The ParaView code base is designed in such a way that all of its components can be reused to quickly develop vertical applications. This flexibility allows ParaView developers to quickly develop applications.

    Input/Output and File Format

    • Supports a variety of file formats including: VTK (new and legacy, all types including parallel, ascii and binary, can read and written).
    • Various polygonal file formats including STL and BYU (by default, read only, other VTK writers can be added by writing XML description).
    • Many other file formats are supported. See ParaView Readers and ParaView Writers for a full list.

    CMake is a family of tools designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files. CMake generates native makefiles and workspaces that can be used in the compiler environment of your choice. ParaView utilizes CMake for the software compilation process.


    ParaView is used as the visualization platform for the Modeling software OpenFOAM (Open Field Operation and Manipulation).It is primarily a C++ toolbox for the customisation and extension of numerical solvers for continuum mechanics problems, including computational fluid dynamics (CFD). It comes with a growing collection of pre-written solvers applicable to a wide range of problems.

    First major general-purpose CFD package to use polyhedral cells. This functionality is a natural consequence of the hierarchical description of simulation objects.

    OpenFOAM compares favourably with the capabilities of most leading general-purpose commercial closed-source CFD packages. It relies on the user’s choice of third party pre- and post-processing utilities, and ships with:

    • a plugin (paraFoam) for visualisation of solution data and meshes in ParaView.
    • a wide range of mesh converters allowing import from a number of leading commercial packages
    • an automatic hexahedral mesher to mesh engineering configurations

    OpenFOAM was conceived as a continuum mechanics platform but is ideal for building multi-physics simulations.

    OpenCFD develop OpenFOAM in the Linux/UNIX operating system because: we believe it is the best platform for this kind of high end simulation code development and operation; Linux is efficient, robust, reliable and flexible and undergoes rapid development and improvement; Linux is open source, like OpenFOAM; Linux is very effective for parallel operation on Beowulf clusters.

    OpenFOAM is open source software so people can freely compile it on any operating system they choose. Most OpenFOAM users are running Linux, so this site offers the download of binaries for selected Linux systems.

    As the present time we are unaware of any binary distributions for Windows or MacOSX. However, ports to these operating systems have been the subject of debate on the OpenFOAM discussion site, which may provide the best source of information on the matter.

    OpenFOAM uses finite volume numerics to solve systems of partial differential equations ascribed on any 3D unstructured mesh of polyhedral cells.

    Mesh generation

    OpenFOAM applications handle unstructured meshes of mixed polyhedra with any number of faces: hexahedra, tetrahedra, degenerate cells, basically anything.

    Mesh generation is made simple by the fact that a cell is simply represented as a list of faces and a face as a list of vertices: this makes mesh handling very easy even for complex meshes with, say, embedded refinement or complex shapes near the boundary.

    OpenFOAM is supplied with the following mesh generator tools that run in parallel.

    Mesh generation tools

    blockMesh A multi-block mesh generator
    extrude2DMesh Takes 2D mesh (all faces 2 points only, no front and back faces) and creates a 3D mesh by extruding with specified thickness
    extrudeMesh Extrude mesh from existing patch (by default outwards facing normals; optional flips faces) or from patch read from file
    snappyHexMesh Automatic split hex mesher. Refines and snaps to surface

    The main mesh generators cover two extremes: snappyHexMesh, that can mesh to complex CAD surfaces; blockMesh a simple file-driven block mesh generator.

    Mesh manipulation

    OpenFOAM is supplied with several utilties that perform mesh checking and manipulation. The full list of utilties is given below

    Mesh manipulation

    attachMesh Attach topologically detached mesh using prescribed mesh modifiers
    autoPatch Divides external faces into patches based on (user supplied) feature angle
    cellSet Selects a cell set through a dictionary
    checkMesh Checks validity of a mesh
    createBaffles Makes internal faces into boundary faces. Does not duplicate points, unlike mergeOrSplitBaffles
    createPatch Utility to create patches out of selected boundary faces. Faces come either from existing patches or from a faceSet
    deformedGeom Deforms a polyMesh using a displacement field U and a scaling factor supplied as an argument
    faceSet Selects a face set through a dictionary
    flattenMesh Flattens the front and back planes of a 2D cartesian mesh
    insideCells Picks up cells with cell centre ’inside’ of surface. Requires surface to be closed and singly connected
    mergeMeshes Merge two meshes
    mergeOrSplitBaffles Detects faces that share points (baffles). Either merge them or duplicate the points
    mirrorMesh Mirrors a mesh around a given plane
    moveDynamicMesh Mesh motion and topological mesh changes utility
    moveEngineMesh Solver for moving meshes for engine calculations.
    moveMesh Solver for moving meshes
    objToVTK Read obj line (not surface!) file and convert into vtk
    pointSet Selects a point set through a dictionary
    refineMesh Utility to refine cells in multiple directions
    renumberMesh Renumbers the cell list in order to reduce the bandwidth, reading and renumbering all fields from all the time directories
    rotateMesh Rotates the mesh and fields from the direcion n1   \special {t4ht= to the direction n2   \special {t4ht=
    setSet Manipulate a cell/face/point set interactively
    setsToZones Add pointZones/faceZones/cellZones to the mesh from similar named pointSets/faceSets/cellSets
    splitMesh Splits mesh by making internal faces external. Uses attachDetach
    splitMeshRegions Splits mesh into multiple regions
    stitchMesh ’Stitches’ a mesh
    subsetMesh Selects a section of mesh based on a cellSet
    transformPoints Transforms the mesh points in the polyMesh directory according to the translate, rotate and scale options
    zipUpMesh Reads in a mesh with hanging vertices and zips up the cells to guarantee that all polyhedral cells of valid shape are closed

    Mesh motion

    OpenFOAM adopts a novel approach to mesh motion by defining it in terms of the boundary motion which is extremely robust.

    The solver need only define the the motion of the boundary and everything else will be done automatically. The open architecture of OpenFOAM solver codes allows quick and efficient implementation: mesh motion can be based on any solution variable, either local or integrated and by dynamically adjusted during the run.

    Mesh motion is also transparently integrated with top-level models: the model writer does not see the additional complexity, which is conveniently packaged within the discretisation operators.

    For examples of automated mesh motion in OpenFOAM, see Solutions

    Mesh conversion

    OpenFOAM accepts meshes generated by any of the major mesh generators and CAD systems. Listed below are converter utlities for the major commercial mesh generators. Note that it is also possible to import the meshes from most general purpose mesh generators since they will export in a format read by one of the converters.

    Mesh converters

    ansysToFoam Converts an ANSYS input mesh file, exported from I-DEAS, to OPENFOAM®format
    cfx4ToFoam Converts a CFX 4 mesh to OPENFOAM®format
    fluent3DMeshToFoam Converts a Fluent mesh to OPENFOAM®format
    fluentMeshToFoam Converts a Fluent mesh to OPENFOAM®format including multiple region and region boundary handling
    foamMeshToFluent Writes out the OPENFOAM®mesh in Fluent mesh format
    foamToStarMesh Reads an OPENFOAM®mesh and writes a PROSTAR (v4) bnd/cel/vrt format
    gambitToFoam Converts a GAMBIT mesh to OPENFOAM®format
    gmshToFoam Reads .msh file as written by Gmsh
    ideasUnvToFoam I-Deas unv format mesh conversion
    kivaToFoam Converts a KIVA grid to OPENFOAM®format
    mshToFoam Converts .msh file generated by the Adventure system
    netgenNeutralToFoam Converts neutral file format as written by Netgen v4.4
    plot3dToFoam Plot3d mesh (ascii/formatted format) converter
    polyDualMesh Calculate the dual of a polyMesh. Adheres to all the feature and patch edges
    sammToFoam Converts a STAR-CD SAMM mesh to OPENFOAM®format
    star4ToFoam Converts a STAR-CD (v4) PROSTAR mesh into OPENFOAM®format
    starToFoam Converts a STAR-CD PROSTAR mesh into OPENFOAM®format
    tetgenToFoam Converts .ele and .node and .face files, written by tetgen
    writeMeshObj For mesh debugging: writes mesh as three separate OBJ files which can be viewed with e.g. javaview

    FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

    FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

    FreeSurfer is brought to you by the Athinoula A. Martinos Center for Biomedical Imaging. Support for this research was provided in part by the National Center for Research Resources (P41-RR14075, R01 RR16594-01A1 and the NCRR BIRN Morphometric Project BIRN002, U24 RR021382), the National Institute for Neurological Disorders and Stroke (R01 NS052585-01), the National Institute of Biomedical Imaging and Bioengineering, as well as the Mental Illness and Neuroscience Discovery (MIND) Institute and is part of the National Alliance for Medical Image Computing (NA-MIC) funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

    FreeSurfer Beginners Guide

    FreeSurfer is a freely available software package developed by investigators at the Athinoula A. Martinos Center for Biomedical Imaging used for a number of procedures including:

    1. Creation of computerized models of the brain from magnetic resonance imaging (MRI) data. link
    2. Processing of functional magnetic resonance imaging (fMRI) data. link
    3. Measuring a number of morphometric properties of the brain including cortical thickness and regional volumes. link
    4. Intersubject averaging of structural and functional data using a procedure that aligns individuals based on their cortical folding patterns for optimal alignment of homologous neural regions. link

    Machine Requirements

    To run FreeSurfer, you will need either a PC running Linux or a Macintosh running OS X.

    FreeSurfer consumes a lot of processor time, memory resources and disk space, so it is recommended to run FreeSurfer on as powerful a machine as you have available. For example, at MGH we typically run Linux CentOS 4 on 2.5GHz dual processor AMD Opterons with 4 to 8 GB of DDR SDRAM, and 250GB of disk space.


    The FreeSurfer tools deal with two main types of data: volumetric data (volumes of voxels) and surface data (polygons that tile a surface). The talks and tutorials should familiarize you with FreeSurfer’s volume and surface processing streams, the recommended workflow to execute these, and many of their component tools. The tutorials also describe some of FreeSurfer’s tools for registering volumetric datasets, performing group analysis on morphology data, and integrating multi-modal output with FreeSurfer (overlaying color coded parametric maps onto the cortical surface and visualizing plotted results). After completing the tutorials, you should be able to:

    • perform surface reconstructions;
    • generate subcortical segmentations;
    • fix errors encountered during the volume or surface processing;
    • overlay functional data onto surfaces;
    • perform group analysis of structural (e.g. thickness) and functional data.

    logiciels du laboratoire Jean Kuntzmann

    Les liens qui suivent pointent vers les logiciels développés dans nos différentes équipes:

    Souvent ils utilisent des outils de developpement


    AMIRA (juil. 2007) AMIRA is an Advanced 3D Visualization and Volume Modeling.
    PPM (juil. 2007) The acronym PPM stands for Parallel Particle Mesh library. PPM is a software layer between the Message Passing Interface (MPI) and codes for simulations of physical systems using hybrid particle-mesh methods.
    Basilic (dec. 2006) Basilic est un serveur de bibliographie pour les équipes de recherche. Il automatise et facilite la diffusion des publications scientifiques sur Internet, en générant automatiquement des pages webs à partir d’une base de données.
    DCINPW (dec. 2006) Dynamic Canvas for Immersive Non-Photorealistic Walkthroughs
    Freestyle (dec. 2006) Freestyle est un logiciel permettant de faire du rendu non photoréaliste de scènes 3D à base de lignes.
    libQGLViewer (dec. 2006) libQGLViewer est une bibliothèque GPL écrite en C++, basée sur openGL et Qt, qui permet de rapidement développer des applications de visualisation 3D.
    SciPres (dec. 2006) SciPres est un système pour créer des présentations animées.
    TiffIO (dec. 2006) TiffIO est un plugin qui permet à n’importe quelle application basée sur la bibliothèque Qt de lire/écrire des images au format TIFF dans des QImages.
    VRender (dec. 2006) VRender permet de faire du rendu vectoriel de données 3D telles qu’elles apparaissent dans une fenêtre OpenGL au format Postscript, XFig (et bientôt SVG).
    X3DToolKit (dec. 2006) X3DToolKit est une bibliothèque GPL écrite en C++ qui permet de charger, d’afficher et de traiter des scènes 3D au format X3D.


    HUMANS (janv. 2007) Toolbox pour la simulation des humanoïdes
    MODULOPT (janv. 2007) librairie d’optimisation
    SICONOS (janv. 2007) plateforme pour la simulation des systèmes dynamiques non-réguliers
    GIVARO (sept. 2005) Une bibliothèque générique pour les corps finis et leurs extensions
    Simplicial Homology (oct. 2004) Un module proposé pour GAP pour le calcul de groupes d’homologies de complexes simpliciaux
    FFLAS (juil. 2004) Finite Field Linear Algebra Subroutines
    LinBox (août 2002) Une bibliothèque générique pour l’algèbre linéaire exacte
    FRIDAY (nov. 2000) Systèmes dynamiques.
    DAE (nov. 1999) Equations Différentielles Algébriques
    EQDL (nov. 1999) Systèmes et Equations Différentiels Linéaires
    LAMEX (août 1996) Systèmes dynamiques


    Life (mars 2009) une librairie pour la résolution d’équations aux dérivées partielles en 1D,2D et 3D par des méthodes de Galerkin de type h/p.
    NAUTil (mars 2009) von Neumann Analysis Utilities : routines Maple pour l’automatisation
    de l’analyse de stabilité linéaire de schémas aux différences finies.
    SPASS (mars 2009) Signal Processing for ASynchronous Systems : routines Matlab pour le l’échantillonnage non uniforme et le traitement du signal asynchrone.


    SOFA (fev. 2007) Sofa est une librairie C+ open souce pour la modélisation et la simulation de scènes mécaniques comportant des modèles très divers en interaction…


    detectors (dec. 2006) A joint comparison of affine covariant regions by LEAR, Oxford, Leuven and Prague (the test setup and the binaries.
    IPLD (dec. 2006) Interest Point Detectors & Test Sequences
    KAS (dec. 2006) Groups of adjacent contour segments: sofware for detecting Vitto’s local shape features.
    Part-Detect (dec. 2006) Scale-invariant Shape Features for Recognition of Object Categories
    Point detector (dec. 2006) an Interest Point Destector Software
    Statlearn (dec. 2006) Statlearn is a MatLab toolbox for easy manipulation of different classification methods (supervised learning) and multidimensional distributions (unsupervised learning), developed by Guillaume Bouchard.


    Géodésique (nov. 2002) Calcul de Géodésiques.


    Dassflow (janv. 2007) logiciel de simulation en hydraulique fluviale
    AGRIF (dec. 2006) Logiciel de raffinement adaptatif de maillages structurés
    Rheolef (dec. 2006) Environnement de calcul par éléments finis


    Matlab Wavelet Denoising Toolbox (mars 2008) Un ensemble de procédures (scripts) pour le débruitage de signaux bruités à
    l’aide de méthodes diverses de décomposition en ondelettes (déterministes et bayésiennes)
    sont implémentées et discutées.
    Mouvement Brownien Fractionnaire et Multifractionnaire (mars 2008) Autour des mouvements browniens fractionnaires et multifractionnaires :
    Plusieurs procédures (scripts) pour simuler une trajectoire discrétisée d’un mouvement brownien fractionnaire ou multifractionnaire et en estimer les param\`etres sont implémentées
    et/ou discutées en S-plus et/ou Matlab.
    LogiFiab (janv. 2007) LogiFiab met en oeuvre les principaux modèles probabilistes et tests statistiques pour l’évaluation de la fiabilité des logiciels.
    Smoothing Toolbox (nov. 2005) Boite a outils Matlab pour le lissage et la regression non
    Empirical Bayes Thresholding (nov. 2005) Selection de seuil pour l’estimateur des ondelettes
    par Bayes empirique
    BLISS (nov. 2005) Programme de Séparation Aveugle de Sources
    MacSurvival (dec. 1996) Implémentation de techniques d’analyse des données censurées. Unique logicile de survie sur Mac incluant des méthodes non paramétriques d’estimation lisse du taux de hasard

    U3D and matlab file exchange; Export triangulated mesh into a pdf with a 3D interactive object.


    Export triangulated mesh into a pdf with a 3D object. The matlab mesh is converted to IDTF with matlab code. The IDTF file is converted to u3d with an external binary file. The u3d file can then be embedded into a pdf with pdflatex and the movie15 package. The user can then interact with the mesh (zoom, rotate etc.) from adobe reader. The package contains demo data and example of output.

    The code of the IDTF to U3D converter can be obtained at :

    The toolbox has been tested on mac intel, linux and windows.

    To test run the script : demo_mesh2pdf.m

    MATLAB release MATLAB 7 (R14)
    Other requirements The windows version requires to install MeshLab :


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