Changes between Version 6 and Version 7 of WikiStart


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Timestamp:
Oct 12, 2016, 4:56:17 PM (10 years ago)
Author:
henrik
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  • WikiStart

    v6 v7  
    1 = Welcome to the Organism/Tissue Simulator software page =
     1= Welcome to the Organism-Tissue Simulator software page =
    22
    3 The Organism/Tissue Simulator is a C++ software for simulating biological systems. It
     3The Organism-Tissue Simulator is a C++ software for simulating biological systems. It
    44mainly focuses on systems with multiple cells/compartments, and includes
    55biochemical as well as mechanical and cell proliferation rules for numerically simulating the system dynamics.
    … …  
    77The software is currently divided into two separate codes:
    88
    9 Organism : used for simulating cells with geometries that can be described by a fixed number of variables and parameters.
    10 Examples are cells described by Spheres, capped cylinders for rod-shaped cells, and budding yeast shapes.
     9'''Organism''' : used for simulating cells with geometries that can be described by a fixed number of variables and parameters.
     10Examples are cells described by Spheres, Capped cylinders for rod-shaped cells, and Budding (yeast) shapes. It also can be used for simulations on geometries extracted from confocal data, where it uses information on cell volumes cell-cell connections (walls) and their areas. Example papers using these different approaches are:
    1111
    12 It is assuming a deterministic system and uses an ''Ordinary Differential Equation'' approach.
     12Jönsson et al (2006) ''PNAS''
     13Cho, Jönsson et al (2006) ''PLoS Biology''
     14Jönsson and Levchenko (2005) ''Multiscale Modeling and Simulation''
     15Gruel et al (2016) ''Science Advances''
     16
     17'''Tissue''' : used for simulating vertex-based cell geometries including finite element mechanical models. A cell wall (cell in 2.5D) is defined by a list of vertices defining a polygon. Example papers using this software are:
     18
     19Hamant, Heisler, Jönsson et al (2008) ''Science''
     20Bozorg et al (2014) ''PLoS Comp Biol''
    1321
    1422Some of the features of the software are:
    1523
    16 * It includes several numerical solvers for the ODEs.
     24* It includes several numerical solvers for the ordinary differential equations, also with noise, and for stochastic simulations (Organism).
    1725
    18 * It has an optimization and analyze environment.
     26* It includes a library of common biochemical, growth, division and mechanical rules.
    1927
    20 * It includes a library of common biochemical and mechanical rules.
     28* Models are defined within a specific model file - no need for recompilation when models are changed.
    2129
    22 * It is developed such that it should be easy for a programmer to define
    23 new reaction- division- etc. rules.
     30* The code is compartmentalised such that it should be easy for a programmer to define
     31additional user-specific reaction- division- etc. rules.
    2432
    2533* It is and has been used to simulate growing plant tissue, and yeast and
    2634bacterial cell colonies.
    2735
     36* It includes visualisation and analysis tools.
     37
     38* it includes an optimisation environment where data from multiple mutants can be used to define a cost function.
     39
    2840The software is mainly developed at the Computational Biology & Biological
    29 Physics group at Lund University. Contact: henrik@thep.lu.se.
     41Physics group at Lund University and the Computational Morphodynamics group at the Sainsbury Laboratory, University of Cambridge. Contact: henrik.jonsson@slcu.cam.ac.uk.
    3042
    3143= Binaries =
    3244
    33 There are two main binaries. ''simulator'' which is simulating an organism
    34 model, and ''optimizer'' which is used to optimize model parameters.
     45There are three main binaries. ''simulator'' which is simulating a single organism-tissue
     46model. For the Organism code there is an ''optimizer'' binary which is used to optimise model parameters towards a data template, and ''newman'' which is used to visualise model output.
     47For the Tissue code, the preferred viualisation tool is Paraview.
    3548
    3649'''Simulator'''
    … …  
    7790= Compilation =
    7891
    79 The code can be compiled by using make or scons. Both a ''Makefile'' and
    80 a ''SConstruct'' file can be found found in the $ORGANISM/src directory. The
    81 code is ANSI-compatible and has been tested to compile on Linux, Mac OSX and
    82 Windows (using Cygwin) platforms.
    83 
    84 
    85 
     92The code can be compiled by using make. A Makefile can be found in the $ORGANISM/src directory. The
     93code is ANSI-compatible and has been tested to compile on Linux (default for the provided Makefile), Mac OS X and
     94Windows (using Cygwin) platforms. It is dependent on boost and for plotting OpenGL.