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@MathCancer MathCancer released this 03 Nov 02:44
· 1726 commits to master since this release
1.2.1
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PhysiCell: PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D
Multicellular Systems.

Version: 1.2.1
Release date: 1 September 2017

Homepage: http://PhysiCell.MathCancer.org
Downloads: http://PhysiCell.sf.net

Summary:
This release introduces a improved MultiCellDS outputs, new matlab
functions to read the MultiCellDS outputs, experimental functions
for povray routines (for 3-D raytracing), some bugfixes, and
new sample projects in cancer heterogeneity, synthetic multicellular
bioengineering, and cancer immunology.

PhysiCell is currently under scientific peer review.

Major new features and changes:

  • Updated save_PhysiCell_to_MultiCellDS_xml_pugi() to save much more
    phenotype information and all custom variables for each cell.

  • Updated read_MultiCellDS_XML.m (in ./matlab) to read these
    newly expanded data files.

  • Included new matlab functions for fast 3-D data exploration:

    simple_plot.m -- quickly plots (as a surface) all the cells
    simple_cutaway_plot.m -- same as above, but with a cutaway view
    composite_cutaway_plot.m -- plots cutaway view of live and dead
    cells, colored separately.

  • Wrote new POV-ray functions for future raytracing utilities. See
    ./modules/PhysiCell_POV.*

  • Add the following new sample projects:

    biorobots: simulates a system of director, worker, and cargo
    cells that coordinate to deliver cellular cargo to the
    directors. Uses motility, custom mechanics, and other functions.

     build via: make biorobots-sample && make project

    cancer biorobots: modifies the above project so that worker
    cells take cargo to hypoxic tumor regions. cargo cells
    release a drug once they are detached from worker cells.
    tumor cells have a damage and apoptosis model.

     build via: make cancer-biorobots-sample && make project

    heterogeneity: simulates proliferation of a heterogeneous
    tumor. Note the loss of symmetry and selection/evolution.

     build via: make heterogeneity-sample && make project

    cancer immunology: simulates an immune system attack on a
    tumor with heterogeneous proliferation and immunogenicity
    characteristics. In 3D!

     build via: make cancer-immune-sample && make project

Minor new features and changes:

  • Added double NormalRandom( double mean, double standard_deviation )
    to PhysiCell_utilities.* This will generate normally-distributed
    random numbers.

  • Includes a sneak preview of BioFVM 1.1.7, which includes bugfixes on
    how boundary conditions were initialized.

bugfixes:

  • Removed annoying "cout" lines in:

    void standard_live_phase_entry_function(Cell*,Phenotype&,double).

    They were leftover from debugging. Sorry!

  • In the templates, we updated to:

      while( t < t_max + 0.1*diffusion_dt )
  {

    so that the simulations run all the way to the final time,
    instead of exiting too early by dt time.

  • Fixed a bug in Motility::Motility() where the migration bias was
    initialized to (1,0,0).

  • Made adhesion and repulsion symmetric across cells (in add_potentials)

  • got rid of debug_temp_a in (in add_potentials)

  • if default_microenvironment_options.simulate_2D == true, we now
    set velocity[2] = 0.0 in the velocity functions.

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