Index

Version 4.x (Python 3.x)

• CC3D 4.2.3 (Aug 22, 2020)

• CC3D 4.2.2 (Jul 25, 2020)

• CC3D 4.2.1 (Jun 8, 2020)

• CC3D 4.2.0 (May 2, 2020)

• CC3D 4.1.1 (Jan 18, 2020)

• CC3D 4.1.0 (Sep 21, 2019)

• CC3D 4.0.0 (Aug 13, 2019)

Version 3.x (Python 2.x)

• CC3D 3.7.9 (Apr 30, 2019)

• CC3D 3.7.8

• CC3D 3.7.7

• CC3D 3.7.6

• CC3D 3.7.5

• CC3D 3.7.4

• CC3D 3.7.3

• CC3D 3.7.2

• CC3D 3.7.1

• CC3D 3.7.0

• CC3D 3.6.2

CC3D Version 4.2.3 (Aug 22 2020)

We are pleased to announce new version 4.221 of our software CompuCell3D. This a bug-fix release that includes the following features and bug-fixes:

Improvements and new features

• Added on_stop function to steppable - called if user stops the simulation
• Added ability to open zipped project from both Player and Twedit++
• Improved commenting / uncommenting of XML scripts
• Added more natural syntax to refer to cell types

  • e.g., self.cell_type.Condensing

• Added pre-check for cell types and fields
• Added Add Steppable ... function to CC3D Python menu, making it easier to add steppables in Twedit

Multiple bug fixes including

• Fixed settings handling in Twedit++
• Fixed display of line numbers in Twedit++
• Fixed issues with 2.5D simulations where dim z=2
• Fixed behavior of cell_list_by_cell type when using nested loops
• Improved random seed generation (matters if two identical simulations are started within less than a second of each other)

Known Issues

• GPU solvers on OSX 10.14 or higher may not work properly

Binary distribution packages

Windows - 32-bit and 64-bit

• CompuCell3D 4.2.3 - Windows (select one of the exe files) Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D

IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder

Mac OS X - binaries

• CompuCell3D 4.2.3 - Mac OS X Download
  (Note: Don't download the version using the green box, scroll down to the directly listing and download the .zip file.)

Installation Instructions for Mac OSX Binaries (not needed if you download the binary above)

Linux

We are providing binaries for 64 bit Ubuntu and RedHat (you should not need to compile anything)

• CompuCell3D 4.2.3 - Linux (Ubuntu/RedHat) Download

CC3D Version 4.2.2 (July 25, 2020)

We are pleased to announce new version 4.221 of our software CompuCell3D. This a bug-fix release that includes the following features and bug-fixes:

Improvements and new features

• Added ability top open zipped .cc3d project directly from Twedit++ - no need to do unzipping using 3rd party tools
• Added saving of simulation layout on simulation stop or simulation finish events
• Added automatic zip file name fill-in in Twedit++ when zipping .cc3d project
• Added Simulation menu action to reset global settings - as of now users can reset simulation-specific and global settings directly from Player menu
• Added option to reset Twedit++ settings directly from Twedit++ GUI

Multiple bug fixes including

• Fixed saving of windows layout - including plots and steering panel
• Fixed screenshot color issues - as of now coloring is based on specification inside screenshot description file, and not on current player settings
• Fixed handling of secretion in ReactionDiffusionSolverFE
• Fixed "Check for New Version" functionality in the player
• Fixed behavior of simulations that use plots but are run in gui-less mode
• Fixed Twedit++ zoom in / zoom out issues
• Fixed CC3D version printout issues

Known Issues

• GPU solvers on OSX 10.14 or higher may not work properly

Binary distribution packages

Windows - 32-bit and 64-bit

• CompuCell3D 4.2.2 - Windows (select one of the exe files) Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D

IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder

Mac OS X - binaries

• CompuCell3D 4.2.2 - Mac OS X Download
  (Note: Don't download the version using the green box, scroll down to the directly listing and download the .zip file.)

Installation Instructions for Mac OSX Binaries (not needed if you download the binary above)

Linux

We are providing binaries for 64 bit Ubuntu and RedHat (you should not need to compile anything)

• CompuCell3D 4.2.2 - Linux (Ubuntu/RedHat) Download

CC3D Version 4.2.1 (June 8, 2020)

We are pleased to announce new version 4.2.1 of our software CompuCell3D. This a bug-fix release that includes the following features and bug-fixes:

Improvements and new features

• Added new convenience function to FieldSecretor class to compute total concentration "seen" by a cell as well as total amount of field in the entire lattice

Multiple bug fixes including

• Fixed Replay of saved simulation snapshots
• Fixed simulation shutdown function call sequence to avoid crashes after last MCS was not a multiple of screen update frequency

Known Issues

• GPU solvers on OSX 10.14 or higher may not work properly

Binary distribution packages

Windows - 32-bit and 64-bit

• CompuCell3D 4.2.1 - Windows (select one of the exe files) Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D

IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder

Mac OS X - binaries

• CompuCell3D 4.2.1 - Mac OS X Download
  (Note: Don't download the version using the green box, scroll down to the directly listing and download the .zip file.)

Installation Instructions for Mac OSX Binaries (not needed if you download the binary above)

Linux

We are providing binaries for 64 bit Ubuntu and RedHat (you should not need to compile anything)

• CompuCell3D 4.2.1 - Linux (Ubuntu/RedHat) Download

---

CC3D Version 4.2.0 (May 2, 2020)

We are pleased to announce new version 4.2.0 of our software CompuCell3D. This release includes the following bug fixes and new features:

Multiple bug fixes including

• fixing CC3D GUI behavior with multiple monitors
• fixing contour lines plotting
• fixing display of chemical/scalar fields
• floating windows layout now supported on all platforms
• dmg-based installer for OSX 10.14+. Solves previous issues with CC3D installations on newer OSX systems

Improvements and new features

• New floating layout that limits windows clutter (immpotant for OSX users)
• Added persistent bias to Bias Vector Steppable
• Added Screenshot API
• Added cell type name accessor to Python steppable
• Added Fluctuation Compensator to DiffusionSolverFE and ReactionDiffusionSolverFE
• Added effective energy data Python accessor
• Added Focal Point Plasticity time tracking data
• Added Focal Point Plasticity link initiator data
• Added PDE test-suite
• Improvements to CallableCC3D module (input passing)

Known Issues

• GPU solvers on OSX 10.14 or higher may not work properly

Binary distribution packages

Windows - 32-bit and 64-bit

• CompuCell3D 4.2.0 - Windows Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D

IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder

Mac OS X - binaries

• CompuCell3D 4.2.0 - Mac OS X Download
  (Note: Don't download the version using the green box, scroll down to the directly listing and download the .zip file.)

Installation Instructions for Mac OSX Binaries (not needed if you download the binary above)

Mac Security Problem: If you are using Mac OS 10.15.x you may have problems running CompuCell3D because of Apple's increassingly onerous security measures. If you encounter problems please contact us at <jsluka AT indiana DOT edu>. CC3D 4.2.0 should fix this problem.

Linux

We are providing binaries for 64 bit Ubuntu and RedHat (you should not need to compile anything)

• CompuCell3D 4.2.0 - Linux (Ubuntu/RedHat) Download

CC3D Version 4.1.1 (Jan. 18, 2020)

We are pleased to announce new version 4.1.1 of our software CompuCell3D.

Important Because we switched from Python 2 to Python 3 your old simulations will require minor modifications. Please see https://pythonscriptingmanual.readthedocs.io/en/4.0.0/transition_to_cc3d_4.html for instructions on how to port your simulations. If you have questions or require assistance please reach out to us on our user support forum https://www.reddit.com/r/CompuCell3D/

Important We suggest that as you move to CC3D 4.0.0+ you keep old installation of CC3D (version 3.7.x) in place in order to ensure that you can run your simulations during transitions period. CompuCell3D 4.0.0+ stores settings in different place from earlier version so you can safely run new and older versions side-by-side.

New Features

• Added support for specifying Reaction-Kinetics models in Antimony and CellML (Windows and OSX)
• Fixed parameter scan to allow runs with multiple workers
• Added callable API allowing CC3d to be called as a function returning values
• Fixed restart files issue
• Fixed PIFF dumper
• Fixed hover over text in Player
• Added support for developing custom C++ steppables and plugins on OS
• Expanded compilation documentation for all 3 platforms
• Improved data passing between steppables
• Added optional comments in code snippets
• Improved interface with fpp plugin and new accessible plugin data in steppables

• Added access to BoxWatcher data in steppables

• Fixed domain resizing

Binary distribution packages:

Windows - 32-bit and 64-bit

• CompuCell3D 4.1.1 - Windows Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D

IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder

Mac OS X - binaries

• CompuCell3D 4.1.1 - Mac OS X Download (Note: Don't download the version using the green box, scroll down to the directly listing and download the .zip file.)

Installation Instructions for Mac OSX Binaries (not needed if you download the binary above)

Mac Security Problem: If you are using Mac OS 10.15.x you may have problems running CompuCell3D because of Apple's increassingly onerous security measures. If you encounter problems please contact us at <jsluka AT indiana DOT edu>.

Linux

We are providing binaries for 64 bit Ubuntu and RedHat (you should not need to compile anything)

• CompuCell3D 4.1.1 - Linux (Ubuntu/RedHat) Download

CC3D Version 4.1.0 (Sept. 21, 2019)

We are pleased to announce new version 4.1.0 of our software CompuCell3D.

Important Because we switched from Python 2 to Python 3 your old simulations will require minor modifications Please see https://pythonscriptingmanual.readthedocs.io/en/4.0.0/transition_to_cc3d_4.html for instructions on how to port your simulations. If you have questions or require assistance please reach out to use on our user support forum https://www.reddit.com/r/CompuCell3D/

Important We suggest that as you move to CC3D 4.0.0+ you keep old installation of CC3D (version 3.7.x) in place in order to ensure that you can run your simulations during transitions period. CompuCell3D 4.0.0+ stores settings in different place from earlier version so you can safely run new and older versions side-by-side.

New Features

• New, intuitive way to launch parameter scans
• Added 3D vascularized tumor demo from Shirinifard PLoS One 2009
• Added basic, in-player simulation stats output

• Added "WeightEnergyByDistance" in all contact energy plugins

• Expanded Developer's manual and added new, documented DeveloperZone steppables examples

• Added convenience Michaelis-Menten and Hill functions to SteppableBasePy

• Multiple bug fixes (including ability to resize screenshots)

Binary distribution packages:

Windows - 32-bit and 64-bit

• CompuCell3D 4.1.0 - Windows Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D

IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder

Mac OS X - binaries

• CompuCell3D 4.1.0 - Mac OS X Download

(Note: Don't download the version using the green box, scroll down to the directly listing and download the .zip file.)

Installation Instructions for Mac OSX Binaries (not needed if you download the binary above)

Linux

We are providing binaries for 64 bit Ubuntu and RedHat (you should not need to compile anything)

• CompuCell3D 4.1.0 - Linux (Ubuntu/RedHat) Download

CC3D Version 4.0.0 (Aug. 13, 2019)

We are pleased to announce completely new version 4.0.0 of our software CompuCell3D. Starting from version 4.0.0 we are moving to Python 3 and will no longer develop Python 2 - based CompuCell3D. We will provide support for older version but we encourage all users to move to the new version. We have made significant improvements in this new version that make using CompuCell3D even easier than before

Important Because we switched from Python 2 to Python 3 your old simulations will require minor modifications Please see https://pythonscriptingmanual.readthedocs.io/en/4.0.0/transition_to_cc3d_4.html for instructions on how to port your simulations. If you have questions or require assistance please reach out to use on our user support forum https://www.reddit.com/r/CompuCell3D/

Important We suggest that as you move to CC3D 4.0.0+ you keep old installation of CC3D (version 3.7.x) in place in order to ensure that you can run your simulations during transitions period. CompuCell3D 4.0.0 stores settings in different place from earlier version so you can safely run new and older versions side-by-side.

New Features

• Python 3 - based code
• Simpler specification of simulation - new , simpler API
• More intuitive specification of parameter scans
• Better support and integration with 3rd party Python packages (numpy, pandas, scipy)
• Multiple bug fixes

Binary distribution packages:

Windows - 32-bit and 64-bit

• CompuCell3D 4.0.0 - Windows Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D

IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder

Mac OS X - binaries

• CompuCell3D 4.0.0 - Mac OS X Download

(Note: Don't download the version using the green box, scroll down to the directly listing and download the .zip file.)

Installation Instructions for Mac OSX Binaries (not needed if you download the binary above)

Linux

We are providing binaries for 64 bit Ubuntu and RedHat (you should not need to compile anything)

• CompuCell3D 4.0.0 - Linux (Ubuntu/RedHat) Download

CC3D Version 3.7.9 (Apr 30, 2019)

CC3D 3.7.9 is ready for download.

IMPORTANT: This is a release candidate. It is fully functional new version of CompuCell3D. Before making it an official release we want to give users an opportunity to try it on their machines and report any bugs on our Q&A page: CC3D - AllAnswered

New Features

• New, intuitive handling of screenshots. Adjust graphical configuration in the Player, click "Camera" button and from now on every run of your simulation will have screenshots taken.

• Support for screenshots on clusters, and in the non-GUI-based runs (see manual) for how to use this feature.

• Vastly improved Boundary Walker algorithm that provides major speedups for simulations with either very large cells or with very few cells on a large lattice
• Refactored Player code
• Multiple bug fixes

Binary distribution packages:

Windows - 32-bit and 64-bit

• CompuCell3D 3.7.9 - Windows Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D

IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder

Mac OS X - binaries

• CompuCell3D 3.7.9 - Mac OS X Download

(Note: Don't download the version using the green box, scroll down to the directly listing and download the .zip file.)

Installation Instructions for Mac OSX Binaries (not needed if you download the binary above)

Linux

We are providing binaries for 64 bit Ubuntu and RedHat (you should not need to compile anything)

• CompuCell3D 3.7.9 - Linux (Ubuntu/RedHat) Download

CC3D Version 3.7.8

New Features

• Python parameter Steering via Interactive Sliders
• Multiple Bug Fixes

Binary distribution packages:

Windows - 32-bit and 64-bit

IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder

• CompuCell3D 3.7.8 - Windows Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D:

Mac OS X - binaries

Installation Instructions for Mac OSX Binaries

• CompuCell3D 3.7.8 - Mac OS X Download

Linux

We are providing binaries for 64 bit Ubuntu and RedHat

• CompuCell3D 3.7.8 - Linux (Ubuntu / RedHat ) Download

Most Linux users choose to compile cc3d from source. Please take a look at our tutorials:

• Building and installing 3.7.8 from source on Ubuntu Linux is easily done by following our Ubuntu Linux step-by-step tutorial or RedHat/CentOS tutorials.

• You may also try conda-based installation method Conda-based installation

CC3D 3.7.7

New Features

• Improved handling of Player settings - based on SQLite database

  • NOTE: If Twedit++ or Compucell3D crashes when trying to run an old xxx.cc3d setup file then delete the _settings.xml file from the Simulation directory.

• Significantly faster connectivity plugin that works in 2D , 3D and on any type of lattice
• Multiple bug-fixes

Binary distribution packages:

Windows - 32-bit and 64-bit

IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder

• CompuCell3D 3.7.7 - Windows Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-GPU version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D:

Mac OS X - binaries

Installation Instructions for Mac OSX Binaries

• CompuCell3D 3.7.7 - Mac OS X Download

Linux

Most Linux users choose to compile cc3d from source. Please take a look at our tutorials:

• Building and installing 3.7.7 from source on Ubuntu Linux is easily done by following our Ubuntu Linux step-by-step tutorial or RedHat/CentOS tutorials.

We will provide binaries for 64 bit Ubuntu (14.04 and 16.04), RedHat CentOS soon

CC3D Version 3.7.6

CC3C 3.7.6 includes improved Player and Twedit++ (we migrated development to PyQt5). We also changed plotting backend in the Player which may cause your older python code to throw an error when processing plotting section. Please follow this tutorial to fix your plots. Remember that 3.7.5 is fully functional version and if you experience any issues with 3.7.6 downgrading to 3.7.5 will be OK for now

New Features

• Windows, OSX, Linux versions ship with bundled Python distributions
• Simplified Player menus
• We added parameter optimization module based on user-defined cost function (we will develop tutorials soon)
• One installer should work on all versions of OSX starting with 10.9 (Mavericks)
• Starting from this version we will be only providing binaries for 64-bit Long Term Support Ubuntu releases (14.0 16.04 etc). Keep in mind that CC3D can be easily compiled on any linux distribution
• Bug fixes in Twedit++

• RoadRunner was upgraded to the latest version.

• IMPORTANT: The RR upgrade eliminates the need to set steps options in in the Steppable file. If you have step options set remove it from your script

Binary distribution packages:

Windows - 32-bit and 64-bit

• CompuCell3D 3.7.6 - Windows Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D:

Mac OS X - binaries

Installation Instructions for Mac OSX Binaries

• CompuCell3D 3.7.6 - Mac OS X Download

Linux

We are providing binaries for 64 bit Ubuntu (14.04 and 16.04). We will release RedHat CentOS binaries soon

• CompuCell3D 3.7.6 - Linux (Ubuntu) Download

Most Linux users choose to compile cc3d from source. Please take a look at our tutorials:

• Building and installing 3.7.6 from source on Ubuntu Linux is easily done by following our Ubuntu Linux step-by-step tutorial or RedHat/CentOS tutorials.

CC3D Version 3.7.5

This version includes improved player and many convenience features in Python scrip ting which make model development much easier.

New Features

• Windows versions ship with bundled Python distributions

• We added support for OSX 10.11 - ElCapitan

• Starting from this version we will be only providing binaries for 64-bit Long Term Support Ubuntu releases (14.0 16.04 etc). Keep in mind that CC3D can be easily compiled on any linux distribution
• Player has been improved and users can add axes for better visualization

• RoadRunner was upgraded to the latest version.

• IMPORTANT: The RR upgrade eliminates the need to set steps options in in the Steppable file. If you have step options set remove it from your script

Binary distribution packages:

Windows - 32-bit and 64-bit

• CompuCell3D 3.7.5 - Windows Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D:

• Non-GPU CompuCell3D 3.7.5 - Windows Download

Mac OS X - including ElCapitan binaries

Installation Instructions for Mac OSX Binaries

• CompuCell3D 3.7.5 - Mac OS X Download

Linux

Installation Instructions for Linux Binaries

• CompuCell3D 3.7.5 - Linux Download

• If the above packages are not suitable, building and installing 3.7.5 from source on Linux is easily done by following our Linux step-by-step tutorial .

CC3D Version 3.7.4

This version includes improved player and many convenience features in Python scripting which make model development much easier.

New Features

• Player has been improved and has new layout with floating windows. This is the default and recommended setting for Mac users. Check here

• Player settings are stored individually with each simulation. Thus several simulations running in parallel may have different set of settings. Previously there was one global setting file which made it inconvenient to run multiple simultaneous simulations with different settings
• Window layout is saved in the settings each time user stops the simulation. This feature allows simulation to open in exactly the same state it was before user stopped simulation run.
• Automatic cell labeling using scalar or vector cell attribute
• Simplified access to cell python dictionary - not you type cell.dict
• Simplified histograms and scientific plots setup
• Added ability to subscribe/unsubscribe to CompuCell3D mailing list from the Player

Binary distribution packages:

Windows

• CompuCell3D 3.7.4 - Windows Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D:

• Non-GPU CompuCell3D 3.7.4 - Windows Download

Mac OS X

Installation Instructions for Mac OSX Binaries

• CompuCell3D 3.7.4 - Mac OS X Download

Linux

Installation Instructions for Linux Binaries

• CompuCell3D 3.7.4 - Linux Download

• If the above packages are not suitable, building and installing 3.7.3 from source on Linux is easily done by following our Linux step-by-step tutorial .

CC3D Version 3.7.3

This is mainly bug fix release. Our users discovered several annoying bugs - nothing dramatic, just annoyances in Player, Twedit++ and Python scripting interface.

New Features

• paramScan script that runs parameter scan in a fault-tolerant way.
• New format to save plot data (csv)
• Easier computations on he lattice with new hex2Cartesian and cartesin2Hex Py Steppable Base functions
• Option to turn off comments in Python snippets inserted from CC3D Python menu
• Support for VTK6
• Stopped requiring PyQt/Qt for command line runs
• Improved XML code checkers which do sanity checks for XML part of simulation description

Bug Fixes:

• Fixed saving plots and plots data
• Fixed saving .cc3d projects in the new directory aka Save Project As ...
• Fixed visualization scaling for 2D projectsion on hex lattice
• Fixed generation of higher neighbor orders on demand. Current implementation was good up to 8th nearest neighbor. Now we can use 20 or 30 or higher
• Fixed how secretion plugin=- related bottleneck in openMP see manual for more details

Binary distribution packages:

Windows

• CompuCell3D 3.7.3 - Windows Download

Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D:

• Non-GPU CompuCell3D 3.7.3 - Windows Download

Mac OS X

Installation Instructions for Mac OSX Binaries

• CompuCell3D 3.7.3 - Mac OS X Download

Linux

Installation Instructions for Linux Binaries

• CompuCell3D 3.7.3 - Linux Download

• If the above packages are not suitable, building and installing 3.7.3 from source on Linux is easily done by following our Linux step-by-step tutorial .

CC3D Version 3.7.2

New Features

• Improved roadrunner SBML Solver - faster than before and with more user-configurable options
• Improved GPU and CPU PDE Solvers - fixed small bugs on hex lattice with non-periodic boundary conditions
• Updated Twedit helper menu
• Fixed OSX player freeze when replaying VTK files
• Added min/max functions to the chemical field for faster performance

Binary distribution packages:

Windows

• CompuCell3D 3.7.2 - Windows Download

Mac OS X

Installation Instructions for Mac OSX Binaries

• CompuCell3D 3.7.2 - Mac OS X Download

Linux

Installation Instructions for Linux Binaries

• CompuCell3D 3.7.2 - Linux Download

• If the above packages are not suitable, building and installing 3.7.2 from source on Linux is easily done by following our Linux step-by-step tutorial .

BionetSolver is deprecated as of 3.7.2

Starting with 3.7.2 we will discontinue upgrades, bug fixes etc for Bionet-Solver. However, we will continue bundling it with binary packages for most platforms (OSX 10.9 is an exception due to compilation issues) but we ask CC3D users to consider using SBML-Solver which is a much better choice for working with SBML models inside CC3D. To get started with SBML-Solver please see Python Scripting Manual for CompuCell3D 3.7.2

CC3D Version 3.7.1

New Features

• LLVM-based RoadRunner as a backend for SBML Solver

• Parameter Scans (instructions will appear soon)
• Improved Twedit
• On Windows switched compilers from VS2008 to VS 2010
• Added Serialization of SBMLSolver objects
• Fixed memory leaks in the Player
• Added proper cleanup functions to Simulator

Binary distribution packages:

Windows

• CompuCell3D 3.7.1 - Windows Download

Mac OS X

• CompuCell3D 3.7.1 - Mac OS X Download

Linux

Installation Instructions for Linux Binaries

• CompuCell3D 3.7.1 - Linux Download

• If the above packages are not suitable, building and installing 3.7.1 from source on Linux is easily done by following our Linux step-by-step tutorial .

CC3D Version 3.7.0

New Features

• GPU Reaction-Diffusion Solvers (explicit and implicit)

• RoadRunner-based SBMLsolvers

• Simplified and improved Steppable API (backward compatibility maintained)
• Numpy-based syntax for field manipulation
• Demo integration with Dolfin- works on linux only

Binary distribution packages:

Windows

• CompuCell3D 3.7.0 - Windows Download

Mac OS X

• CompuCell3D 3.7.0 - Mac OS X Download

Linux

Installation Instructions for Linux Binaries

• CompuCell3D 3.7.0 - Linux Download

• If the above packages are not suitable, building and installing 3.7.0 from source on Linux is easily done by following our Linux step-by-step tutorial .

CC3D Version 3.6.2

Binary distribution packages:

Windows

• CompuCell3D 3.6.2 - Windows Download

Mac OS X

• CompuCell3D 3.6.2 - Mac OS X Download

• separate binary distributions are available for: 10.8 Mountain Lion 64bit (OpenCL GPU accelerated) intel systems, for 10.6 Snow Leopard and newer 64 bit intel systems, and for 10.5.8 Leopard and newer 32bit intel systems

Linux

• CompuCell3D 3.6.2 - Linux Download

• If the above packages are not suitable, building and installing 3.6.2 from source on Linux is easily done by following our Linux step-by-step tutorial .