This is a program for simulating cortical microtubule dynamics (CMT) on experimentally extracted microscopic images of cell

Application:

https://www.sciencedirect.com/science/article/pii/S0960982218309242

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005959

Testing and contributing is very welcome, especially if you can contribute with new algorithms and features.

NOTE: You need a compiler that supports the C++ 14 standard as a minimum.

corticalsim3D depends on Eigen and Boost (however, the latter will be dropped soon). In addition, you will need Meson to build the executables, as well as a fairly recent C++ compiler (GCC or Clang) supporting the C++ 14 standard. The following instructions outline the process of installing the dependencies on different platforms, as well as compiling and installing the corticalsim3D package itself.

Most dependencies need to be installed manually on Windows.

1. GCC

   1. Download MinGW
   2. Run mingw-xx.exe (this will create a folder called MinGw)
   3. Copy the MinGw folder to C:\
   4. Add C:\MinGW and C:\MinGW\bin to the system path

2. Eigen

   1. Download Eigen
   2. Extract eigen-3.4.0 folder and rename it to Eigen
   3. Copy the Eigen folder to C:\Program Files

3. Boost

   Download and install Boost.

   NOTE: The Boost dependency will be deprecated and removed soon.

4. Meson

   Use the official Meson installer for Windows. The installer also bundles the Ninja dependency, so you don't have to install that separately.

Please use your package manager to install all the dependencies. Most Linux distributions provide packages for GCC, Meson, Ninja, Boost and Eigen.

Instructions for Ubuntu (to be confirmed, may be incomplete):

sudo apt update && apt upgrade
sudo apt install gcc libboost-filesystem-dev libeigen3-dev meson ninja-build cmake

1. First, clone the corticalsim3D repository:

   git clone https://github.com/NLeSC/corticalsim3D

   NOTE: It is recommended that you do not enter the corticalsim3D directory. The next steps assume an out-of-source build setup, meaning that the directory (where the package will be compiled) will be outside the source tree. This has several advantages, such as precluding the possibility of accidentally committing build artefacts to the repository.

2. Configure the build with meson:

   meson setup build corticalsim3D

   This command uses the Meson build system to bootstrap everything that we need for the compilation into a directory called build from the sources located in the corticalsim3D directory.

3. Enter the build directory and compile the source:

   meson compile -C build

   This will generate an executable file called corticalsim3d in the current directory (build).

Run the corticalsim3d executable with the corticalsim3D/config/parameters_ARRAY.txt parameter file as the first argument:

./build/corticalsim3d ./corticalsim3D/config/parameters_ARRAY.txt

• Reproduce the installation instructions for Windows and update them as necessary.
• Add specific installation instructions for dependencies for different Linux distributions (Ubuntu, Debian, Arch...).
• Add installation instructions for MacOSX.
• Meson: Option to install the executable into a custom directory