modelCMT (cortical microtubule dynamics)

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

Note

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

WINDOWS

install gcc/g++

download Mingw: https://nuwen.net/mingw.html

  run mingw-xx.exe -> this will create a folder MinGw
  
  copy MinGw to C:\
   
  add environment variable: C:\MinGW or C:\MinGW\bin

install eigen:

download eigen: https://drive.google.com/file/d/1VFLlKJI9EaSP9VUaeV8vmPQYkqdIIJPg/view?usp=sharing

  extract "eigen-3.4.0" folder and rename it to "Eigen"

  copy "Eigen" folder to C:\Program Files 

install boost:

download boost: https://drive.google.com/file/d/1apu5_am2kJj7HvXJNPhn30k_ryi3gJDf/view?usp=sharing

  extract "boost_1_77_0" folder and rename it to "Boost"

  copy "Boost" to C:\Program Files 

get the source code

Option 1: Download the package from the Github: https://github.com/HiBandan/modelCMT/archive/refs/heads/main.zip

Option 2: Clone from terminal:

git clone https://github.com/HiBandan/modelCMT.git

install Code::Blocks:

https://code-blocks.en.uptodown.com/windows

run

open (with Code::Blocks): modelCMT_WINDOWS.cbp

Projects -> modelCMT.cbp -> add files
    -> modules/cppFiles (all files except 'inline.cpp')
    -> modules/headFiles (all files)
    -> modules/paramFiles (all files)
    
settings -> compiler -> search directories (compiler) -> add 

    -> C:\Program Files\Eigen 
    -> C:\Program Files\Boost 

project -> 

  set program’s arguments: ./modules/paramFiles/parameters_ARRAY.txt
  build options -> search directories -> compiler -> add -> modules/cppFiles 
  build options -> search directories -> compiler -> add -> modules/headFiles
  build options -> linker settings -> add -> boost_system
  build options -> linker settings -> add -> boost_filesystem
  build options -> linker settings -> add -> libboost_filesystem
  
run 

LINUX

install gcc/g++

   sudo apt update
   sudo apt install build-essential

install eigen:

download eigen: https://drive.google.com/file/d/1VFLlKJI9EaSP9VUaeV8vmPQYkqdIIJPg/view?usp=sharing

  extract "eigen-3.4.0" folder and rename it to "Eigen"

  copy "Eigen" folder to /usr/local/include

install boost:

download boost: https://drive.google.com/file/d/1apu5_am2kJj7HvXJNPhn30k_ryi3gJDf/view?usp=sharing

  extract "boost_1_77_0" folder and rename it to "Boost"

  copy "Boost" to /usr/local/include

get the source code

Option 1: Download the package from the Github: https://github.com/HiBandan/modelCMT/archive/refs/heads/main.zip

Option 2: Clone from terminal:

git clone https://github.com/HiBandan/modelCMT.git

install Code::Blocks:

sudo add-apt-repository ppa:damien-moore/codeblocks-stable

sudo apt update

sudo apt install codeblocks codeblocks-contrib

run

open (with code-block): modelCMT_LINUX.cbp

Projects -> modelCMT.cbp -> add files
  -> modules/cppFiles (all files except 'inline.cpp')
  -> modules/headFiles (all files)
  -> modules/paramFiles (all files)

settings -> compiler -> search directories (compiler) -> add 

    -> /usr/local/include/Eigen
    -> /usr/local/include/Boost 
   
project -> 

  set program’s arguments: ./modules/paramFiles/parameters_ARRAY.txt
  build options -> search directories -> compiler -> add -> modules/cppFiles 
  build options -> search directories -> compiler -> add -> modules/headFiles
  build options -> linker settings -> add -> boost_system
  build options -> linker settings -> add -> boost_filesystem
  build options -> linker settings -> add -> libboost_filesystem

run