spQSP-IO

User manual for spatial quantitative systems pharmacology for immuno-oncology (spQSP-IO)

Ubuntu Operating System Configuration (Only required for Windows User)

This step helps to setup the Ubuntu operating system in for Windows user via virtual machine.

1. The virtual machine host: VirtualBox is available at https://www.virtualbox.org/ 2 . The Ubuntu Desktop image (Latest version 20.04.2) is available at http://www.releases.ubuntu.com/20.04/
2. Enter the “Oracle VM VirtualBox Manager”, press “New” to create the virtual machine with all default settings. (Recommend allocate 20 GB for storage and 2 GB of RAM)

Notice: All following operations should be done in the Linux operating systems (the virtual machine), NOT Windows.

Required Library Installation

Libraries: SUNDIALS: version:4.0.1; Boost: version 1.70.0

-SUNDIALS

1. Download is available at: https://computing.llnl.gov/projects/sundials/sundials-software
   The following files are downloaded: sundials-4.0.1.tar.gz

2. Decompress Archieve:
   $ tar xzf sundials-4.0.1.tar.gz

3. Install cmake if not already available:
   $ sudo apt install cmake-curses-gui

4. Create install and build directories:
   $ mkdir -p ~/lib/sundials-4.0.1 $ mkdir -p ~/Downloads/sundials-build $ cd ~/Downloads/sundials-build

5. Configuration
   $ ccmake ~/Downloads/sundials-4.0.1
   Press c key to enter configuration interface Set install directory: CMAKE_INSTALL_PREFIX set to ~/lib/sundials-4.0.1 Set example install directory: EXAMPLE_INSTALL_PATH set to ~/lib/sundials-4.0.1/examples Press c repeatedly to process configuration; press g to generate Makefile and exit configuration.

6. Build
   From ~/Downloads/sundials-build/
$ make
$ make install

-Boost Version 1.70.0

1. Source code available at: https://www.boost.org/users/history/version_1_70_0.html
   The following files are downloaded:
   boost_1_70_0.tar.gz

2. Decompress the archive:
   $ tar xzf boost_1_70_0.tar.gz
   

Official instructions is available at: https://www.boost.org/doc/libs/1_70_0/more/getting_started/unix-variants.html

3. Building separately-compiled boost libraries
   $ cd ~/Downloads/boost_1_70_0
$ ./bootstrap.sh --prefix=$HOME/lib/boost_1_70_0
$ ./b2 install
   

Model Simulation

The Makefile of this model is available at: ~/TNBC_omics/TNBC_single/linux/
$ make TNBC_s_sim
$ ./TNBC_s_sim -h
For all options to configure the simulation