Installation

Build from source

To build SBNE from its source code you need to:

Build libSBML from source (with enabled layout and render packages)

As SBNE depends on libSBML, first, it is required to build the latest version of libSBML from its source. In doing so, this video and instruction page can come in handy for you. As, for SBNE, we need to build libSBML with its Layout and Render extensions, while following these instructions, you must remember to check ENABLE_LAYOUT and ENABLE_RENDER boxes in CMake-gui configuration of libSBML.

Build SBNE from source

The steps to build SBNE from its source code are as follows:

  • Create a directory for your entire SBNE project. This directory has to be placed in somewhere not admin-blocked and is recommended to have the following file structure:

    <root directory>
├── build
├── install
├── source

  • Clone or download SBNE source to <root directory>/source.

  • Download and Install CMake and then open CMake-gui.

    • Select <root directory>/source/sbne-main (where the top-level CMakeLists.txt is located) as the source directory.

    • Select <root directory>/build as the build (binary) directory.

    • Click “Configure” button and choose your compiler.

      Note

      At this step, CMake requires you to set the value of sbml_DIR or libsbml_DIR (depneding on your operationg system) to the directory where sbml-config.cmake or libsbml-config.cmake is located under the install directory of libSBML.

    • Set CMAKE_INSTALL_PREFIX to <root directory>/install.

    • Check USE_GRAPHVIZ box if you want your SBNE to layout the network of models by Graphviz layout algorithms.

      Note

      To integrate graphivz libraries into SBNE, you must have already installed Graphviz development tools. If you have done so, you can check USE_GRAPHVIZ box at this step, and then CMake requires you to set the value of GRAPHVIZ_PREFIX to the root directory where graphviz is installed on your machine.

    • Check WITH_PYTHON box if you want to build the language bindings for Python.

      Note

      If you check WITH_PYTHON box at this step, CMake will provide you with PYTHON_INSTALL_IN_PREFIX and PYTHON_INSTALL_WITH_SETUP options later. By checking the box associated with the former option, Python binidngs are installed in <root directory>/install/lib/pyhton[version]/site-packages/libsbne and by checking the box associated with the latter one they will be installed to the standard location for third-party Python modules.

    • Check WITH_GUI box if you want to build SBNE-GUI.

      Note

      To build SBNE-GUI, Qt5 development tools are needed to be already installed on your machine. In that case, if you check WITH_GUI box at this step, CMake requires you later to set the value of Qt5_DIR to the directory where Qt5Config.cmake and other Qt dependencies are located.

    • Click “Configure” button time and again until no red variable row remains.

    • Click “Generate” button.

  • Now that you have figured out all the configuration settings, all you need is building the project as follows:

    • On Windows, you can either click on “Open Project” button on CMake-gui or open the generated .sln file in <root directory>/build in Visual Studio. Once Visual Studio is launched, change the configuration to “Release”, and build ALL-BUILD and INSTALL.

    • On macOS and Linux, simply go to <root directory>/build and run make and then make install on terminal.

Install Python package

The Python bindings of SBNE API can be installed using a “pip install” as a collection of pip packages (currently on TestPyPI):

$ pip install -i https://test.pypi.org/simple/ libsbne

Download SBNE binaries

Installation with precompiled binaries is provided for users who intend to use SBNE without changing its source code. Using Qt Installer Framework, we have created installers for Microsoft Windows (.exe), macOS (.dmg), and Linux (.run) platforms, which are available in the Releases page of the repository on GitHub.