pyvcell-odesolver 0.9.0

Virtual Cell CVODE / IDA based ODE solver

The Virtual Cell Project

The Virtual Cell is a modeling and simulation framework for computational biology. For details see http://vcell.org and http://github.com/virtualcell.

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vcell-ode

Virtual Cell ODE virtualcell/vcell-ode is a collection of numerical simulation libraries and protocols used to process ODEs in the Virtual Cell framework virtualcell/vcell).

Building VCell ODE

There are two ways to build VCell ODE, but both start out the same way

Step 1: Acquire the source-code

The source code can be found online at the GitHub repository. git clone https://github.com/virtualcell/vcell.git

Step 2: Install Dependencies

You will need to acquire a unix-style C and C++ compiler suite in order to build VCell ODE. Traditionally, this project uses CLang + Mold, but other compiler suites may work. Additionally, you'll need to install the other dependencies for VCell ODE, which can be done in one of two ways:

Method 1: Conan Toolchain (Recommended)

The VCell ODE project uses the C++ dependency management system called conan to handle dependency management when building VCell ODE. We provide a number of conan-profiles that will provide conan the information need to automatically build the desired toolchain for cmake.

Method 2: Manual Dependency Installation

If you'd rather manually install all the dependencies build-tools to create VCell CLI, you'll need the following:

Dependencies

• If you want live messaging while the solver runs: libcurl (add -DOPTION_TARGET_MESSAGING to cmake call below)

Build Tools

• cmake to perform the build configuration
• ninja (or equivalent) to perform the actual build process

Step 3: Invoke the Build

In a shell with conan and/or the other build tools in path, navigate to the project's root directory and run the following commands (tested in bash on unix and powershell on windows)

Note that if using conan, you'll need to define a profile. use conan profile detect --force to generate one automatically, or use one of the provided ones in <project_root>/conan-profiles link to further reading on the official conan website.

Powershell

    mdkir build # Must do if not using conan
    conan install . --output-folder build --build=missing # If building using conan's help
    cd build
    ./conanbuild.ps1 # If building using conan's help
    cmake -B . -S .. -G "Ninja" -DCMAKE_TOOLCHAIN_FILE="conan_toolchain.cmake" -DCMAKE_BUILD_TYPE=Release
    cmake --build . --config Release

    mdkir build # must do if not building conan
    conan install . --output-folder build --build=missing # If building using conan's help
    cd build
    ./conanbuild.sh # If building using conan's help
    cmake -B . -S .. -G "Ninja" -DCMAKE_TOOLCHAIN_FILE="conan_toolchain.cmake" -DCMAKE_BUILD_TYPE=Release
    cmake --build . --config Release

Step 4: Manual user/system install

Currently, VCell ODE does not have an automated installation script. You will either need to move the resulting executables in <project_root>/build/bin to an appropriate folder in path, or put said folder into path for your computer.