https://github.com/virtualcell/vcell-ode
The ODE focused solvers VCell utilizes in it's main applications
https://github.com/virtualcell/vcell-ode
Last synced: 4 months ago
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The ODE focused solvers VCell utilizes in it's main applications
- Host: GitHub
- URL: https://github.com/virtualcell/vcell-ode
- Owner: virtualcell
- Created: 2025-06-04T16:31:27.000Z (about 1 year ago)
- Default Branch: master
- Last Pushed: 2025-12-18T18:05:54.000Z (6 months ago)
- Last Synced: 2025-12-20T07:02:53.404Z (6 months ago)
- Language: C
- Size: 84.7 MB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 4
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Metadata Files:
- Readme: README.md
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README
## 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.
---
# vcell-ode
Virtual Cell ODE [virtualcell/vcell-ode](https://github.com/virtualcell/vcell-ode) is a collection of numerical
simulation libraries and protocols used to process ODEs in the Virtual Cell framework [virtualcell/vcell](https://github.com/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 `/conan-profiles` [link](https://docs.conan.io/2/reference/config_files/profiles.html)
to further reading on the official `conan` website.
#### Powershell
```pwsh
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
```
```bash
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 `/build/bin` to an appropriate folder in path, or put said folder into path for your computer.