SpatialKappa
14 September 2012
Copyright © 2012 DemonSoft.org
<http://www.demonsoft.org/>
Copyright © 2014-2019 David C Sterratt
INTRODUCTION
This project contains an implementation of a syntactic extension of Kappa to allow expression of location and transport in models. A user manual is available here.
Feel free to add bug reports or feature requests here.
INSTALLATION
Either
- Run the standalone jar file (SpatialKappa-v2.1.3.jar)
- Install the python interface using pip:
pip install SpatialKappaand then test usingpython -m unittest SpatialKappa.tests. Within pythonhelp(SpatialKappa)gives the list of model-building and control functions.
COMPILATION
To make the SpatialKappa.jar file either:
- Import this code as an Ecclipse project; or
- Install ant (
sudo apt install ant openjdk-7-jdkon Debian/Ubuntu) and runmake all
To install the python interface, cd into the python directory, and follow the instructions in python/INSTALL.md
LICENSE
This project is licenced under the GNU Lesser General Public Licence Version 3 (LGPLv3), included as LICENSE.html.
Included third party libraries are released under their respective licences, listed below:
| Library | Home site | License |
|---|---|---|
| Antlr v3.2 | http://www.antlr.org | http://www.antlr.org/license.html |
| jlfgr v1.0 | http://java.sun.com/developer/techDocs/hi/repository/ | Included in archive |
| commons io v1.4 | http://commons.apache.org/io/ | http://commons.apache.org/io/license.html |
| jcommon v1.0.16 | http://www.jfree.org/jcommon/ | http://www.gnu.org/licenses/lgpl.html |
| jfreechart v1.0.13 | http://www.jfree.org/jfreechart/ | http://www.gnu.org/licenses/lgpl.html |
| EasyMock v3.0 | http://easymock.org/ | http://easymock.org/License.html |
| CgLib v2.2 | http://cglib.sourceforge.net/ | http://www.apache.org/foundation/licence-FAQ.html |
| Objenesis v1.2 | http://objenesis.googlecode.com/svn/docs/index.html | http://objenesis.googlecode.com/svn/docs/license.html |
| ASM v3.3.1 | http://asm.ow2.org/index.html | http://asm.ow2.org/license.html |
ACKNOWLEDGEMENTS
The development of Spatial Kappa was funded in part by SynthSys. SynthSys is a Centre for Integrative Systems Biology (CISB) funded by BBSRC and EPSRC, reference BB/D019621/1.
This open source software code was developed with funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement nos. 241498 (EUROSPIN project), 242167 (SynSys-project) and 604102 (Human Brain Project), and in the Human Brain Project, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No. 720270 and No. 785907 (Human Brain Project SGA1 and SGA2).
DISCLAIMER
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
