Spatial Kappa
14 September 2012INTRODUCTION
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.
Note that the project makes use of the ANTLR IDE Eclipse plugin to generate the parser. If building the project from source, you'll need similar, or generate the parser from the ANTLR grammar manually.
DOWNLOADS
The project is hosted on github at https://github.com/donal-s/SpatialKappa. Downloads of the latest versions are available here.
USERS
The simulator was used by the 2010 Edinburgh iGEM team to run the computational models of the project. I'm now looking to expand the tool to be more useful for general users. Comments and suggestions are appreciated.
LICENSE
This project is licenced under the GNU Lesser General Public Licence Version 3 (LGPLv3), included as LICENSE. 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.
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.