start of the project

.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto
+
+# Custom for Visual Studio
+*.cs     diff=csharp
+*.sln    merge=union
+*.csproj merge=union
+*.vbproj merge=union
+*.fsproj merge=union
+*.dbproj merge=union
+
+# Standard to msysgit
+*.doc	 diff=astextplain
+*.DOC	 diff=astextplain
+*.docx diff=astextplain
+*.DOCX diff=astextplain
+*.dot  diff=astextplain
+*.DOT  diff=astextplain
+*.pdf  diff=astextplain
+*.PDF	 diff=astextplain
+*.rtf	 diff=astextplain
+*.RTF	 diff=astextplain

.gitignore

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+#################
+## Eclipse
+#################
+
+*.pydevproject
+.project
+.metadata
+bin/
+tmp/
+*.tmp
+*.bak
+*.swp
+*~.nib
+local.properties
+.classpath
+.settings/
+.loadpath
+
+# External tool builders
+.externalToolBuilders/
+
+# Locally stored "Eclipse launch configurations"
+*.launch
+
+# CDT-specific
+.cproject
+
+# PDT-specific
+.buildpath
+
+
+#################
+## Visual Studio
+#################
+
+## Ignore Visual Studio temporary files, build results, and
+## files generated by popular Visual Studio add-ons.
+
+# User-specific files
+*.suo
+*.user
+*.sln.docstates
+
+# Build results
+[Dd]ebug/
+[Rr]elease/
+*_i.c
+*_p.c
+*.ilk
+*.meta
+*.obj
+*.pch
+*.pdb
+*.pgc
+*.pgd
+*.rsp
+*.sbr
+*.tlb
+*.tli
+*.tlh
+*.tmp
+*.vspscc
+.builds
+*.dotCover
+
+## TODO: If you have NuGet Package Restore enabled, uncomment this
+#packages/
+
+# Visual C++ cache files
+ipch/
+*.aps
+*.ncb
+*.opensdf
+*.sdf
+
+# Visual Studio profiler
+*.psess
+*.vsp
+
+# ReSharper is a .NET coding add-in
+_ReSharper*
+
+# Installshield output folder
+[Ee]xpress
+
+# DocProject is a documentation generator add-in
+DocProject/buildhelp/
+DocProject/Help/*.HxT
+DocProject/Help/*.HxC
+DocProject/Help/*.hhc
+DocProject/Help/*.hhk
+DocProject/Help/*.hhp
+DocProject/Help/Html2
+DocProject/Help/html
+
+# Click-Once directory
+publish
+
+# Others
+[Bb]in
+[Oo]bj
+sql
+TestResults
+*.Cache
+ClientBin
+stylecop.*
+~$*
+*.dbmdl
+Generated_Code #added for RIA/Silverlight projects
+
+# Backup & report files from converting an old project file to a newer
+# Visual Studio version. Backup files are not needed, because we have git ;-)
+_UpgradeReport_Files/
+Backup*/
+UpgradeLog*.XML
+
+
+
+############
+## Windows
+############
+
+# Windows image file caches
+Thumbs.db
+
+# Folder config file
+Desktop.ini
+
+
+#############
+## Python
+#############
+
+*.py[co]
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+
+#Translations
+*.mo
+
+#Mr Developer
+.mr.developer.cfg
+
+# Mac crap
+.DS_Store

readme.md

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+# Spatial SBML
+This project contains a library, as well as a front end application for spatial simulation of SBML Models (using [SBML Level 3](http://sbml.org/Documents/Specifications) with the [Spatial package](http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Spatial_Geometries_and_Spatial_Processes "Spatial package") ). This project is made possible in cooperation with the [Funahashi Lab](http://fun.bio.keio.ac.jp/) who developed the simulator. (The initial presentation from COMBINE 2011 can still be found online [here](http://co.mbine.org/events/COMBINE_2011/agenda?q=system/files/2011-09-04-combine-funahashi-spatial-simulator.pdf).) 
+
+## How to build
+This project uses CMake, as such building ought to be as easy as running:
+
+```
+mkdir build  
+cd build  
+cmake -DBUILD_UI=ON <directory with sources>  
+make  
+make install
+```
+
+## Running the GUI
+Once installed, simply double click SpatialUI, and the following interface will come up.   
+
+![SpatialUI, the interface](http://)
+
+From here, you could simply open one of the example models supplied. We use a custom annotation to store settings such as the last selected species, the colors used for them as well as the bounds. Of course you can open any model in the SBML Spatial format. 
+
+## Libraries
+This project requires the following libraries: 
+
+- [libSBML](http://sbml.org/Software/libSBML) along with a supported xml library (xml2, expat, xerces-c)
+- [Qt4](http://qt-project.org/) for the frontend
+
+## License
+This project is licensed under the BSD license: 
+
+```
+Copyright (c) 2013, Frank T. Bergmann  
+All rights reserved. 
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are 
+met: 
+
+Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer. Redistributions in 
+binary form must reproduce the above copyright notice, this list of 
+conditions and the following disclaimer in the documentation and/or 
+other materials provided with the distribution. 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. 
+
+```