TREMPPI
Toolkit for Reverse Engineering of Molecular Pathways via Parameter Identification
USER GUIDE: http://dibimath.github.io/TREMPPI/
PLEASE DO NOT BUILD FROM THE MASTER BRANCH, IT IS DEVELOPMENT-ONLY! THE STABLE RELEASE CAN BE ACCESSED AT: https://github.com/xstreck1/TREMPPI/releases
Licensed under GNU GPL v3: http://www.gnu.org/licenses/gpl-3.0.en.html
3rd party content
C++ libraries included (see the directory for the specific license):
- sqlite3: http://www.sqlite.org/
- sqlite3pp: https://github.com/iwongu/sqlite3pp/
- json (JsonCPP): http://sourceforge.net/projects/jsoncpp/
JS libraries included (open-source):
- jQuery: http://jqueryui.com/
- jQueryUI: http://jqueryui.com/
- cytoscapeJS: http://cytoscape.github.io/cytoscape.js/
- qTip2: http://qtip2.com/
- paper.js: http://paperjs.org/
- EditableGrid: http://www.editablegrid.net/
BUILDING
Install dependencies, run CMake and then compile with your compiler.
Defines (for CMake, use only if CMake can't find the specified locations):
- BUILD_TEST: use to build testing binary (see below, default off)
- BOOST_ROOT: use to specify boost location (the folder that holds both libraries and headers)
- GTEST_ROOT: use to specify gtest location, only if building gtest
- GECODE_DIR: use to specify gecode constraint solver binary location, do not mix with GECODE_LOCAL
- GECODE_LOCAL: use to specify gecode constraint solver source location, do not mix with GECODE_DIR
- TREMPPI_STATIC: use to build with static version of existing libraries (boost, gecode, etc...), will still depend on the runtime libraries and pythonlib
Dependencies:
- CMake 2.8 (or higher)
- GCC 4.9.0 (or higher) or Visual Studio 2015 (or higher) or Clang 3.4.2 (or higher)
- Boost libraries 1.54.0 (or higher)
- Gecode 4.2.1 (or higher), get here: http://www.gecode.org/
- Python 3.x.x (or higher), compiled for the same architecture (so 32-bit if you compile 32-bit target and 64-bit if you compile 64-bit target)
- Python packages flask-user, libSBML
Optional:
- GTest 1.7.0 (or higher) - only for testing