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

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/

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