Added a new branch called working
Updated loci_tools.jar
Made some small changes to the reaction model scripts
Minor modication
Added the User guide.docx
Extensively updated the Reaction1 model with comments and bug fixes
Cleaned up a few things and deleted old scripts
Made some minor modification to fix Issue #1
Made some minor modifications to fix Issue #2
Removed the NC Transport models, because the Reaction 1 model is the general version of this
Added ReactionModel2
Made some modifications to Reaction model 2.  Issue #3 is now resolved