Style consistency for conditionals

Some conditionals were expressed as "if (...)" while others used
"if(...)". I switched all to the predominant style ["if (...)"].
More style consistency changes
Even more style consistency changes

Mostly changed if statement formatting from this:
"if (...) {"
to this:
"if (...)
 {"

Also fixed some indention problems.
Updated URL
Even more style consistency changes

Changing things like this:
"for( i = 0; i < 10; i++ )"
to this:
"for (i = 0; i < 10; i++)"
and other similar changes.
Updated institution information

Mentions MMBioS and the grant number.
Refactored code in prepare_reactions

Started breaking up the prepare_reactions function to make it a little
easier to maintain and understand.
Removed redundant comment from previous commit