Merge pull request #1 from streppneumo/master

changes to interactive shell
Merge pull request #1 from streppneumo/master

changes to interactive shell
Adding first lipid metabolism rxns
More subsystems added
Tyrosine genes accounted for
Taurine & hypotaurine reactions
New pathways added
Selenocompound underway
More runs and orthologs added
Last changes made
Little edits
Paralog work
Merge pull request #9 from laruer14/master

Summer Metabolic Rxns
Merge pull request #8 from whittaam/master

End of summer work
shorthand parsing, Added class