Update gapAnalysis.py

Added exchange and transport reactions, as well as iterations to growMatch
clean up Jon's fixes to gap analysis
modify tries to set read-only reversibility flag

This flag was made into a read-only property calculated from the upper
and lower bounds, so it should not be directly set anymore.
Merge pull request #51 from aebrahim/modify_reversible_bug

modify tries to set read-only reversibility flag
add doc pages explaining reactions and metabolites

Touched up rst exported from ipython notebooks, which are also included
examples set reversibility

reversibility should not be set, but is calculated from upper and lower
bounds
read only properties for Reaction (genes and mets)

Now users can view the metabolites and genes using reaction.genes and
reaction.metabolites, but these properties are read-only. The value is
still stored in the prefiexed reaction._genes and reaction._metabolites
properties.
Reaction has .reactants and .products properties
depracate Reaction.get_gene()
Merge pull request #53 from aebrahim/reaction_clean

Clean up Reaction class (continued)
Merge pull request #52 from aebrahim/more_docs

More docs
reaction.gene_reaction_rule sets gpr

Instead of calling the function add_gene_reaction_rule to set the gpr,
the gene_reaction_rule can be modified directly, and the setter
automatically will call the gpr parser. This is safer because the gpr
could previously be modified with no effect.

The gene_reaction_rule information is now stored as
_gene_reaction_rule. In order to preserve pickle compatibility, this is
now accounted for in __setstate__
add some unit tests for raection GPR's
one more unit test for reaction gpr
views to read only properties are read only

use frozenset for reaction.genes and dictrpoxy (if possible) for
reaction.metabolites
give species a readonly reactions property

Can be used to get a read-only view of the metabolite reactions
typos in Reaction.py
remove old maps module
add visbio documentation

Examples on how to use visbio with cobrapy to visualize maps.
link to notebooks properly