Added builder class (from tbidbaxlipo)
Added debug message to bng.py output
Option to specify output file basename in bng/run_ssa
Left a colon off the if block
Merge remote-tracking branch 'pysb/master'
keep changes to do_export from leaking

The reset of do_export needs to go *after* the model load, not before.
otherwise if the last model to be loaded changes it to False then that
state will leak out into subsequent tests.
keep noisy distutils output from breaking doctests
as_complex_pattern converts Monomers

This prevents all constructors that depend on as_reaction_pattern
or as_complex_pattern to take MonomerPattern from throwing an error
when given a Monomer instead.

In particular, this resolves issue number #88, in which the Observable
constructor would error when a Monomer was used instead of a
MonomerPattern.
Wrapped integrate.py to 80 chars
Solver's call to lambdify specifies "numpy"

Previously, lambdify would use the built-in math module's
implementations of sympy functions (such as exponentiation)
which would fail when passed numpy arrays (such as the trajectories
resulting from observables. Specifying "numpy" in the call to lambdify
indicates that the numpy implementation of sympy functions are preferred.
minor tutorial cleanups
Updated the Rules section of the tutorial.

Included a tutorial_d which has a single binding rule between Raf and
MEK. Also added an identifier to useful_references.rst so that we could
hyperlink to it.
Fixed a few typos/capitalization issues
updated observables section of tutorial