dfba & bioreactor

1. added id variables to both Organism and Bioreactor
2. changed the output of dFBA to t, V, X, S instead of t, y
removed flux_cone_projection()

removed flux_cone_projection().

it is replaced by flux_envelope()
Revert "removed flux_cone_projection()"

This reverts commit 534949a081e1c0f301054e7b2091cc7cced3abf8.
Merge branch 'master' into kai-branch
dFBA methods now returns a OrderedDict

dFBA methods now returns a OrderedDict containing simulation results
changed  the interface of Bioreactor __init__()

now allows organisms and metabolites to be set after the initial
construction of Bioreactor.
added dFBA_combination() to dfba module
fixed import in examples
added dyssco.py
minor changes to envelope methods interface
removed test case for fluxconeprojection
finished dyscco methods
removed import fluxconeprojection line in test_core
debug: bioreactor.py, dyssco

debugged:
__init__() of bioreactor.py

added:
calculate_yields_from_dfba() in IdealBatch and IdealFedbatch
dyssco.py

added:
calculate_performance()
calculate_performances()
performance2metrics()
Bioreactor_ox

Added a new Bioreactor_ox that extends Bioreactor to include the
oxygen_availability flag.
catching up to Master
resolved conflicts
more conflict resolution