added bioreactor package

created the bioreactor package.
the package should include bioreactor classes and dfba/dymmm
told git to ignore .idea

told git to ignore files in .idea
.idea is used by PyCharm
created bioreactor.py

bioreactor.py contains classes for bioreactor modeling
created framed\examples\basics.py

writing some examples for the basic usage of framed
FBA in basic.py

doing some basic FBA in basic.py
Merge branch 'master' into kai-branch
bioreactor.py -> m-dfba.py

renamed bioreactor.py to m-dfba.py.
m-dFBA stands for "multispecies dFBA".
considering renaming DyMMM framework to m-dFBA.
mv m-dfba.py mdfba.py

changed filename to mdfba.py because python doesn't seem to support
dash "-" in module names
mv init.py __init__.py
added tests directory and test_mdfba.py
added tests/fixtures directory

moved ec_core_model.txt into the fixtures diectory
test cases: mdfba

wrote some test cases for mdfba
mdfba -> dymmm

renamed mdfba back to dymmm.  (silly me)
wrote in dymmm.py

adapted most of dymmm.py to framed
still need to rewrite _ode_RHS
Merge branch 'master' into kai-branch
tests for dymmm

wrote more tests for dymmm
more tests
Merge branch 'master' into kai-branch
tried to write test codes for dymmm.

having some problems with dymmm test.
debugging dymmm