Update visbio.rst

Fix links (convert from markdown to rst)
make sure phenotype phase plane has black plot lines
fix syntax errors in designAnalysis.py
Merge pull request #58 from aebrahim/oven_update

Small oven bugfixes
Corrected test for empty compartment lists in function write_cobra_model_to_sbml_file to allow default compartment lists to be generated when not specified
Grouped together code & comments that deal with compartments in function write_cobra_model_to_sbml_file
fix bug in pFBA from oven
move pFBA from oven to mainline
fix revert_to_reversible rxn/met relationship

need to use model.remove_reactions to make sure reaction/metabolite
awareness is updated
relative imports in parsimonious.py

now that it has been moved out of the oven
unit tests and bugfixes for pFBA/make_reversible
Merge pull request #61 from aebrahim/pFBA

Move pFBA from oven to mainline
Merge pull request #60 from afif-elghraoui/master

Minor Bug Fix in write_cobra_model_to_sbml_file to Allow Default Compartments to be created
small doc formatting bugfixes
reran autodoc script
update pickles
Remove readonly reaction.metabolites dict for now

dictproxy had issues on macs, need a different solution
Merge pull request #64 from aebrahim/fix63

Remove readonly reaction.metabolites dict for now
Merge pull request #7 from opencobra/master

Latest updates from opencobra
merged in updates from opencobra/cobrapy