diff --git a/setup.py b/setup.py
index ebaae0b58..d94e02f51 100644
--- a/setup.py
+++ b/setup.py
@@ -33,14 +33,14 @@
                 'blessings>=1.5.1',
                 'pandas>=0.15.2',
                 'ordered-set>=1.2',
-                'cobra>=0.4',
+                'cobra>=0.4.1',
                 'optlang>=0.3.0',
                 'requests>=2.5.0',
                 'numexpr>=2.4',
                 'networkx>=1.9.1',
                 'six>=1.9.0',
                 'escher>=1.1.2',
-                'IProgress>=0.2',
+                'IProgress>=0.4',
                 'inspyred>=1.0',
                 'lazy-object-proxy>=1.2.0',
                 'palettable>=2.1.1']
@@ -50,7 +50,7 @@
     'swiglpk': ['swiglpk>=1.2.14'],
     'plotly': ['plotly>=1.9.6'],
     'bokeh': ['bokeh>=0.11.1'],
-    'jupyter': ['jupyter>=1.0.0', 'ipywidgets>=4.1.1', 'runipy>=0.1.5'],
+    'jupyter': ['jupyter>=1.0.0', 'ipywidgets>=4.1.1'],
     'test': ['nose>=1.3.7', 'rednose>=0.4.3', 'coverage>=4.0.3'],
     'parallel': ['redis>=2.10.5', 'ipyparallel>=5.0.1'],
     'sbml': ['python-libsbml>=5.13.0', 'lxml>=3.6.0']