diff --git a/fluent b/fluent
index 7162098..a2781d7 100755
--- a/fluent
+++ b/fluent
@@ -1,9 +1,7 @@
 #!/usr/bin/python
 
 import sys
-sys.path.append('system')
 
-import dialogs
 import pygtk
 pygtk.require('2.0')
 import gtk
@@ -11,14 +9,10 @@ import gtk.gdk
 import gtk.glade
 import gnome
 import gnome.ui
-import pango
-import project
-import workflow
-import dataset
-import logger
-import plots
-import navigator
 import scipy
+import pango
+from system import project, workflow, dataset, logger, plots, navigator, dialogs
+
 
 PROGRAM_NAME = 'fluent'
 VERSION = '0.1.0'
diff --git a/system/__init__.py b/system/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/system/dataset.py b/system/dataset.py
index bb14564..95529ae 100644
--- a/system/dataset.py
+++ b/system/dataset.py
@@ -1,4 +1,4 @@
-import logger
+from system import logger
 from scipy import atleast_2d,asarray,ArrayType
 
 
diff --git a/system/dialogs.py b/system/dialogs.py
index 2b87cca..efebc5e 100644
--- a/system/dialogs.py
+++ b/system/dialogs.py
@@ -1,13 +1,11 @@
 import pygtk
 pygtk.require('2.0')
 import gtk
-import gobject
-import logger
-import project
-import workflows
-import workflow
 import sys
 import os
+import gobject
+from system import logger, project, workflow
+import workflows
 
 GLADEFILENAME = 'system/fluent.glade'
 
diff --git a/system/navigator.py b/system/navigator.py
index 8bd3e75..d827124 100644
--- a/system/navigator.py
+++ b/system/navigator.py
@@ -2,9 +2,7 @@
 import gtk
 import gobject
 import plots
-import logger
-import dataset
-import project
+from system import dataset, logger, plots, project
 
 class NavigatorView (gtk.TreeView):
     def __init__(self, project, app):
diff --git a/system/plots.py b/system/plots.py
index d427fc4..1b2f253 100644
--- a/system/plots.py
+++ b/system/plots.py
@@ -1,15 +1,14 @@
 
-import logger
 import pygtk
 import gtk
 import matplotlib
 import scipy
-import project
 from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas
 from matplotlib.axes import Subplot
 from matplotlib.figure import Figure
 from matplotlib.numerix import arange, sin, pi
 from matplotlib.widgets import RectangleSelector
+from system import logger
 
 
 class MainView (gtk.Notebook):
diff --git a/system/project.py b/system/project.py
index 5356b55..8c05c6e 100644
--- a/system/project.py
+++ b/system/project.py
@@ -1,8 +1,8 @@
-import dataset
-import plots
+
 import scipy
 import gobject
 import gtk
+from system import dataset, plots
 
 class Project:
     def __init__(self,name="Testing"):
diff --git a/system/workflow.py b/system/workflow.py
index 5c1eca8..970be89 100644
--- a/system/workflow.py
+++ b/system/workflow.py
@@ -1,8 +1,8 @@
 
 import gtk
-import logger
 import sys
 import os
+from system import logger
 
 def _workflow_classes(modname):
     """Returns a list of all subclasses of Workflow in a given module"""
diff --git a/workflows/go_workflow.py b/workflows/go_workflow.py
index 97d7908..411ca6e 100644
--- a/workflows/go_workflow.py
+++ b/workflows/go_workflow.py
@@ -1,9 +1,6 @@
 import gtk
-import logger
-from annotations import Annotations
-import workflow
-import plots
-import dataset
+from system import dataset, logger, plots, workflow
+from system.annotations import Annotations
 #import geneontology
 #import gostat
 from scipy import array,randn,log
diff --git a/workflows/pca_workflow.py b/workflows/pca_workflow.py
index 4664d9f..91e562f 100644
--- a/workflows/pca_workflow.py
+++ b/workflows/pca_workflow.py
@@ -1,12 +1,10 @@
 import gtk
-import logger
-import workflow as wf
-from workflow import Stage, Function
+import system.workflow as wf
+from system.workflow import Stage, Function
 import pickle
 from scipy import log2,transpose,dot,divide,shape,mean,resize,zeros
 from scipy.linalg import svd,inv,norm,get_blas_funcs,eig
-import plots
-import dataset
+from system import dataset, logger, plots
 
 class PCAWorkflow(wf.Workflow):
     name = 'PCA Workflow'