diff --git a/Introduction.html b/Introduction.html index e35390a..44cf36d 100644 --- a/Introduction.html +++ b/Introduction.html @@ -11766,7 +11766,7 @@

Varialbles and Types
-
In [6]:
+
In [1]:
56*8
@@ -11780,7 +11780,7 @@ 
Varialbles and Types
 
 
-
Out[6]:

+
Out[1]:

 
 
 

@@ -11795,7 +11795,7 @@ 
Varialbles and Types
 

-
In [7]:

+
In [2]:

 

     

 
x=7
@@ -11809,7 +11809,7 @@ 
Varialbles and Types
 
 
-
Out[7]:

+
Out[2]:

 
 
 

@@ -11824,7 +11824,7 @@ 
Varialbles and Types
 

-
In [8]:

+
In [3]:

 

     

 
x+1
@@ -11838,7 +11838,7 @@ 
Varialbles and Types
 
 
-
Out[8]:

+
Out[3]:

 
 
 

@@ -11853,7 +11853,7 @@ 
Varialbles and Types
 

-
In [9]:

+
In [4]:

 

     

 
x^2
@@ -11867,7 +11867,7 @@ 
Varialbles and Types
 
 
-
Out[9]:

+
Out[4]:

 
 
 

@@ -11882,7 +11882,7 @@ 
Varialbles and Types
 

-
In [10]:

+
In [5]:

 

     

 
typeof(x)
@@ -11896,7 +11896,7 @@ 
Varialbles and Types
 
 
-
Out[10]:

+
Out[5]:

 
 
 

@@ -11911,7 +11911,7 @@ 
Varialbles and Types
 

-
In [11]:

+
In [6]:

 

     

 
x/3
@@ -11925,7 +11925,7 @@ 
Varialbles and Types
 
 
-
Out[11]:

+
Out[6]:

 
 
 

@@ -11940,7 +11940,7 @@ 
Varialbles and Types
 

-
In [12]:

+
In [7]:

 

     

 
cos(pi)
@@ -11954,7 +11954,7 @@ 
Varialbles and Types
 
 
-
Out[12]:

+
Out[7]:

 
 
 

@@ -11969,7 +11969,7 @@ 
Varialbles and Types
 

-
In [13]:

+
In [8]:

 

     

 
typeof(ans)
@@ -11983,7 +11983,7 @@ 
Varialbles and Types
 
 
-
Out[13]:

+
Out[8]:

 
 
 

@@ -11998,7 +11998,7 @@ 
Varialbles and Types
 

-
In [14]:

+
In [9]:

 

     

 
im^2
@@ -12012,7 +12012,7 @@ 
Varialbles and Types
 
 
-
Out[14]:

+
Out[9]:

 
 
 

@@ -12027,7 +12027,7 @@ 
Varialbles and Types
 

-
In [15]:

+
In [10]:

 

     

 
typeof(ans)
@@ -12041,7 +12041,7 @@ 
Varialbles and Types
 
 
-
Out[15]:

+
Out[10]:

 
 
 

@@ -12056,7 +12056,7 @@ 
Varialbles and Types
 

-
In [16]:

+
In [11]:

 

     

 
"Hello" * " world"
@@ -12070,7 +12070,7 @@ 
Varialbles and Types
 
 
-
Out[16]:

+
Out[11]:

 
 
 

@@ -12085,7 +12085,7 @@ 
Varialbles and Types
 

-
In [17]:

+
In [12]:

 

     

 
typeof(ans)
@@ -12099,7 +12099,7 @@ 
Varialbles and Types
 
 
-
Out[17]:

+
Out[12]:

 
 
 

@@ -12114,7 +12114,7 @@ 
Varialbles and Types
 

-
In [18]:

+
In [13]:

 

     

 
70//15
@@ -12128,7 +12128,7 @@ 
Varialbles and Types
 
 
-
Out[18]:

+
Out[13]:

 
 
 

@@ -12143,7 +12143,36 @@ 
Varialbles and Types
 

-
In [1]:

+
In [14]:

+

+    

+
true
+

+
+

+

+

+
+

+

+
+
+
Out[14]:

+
+
+

+
true

+

+
+

+
+

+

+
+

+

+

+
In [15]:

 

     

 
12 ≠ 42
@@ -12157,7 +12186,7 @@ 
Varialbles and Types
 
 
-
Out[1]:

+
Out[15]:

 
 
 

@@ -12172,7 +12201,7 @@ 
Varialbles and Types
 

-
In [3]:

+
In [16]:

 

     

 
2 ∈ [6,3,5]
@@ -12186,7 +12215,7 @@ 
Varialbles and Types
 
 
-
Out[3]:

+
Out[16]:

 
 
 

@@ -12201,7 +12230,7 @@ 
Varialbles and Types
 

-
In [19]:

+
In [17]:

 

     

 
typeof(ans)
@@ -12215,11 +12244,11 @@ 
Varialbles and Types
 
 
-
Out[19]:

+
Out[17]:

 
 
 

-
Rational{Int64}

+
Bool

 

 
 

@@ -12230,7 +12259,7 @@ 
Varialbles and Types
 

-
In [20]:

+
In [18]:

 

     

 
"Like in perl you may write x=$x"
@@ -12244,7 +12273,7 @@ 
Varialbles and Types
 
 
-
Out[20]:

+
Out[18]:

 
 
 

@@ -12259,7 +12288,7 @@ 
Varialbles and Types
 

-
In [21]:

+
In [19]:

 

     

 
"... but also $(exp(x))"
@@ -12273,7 +12302,7 @@ 
Varialbles and Types
 
 
-
Out[21]:

+
Out[19]:

 
 
 

@@ -12318,7 +12347,7 @@ 
Functions + Multiple Dispatch
 

-
In [6]:

+
In [20]:

 

     

 
f(x) = x ^ 3
@@ -12332,11 +12361,11 @@ 
Functions + Multiple Dispatch
 
 
-
Out[6]:

+
Out[20]:

 
 
 

-
f (generic function with 2 methods)

+
f (generic function with 1 method)

 

 
 

@@ -12347,7 +12376,7 @@ 
Functions + Multiple Dispatch
 

-
In [7]:

+
In [21]:

 

     

 
f(3)
@@ -12361,7 +12390,7 @@ 
Functions + Multiple Dispatch
 
 
-
Out[7]:

+
Out[21]:

 
 
 

@@ -12376,7 +12405,7 @@ 
Functions + Multiple Dispatch
 

-
In [8]:

+
In [22]:

 

     

 
f("ha ")
@@ -12390,49 +12419,13 @@ 
Functions + Multiple Dispatch
 
 
-

-

-
now in f(x::AbstractString)
-

-

-

-
-
Out[8]:

+
Out[22]:

 
 
 

-
"Hello"

-

-
-

-
-

-

-
+
"ha ha ha "

 

-

-

-
In [15]:

-

-    

-
super(Float)
-

-
-

-

-

-
-

-

 
-
-

-

-
-LoadError: UndefVarError: Float not defined
-while loading In[15], in expression starting on line 1
-

-

 

 
 

@@ -12441,7 +12434,7 @@ 
Functions + Multiple Dispatch
 

-
In [28]:

+
In [23]:

 

     

 
function f(x::AbstractString) 
@@ -12463,7 +12456,7 @@ 
Functions + Multiple Dispatch
 
 
-
Out[28]:

+
Out[23]:

 
 
 

@@ -12478,7 +12471,7 @@ 
Functions + Multiple Dispatch
 

-
In [29]:

+
In [24]:

 

     

 
methods(f)
@@ -12492,10 +12485,10 @@ 
Functions + Multiple Dispatch
 
 
-
Out[29]:

+
Out[24]:

 
 

-3 methods for generic function f:
  •  f(x::AbstractString) at In[28]:2
  •  f(x::AbstractFloat) at In[28]:7
  •  f(x) at In[6]:1

+3 methods for generic function f:
  •  f(x::AbstractString) at In[23]:2
  •  f(x::AbstractFloat) at In[23]:7
  •  f(x) at In[20]:1

 

 
 

@@ -12506,7 +12499,7 @@ 
Functions + Multiple Dispatch
 

-
In [32]:

+
In [25]:

 

     

 
@show f(2.5);
@@ -12535,10 +12528,10 @@ 
Functions + Multiple Dispatch
 

-
In [34]:

+
In [26]:

 

     

-
@show f(Float16(2.5));
+
@show f( Float16(2.5) );
 

 
 

@@ -12564,7 +12557,7 @@ 
Functions + Multiple Dispatch
 

-
In [35]:

+
In [27]:

 

     

 
@show f("abc")
@@ -12597,7 +12590,7 @@ 
Functions + Multiple Dispatch
 

-
In [38]:

+
In [28]:

 

     

 
methods(print)
@@ -12611,7 +12604,7 @@ 
Functions + Multiple Dispatch
 
 
-
Out[38]:

+
Out[28]:

 
 

 18 methods for generic function print:
@@ -12625,7 +12618,7 @@ 
Functions + Multiple Dispatch
 

-
In [36]:

+
In [29]:

 

     

 
methods(println)
@@ -12639,7 +12632,7 @@ 
Functions + Multiple Dispatch
 
 
-
Out[36]:

+
Out[29]:

 
 

 2 methods for generic function println:
@@ -12662,7 +12655,7 @@ 
Composite Types
 

-
In [39]:

+
In [30]:

 

     

 
type Point
@@ -12679,7 +12672,7 @@ 
Composite Types
 

-
In [40]:

+
In [31]:

 

     

 
p = Point(2,3,"Siegfried")
@@ -12693,7 +12686,7 @@ 
Composite Types
 
 
-
Out[40]:

+
Out[31]:

 
 
 

@@ -12708,11 +12701,11 @@ 
Composite Types
 

-
In [41]:

+
In [35]:

 

     

-
function g(p::Point)
-    println("in g(p::Point)")
+
function f(p::Point)
+    println("\nnow in f(x::Point) with p=$p of type $(typeof(p))")
     p.x = p.x + p.y
     return p.name
 end
@@ -12726,39 +12719,11 @@ 
Composite Types
 
 
-
Out[41]:

+
Out[35]:

 
 
 

-
g (generic function with 5 methods)

-

-
-

-
-

-

-
-

-

-

-
In [42]:

-

-    

-
methods(g)
-

-
-

-

-

-
-

-

-
-
-
Out[42]:

-
-

-5 methods for generic function g:
  •  g(y::Int64) at In[29]:2
  •  g(y::AbstractString) at In[29]:7
  •  g(y::AbstractString, z) at In[29]:7
  •  g(p::Point) at In[41]:2
  •  g(y) at In[26]:2

+
f (generic function with 4 methods)

 

 
 

@@ -12769,10 +12734,10 @@ 
Composite Types
 

-
In [43]:

+
In [36]:

 

     

-
methodswith(Point)
+
methods(f)
 

 
 

@@ -12783,10 +12748,10 @@ 
Composite Types
 
 
-
Out[43]:

+
Out[36]:

 
 

-1-element Array{Method,1}:
  •  g(p::Point) at In[41]:2

+4 methods for generic function f:
  •  f(x::AbstractString) at In[23]:2
  •  f(x::AbstractFloat) at In[23]:7
  •  f(p::Point) at In[35]:2
  •  f(x) at In[20]:1

 

 
 

@@ -12797,10 +12762,10 @@ 
Composite Types
 

-
In [44]:

+
In [37]:

 

     

-
g(p)
+
f(p)
 

 
 

@@ -12813,12 +12778,13 @@ 
Composite Types

 

-
in g(p::Point)
+
+now in f(x::Point) with p=Point(5,3,"Siegfried") of type Point
 

 

 

 
-
Out[44]:

+
Out[37]:

 
 
 

@@ -12833,7 +12799,7 @@ 
Composite Types
 

-
In [45]:

+
In [38]:

 

     

 
p
@@ -12847,11 +12813,11 @@ 
Composite Types
 
 
-
Out[45]:

+
Out[38]:

 
 
 

-
Point(5,3,"Siegfried")

+
Point(8,3,"Siegfried")

 

 
 

@@ -12871,7 +12837,7 @@ 
parametric types and methods
 

-
In [46]:

+
In [39]:

 

     

 
type Line{T}
@@ -12890,7 +12856,7 @@ 
parametric types and methods
 

-
In [47]:

+
In [40]:

 

     

 
L1=Line(23,3,4,44,"Julia")
@@ -12904,7 +12870,7 @@ 
parametric types and methods
 
 
-
Out[47]:

+
Out[40]:

 
 
 

@@ -12919,7 +12885,7 @@ 
parametric types and methods
 

-
In [48]:

+
In [41]:

 

     

 
L2=Line(23.777,3.5,4.1,4.0,"Rolf")
@@ -12933,7 +12899,7 @@ 
parametric types and methods
 
 
-
Out[48]:

+
Out[41]:

 
 
 

@@ -12948,11 +12914,11 @@ 
parametric types and methods
 

-
In [49]:

+
In [42]:

 

     

-
function g{T}(x::Line{T}) 
-    println("in g for $T")
+
function f{T}(x::Line{T}) 
+    println("\nnow in f(x::Line{T}) with x=$x of type $(typeof(x))")
     x.name
 end
 

@@ -12965,11 +12931,11 @@ 
parametric types and methods
 
 
-
Out[49]:

+
Out[42]:

 
 
 

-
g (generic function with 6 methods)

+
f (generic function with 5 methods)

 

 
 

@@ -12980,10 +12946,10 @@ 
parametric types and methods
 

-
In [50]:

+
In [43]:

 

     

-
g(L1),g(L2)
+
f(L1),f(L2)
 

 
 

@@ -12996,13 +12962,15 @@ 
parametric types and methods

 

-
in g for Int64
-in g for Float64
+
+now in f(x::Line{T}) with x=Line{Int64}(23,3,4,44,"Julia") of type Line{Int64}
+
+now in f(x::Line{T}) with x=Line{Float64}(23.777,3.5,4.1,4.0,"Rolf") of type Line{Float64}
 

 

 

 
-
Out[50]:

+
Out[43]:

 
 
 

@@ -13026,7 +12994,7 @@ 
Arrays

 

 

 

-
In [37]:

+
In [44]:

 

     

 
A=[1,2,9]
@@ -13040,7 +13008,7 @@ 
Arrays

 

 
 
-
Out[37]:

+
Out[44]:

 
 
 

@@ -13058,10 +13026,10 @@ 
Arrays

 

 

 

-
In [38]:

+
In [45]:

 

     

-
A+2.1
+
A == 2
 

 
 

@@ -13072,14 +13040,11 @@ 
Arrays

 

 
 
-
Out[38]:

+
Out[45]:

 
 
 

-
3-element Array{Float64,1}:
-  3.1
-  4.1
- 11.1

+
false

 

 
 

@@ -13090,7 +13055,7 @@ 
Arrays

 

 

 

-
In [41]:

+
In [46]:

 

     

 
A .== 2
@@ -13104,7 +13069,7 @@ 
Arrays

 

 
 
-
Out[41]:

+
Out[46]:

 
 
 

@@ -13122,7 +13087,39 @@ 
Arrays

 

 

 

-
In [42]:

+
In [47]:

+

+    

+
A+2.1
+

+
+

+

+

+
+

+

+
+
+
Out[47]:

+
+
+

+
3-element Array{Float64,1}:
+  3.1
+  4.1
+ 11.1

+

+
+

+
+

+

+
+

+

+

+
In [48]:

 

     

 
B=[1 2 3; 6 7 4; 6 2 1]
@@ -13136,7 +13133,7 @@ 
Arrays

 

 
 
-
Out[42]:

+
Out[48]:

 
 
 

@@ -13154,7 +13151,7 @@ 
Arrays

 

 

 

-
In [43]:

+
In [49]:

 

     

 
C=[ i*j for i in 1:3, j in 1:4 ]
@@ -13168,7 +13165,7 @@ 
Arrays

 

 
 
-
Out[43]:

+
Out[49]:

 
 
 

@@ -13186,7 +13183,7 @@ 
Arrays

 

 

 

-
In [56]:

+
In [50]:

 

     

 
B * A
@@ -13200,7 +13197,7 @@ 
Arrays

 

 
 
-
Out[56]:

+
Out[50]:

 
 
 

@@ -13218,7 +13215,7 @@ 
Arrays

 

 

 

-
In [57]:

+
In [51]:

 

     

 
#B =rand(500,500)
@@ -13235,12 +13232,12 @@ 
Arrays

 
 

 

-
  0.490006 seconds (285.75 k allocations: 12.694 MB, 1.31% gc time)
+
  0.417821 seconds (288.68 k allocations: 12.865 MB)
 

 

 

 
-
Out[57]:

+
Out[51]:

 
 
 

@@ -13258,7 +13255,7 @@ 
Arrays

 

 

 

-
In [58]:

+
In [52]:

 

     

 
@time svd(B)
@@ -13274,12 +13271,12 @@ 
Arrays

 
 

 

-
  0.226167 seconds (114.64 k allocations: 5.078 MB, 2.76% gc time)
+
  0.195268 seconds (117.06 k allocations: 5.161 MB)
 

 

 

 
-
Out[58]:

+
Out[52]:

 
 
 

@@ -13313,7 +13310,7 @@ 
Dictionary
 

 

-
In [59]:

+
In [53]:

 

     

 
d = Dict( "A"=>6, "B"=> 20)
@@ -13327,7 +13324,7 @@ 
Dictionary
 
 
-
Out[59]:

+
Out[53]:

 
 
 

@@ -13344,7 +13341,7 @@ 
Dictionary
 

 

-
In [60]:

+
In [54]:

 

     

 
d["A"]
@@ -13358,7 +13355,7 @@ 
Dictionary
 
 
-
Out[60]:

+
Out[54]:

 
 
 

@@ -13373,7 +13370,7 @@ 
Dictionary
 

 

-
In [61]:

+
In [55]:

 

     

 
for (key,value) in d
@@ -13412,7 +13409,7 @@ 
Regular Expressions
 

-
In [62]:

+
In [56]:

 

     

 
my_regex = r"[ABC]"
@@ -13445,7 +13442,7 @@ 
Regular Expressions
 

-
In [63]:

+
In [57]:

 

     

 
my_regex =r"(\d+)g"
@@ -13460,7 +13457,7 @@ 
Regular Expressions
 
 
-
Out[63]:

+
Out[57]:

 
 
 

@@ -13484,7 +13481,7 @@ 
Flow Control&#
 

 

 

-
In [64]:

+
In [58]:

 

     

 
for i in 1:5 
@@ -13517,7 +13514,7 @@ 
Flow Control&#
 

 

 

-
In [65]:

+
In [59]:

 

     

 
for i in 1:10
@@ -13570,7 +13567,7 @@ 
Packages

 

 

-
In [66]:

+
In [60]:

 

     

 
Pkg.status()
@@ -13767,6 +13764,19 @@ 
Packages

 

 
+

+

+

+
In [ ]:

+

+    

+
#Pkg.generate("someName")
+

+
+

+

+

+
 

 

 

@@ -13779,7 +13789,7 @@ 
DataFrames
 

 

-
In [67]:

+
In [61]:

 

     

 
using DataFrames
@@ -13794,10 +13804,10 @@ 
DataFrames
 
 
-
Out[67]:

+
Out[61]:

 
 

-
xy
1210.04611913606157114
2220.8373635242857538
3230.9066330243929763
4240.29675648510293584
5250.026788088896794626
6260.5217667751899686
7270.9032616276257022
8280.20058000081954552
9290.784639890245026
10300.6536073175415043

+
xy
1210.5377985654352477
2220.8080711876006776
3230.9541549857881655
4240.33134837317344057
5250.8443261865933054
6260.4257533982368864
7270.8457130119066063
8280.3766193582981403
9290.9043218651444398
10300.5068968925566211

 

 
 

@@ -13808,7 +13818,7 @@ 
DataFrames
 

 

-
In [68]:

+
In [62]:

 

     

 
mean(d[:x]), mean(d[:y])
@@ -13822,11 +13832,11 @@ 
DataFrames
 
 
-
Out[68]:

+
Out[62]:

 
 
 

-
(25.5,0.5177515870161777)

+
(25.5,0.653500382473353)

 

 
 

@@ -13837,7 +13847,7 @@ 
DataFrames
 

 

-
In [69]:

+
In [63]:

 

     

 
using StatsBase
@@ -13852,11 +13862,11 @@ 
DataFrames
 
 
-
Out[69]:

+
Out[63]:

 
 
 

-
0.21569762172381235

+
-0.07597318459490848

 

 
 

@@ -13867,7 +13877,7 @@ 
DataFrames
 

 

-
In [70]:

+
In [64]:

 

     

 
using RDatasets
@@ -13891,7 +13901,7 @@ 
DataFrames
 

 
-
Out[70]:

+
Out[64]:

 
 

 
SepalLengthSepalWidthPetalLengthPetalWidthSpecies
15.13.51.40.2setosa
24.93.01.40.2setosa
34.73.21.30.2setosa
44.63.11.50.2setosa
55.03.61.40.2setosa
65.43.91.70.4setosa

@@ -13905,7 +13915,7 @@ 
DataFrames
 

 

-
In [73]:

+
In [65]:

 

     

 
by(iris, :Species, size)
@@ -13919,7 +13929,7 @@ 
DataFrames
 
 
-
Out[73]:

+
Out[65]:

 
 

 
Speciesx1
1setosa(50,5)
2versicolor(50,5)
3virginica(50,5)

@@ -13933,7 +13943,7 @@ 
DataFrames
 

 

-
In [74]:

+
In [66]:

 

     

 
using DimensionalityReduction
@@ -13949,7 +13959,17 @@ 
DataFrames
 
 
-
Out[74]:

+

+

+
WARNING: Base.FloatingPoint is deprecated, use AbstractFloat instead.
+  likely near /Users/arndt/.julia/v0.4/DimensionalityReduction/src/nmf.jl:10
+WARNING: Base.FloatingPoint is deprecated, use AbstractFloat instead.
+  likely near /Users/arndt/.julia/v0.4/DimensionalityReduction/src/nmf.jl:10
+

+

+

+
+
Out[66]:

 
 
 

@@ -14045,7 +14065,7 @@ 
Graphics - PlotlyJS
 

-
In [75]:

+
In [67]:

 

     

 
using PlotlyJS
@@ -14198,7 +14218,7 @@ 
Graphics - PlotlyJS
 

-
In [76]:

+
In [68]:

 

     

 
nms = unique(iris[:Species])
@@ -14234,16 +14254,16 @@ 
Graphics - PlotlyJS
 
 
-
Out[76]:

+
Out[68]:

 
 

-

+

 
 
@@ -14258,7 +14278,7 @@ 
Graphics - PlotlyJS
 

-
In [ ]:

+
In [69]:

 

     

 
typeof(p1)
@@ -14268,13 +14288,29 @@ 
Graphics - PlotlyJS
+

+
+
+
Out[69]:

+
+
+

+
PlotlyJS.SyncPlot{PlotlyJS.JupyterDisplay}

+

+
+

+
+

+

+
 

 

 

 
In [ ]:

 

     

-
PlotlyJS.savefig(p1, "output_filename.pdf")
+
#PlotlyJS.savefig(p1, "output_filename.pdf")
 

 
 

@@ -14284,7 +14320,7 @@ 
Graphics - PlotlyJS
 

-
In [77]:

+
In [70]:

 

     

 
function clustering_alpha_shapes()
@@ -14340,16 +14376,16 @@ 
Graphics - PlotlyJS
 
 
-
Out[77]:

+
Out[70]:

 
 

-

+

 
 
@@ -14374,7 +14410,7 @@ 
Calling R<
 

 

 

-
In [78]:

+
In [71]:

 

     

 
using RCall
@@ -14387,7 +14423,7 @@ 
Calling R<
 

 

 

-
In [79]:

+
In [72]:

 

     

 
R"rnorm(10)"
@@ -14401,13 +14437,13 @@ 
Calling R<
 

 
 
-
Out[79]:

+
Out[72]:

 
 
 

 
RCall.RObject{RCall.RealSxp}
- [1] -0.2684685  0.5427448 -0.9213678  0.8288000 -0.3974171  1.8959922
- [7]  0.6632521 -0.3106209  1.6267463  0.5812782
+ [1] -1.80862226  0.52612679 -0.30935616  0.16500632 -0.07844949 -0.32057512
+ [7]  0.37502888  0.50023911  0.36234372 -0.09131232
 

 

 
@@ -14419,7 +14455,7 @@ 
Calling R<
 

 

 

-
In [80]:

+
In [73]:

 

     

 
L = 8
@@ -14437,19 +14473,19 @@ 
Calling R<
 

 
 
-
Out[80]:

+
Out[73]:

 
 
 

 
8-element Array{Float64,1}:
- -0.0371922
- -0.164406 
-  1.83884  
-  0.562734 
-  1.63202  
-  0.611594 
-  2.38667  
- -0.608195 

+  1.60154  
+  0.360681 
+  0.552795 
+ -0.0579874
+  0.0642647
+ -0.468992 
+  1.00036  
+  1.91809  

 

 
 

@@ -14460,7 +14496,7 @@ 
Calling R<
 

 

 

-
In [81]:

+
In [74]:

 

     

 
rcopy(R"t.test(rnorm(1000))")
@@ -14474,20 +14510,20 @@ 
Calling R<
 

 
 
-
Out[81]:

+
Out[74]:

 
 
 

 
Dict{Symbol,Any} with 9 entries:
-  :statistic           => 0.10332942684641923
-  symbol("conf.int")   => [-0.05921758561151922,0.06580056524544481]
+  :statistic           => -1.0314510079327326
+  symbol("conf.int")   => [-0.09349989910375861,0.0290728780803126]
   :alternative         => "two.sided"
   :parameter           => 999.0
-  symbol("p.value")    => 0.9177222598844713
+  symbol("p.value")    => 0.3025790137321886
   :method              => "One Sample t-test"
   symbol("data.name")  => "rnorm(1000)"
   symbol("null.value") => 0.0
-  :estimate            => 0.0032914898169627916

+  :estimate            => -0.032213510511723005

 

 
 

@@ -14509,7 +14545,7 @@ 
Calling C/C++
 

 

-
In [82]:

+
In [75]:

 

     

 
ccall( (:clock, "libc"), Int32, ())
@@ -14523,11 +14559,11 @@ 
Calling C/C++
 
 
-
Out[82]:

+
Out[75]:

 
 
 

-
68447842

+
42531843

 

 
 

@@ -14547,7 +14583,7 @@ 
Calling external programs
 

-
In [83]:

+
In [76]:

 

     

 
run(`echo Hello`)
@@ -14574,7 +14610,7 @@ 
Calling external programs
 

-
In [84]:

+
In [77]:

 

     

 
file = "HelloWorld.jl"
@@ -14615,7 +14651,7 @@ 
BioJulia

 

 

-
In [85]:

+
In [78]:

 

     

 
using Bio.Seq
@@ -14631,7 +14667,7 @@ 
BioJulia

 
 
-
Out[85]:

+
Out[78]:

 
 
 

@@ -14647,7 +14683,7 @@ 
BioJulia

 

 

-
In [86]:

+
In [79]:

 

     

 
reverse_complement(seq)
@@ -14661,7 +14697,7 @@ 
BioJulia

 
 
-
Out[86]:

+
Out[79]:

 
 
 

@@ -14677,7 +14713,7 @@ 
BioJulia

 

 

-
In [87]:

+
In [80]:

 

     

 
seq = dna"ACAGCGTAGCT";
@@ -14718,7 +14754,7 @@ 
Vectorization
 

 

-
In [88]:

+
In [81]:

 

     

 
L = 100000000
@@ -14760,9 +14796,9 @@ 
Vectorization

 

-
  0.588814 seconds (8.57 k allocations: 763.363 MB, 24.01% gc time)
-  0.209379 seconds (2.16 k allocations: 108.431 KB)
-  0.187016 seconds (4.43 k allocations: 220.211 KB)
+
  0.796266 seconds (8.56 k allocations: 763.363 MB, 15.37% gc time)
+  0.244972 seconds (2.16 k allocations: 108.509 KB)
+  0.185907 seconds (4.43 k allocations: 220.242 KB)
 

 

 

@@ -14782,7 +14818,7 @@ 
Parallel Computing - Multiple
 

 

 

-
In [89]:

+
In [82]:

 

     

 
procs()
@@ -14796,14 +14832,12 @@ 
Parallel Computing - Multiple
 

 
 
-
Out[89]:

+
Out[82]:

 
 
 

-
3-element Array{Int64,1}:
- 1
- 2
- 3

+
1-element Array{Int64,1}:
+ 1

 

 
 

@@ -14814,7 +14848,7 @@ 
Parallel Computing - Multiple
 

 

 

-
In [90]:

+
In [83]:

 

     

 
addprocs(2)
@@ -14829,16 +14863,14 @@ 
Parallel Computing - Multiple
 

 
 
-
Out[90]:

+
Out[83]:

 
 
 

-
5-element Array{Int64,1}:
+
3-element Array{Int64,1}:
  1
  2
- 3
- 4
- 5

+ 3

 

 
 

@@ -14849,7 +14881,7 @@ 
Parallel Computing - Multiple
 

 

 

-
In [91]:

+
In [84]:

 

     

 
r = remotecall(2, rand, 2, 2)
@@ -14863,11 +14895,11 @@ 
Parallel Computing - Multiple
 

 
 
-
Out[91]:

+
Out[84]:

 
 
 

-
RemoteRef{Channel{Any}}(2,1,33)

+
RemoteRef{Channel{Any}}(2,1,3)

 

 
 

@@ -14878,7 +14910,7 @@ 
Parallel Computing - Multiple
 

 

 

-
In [92]:

+
In [85]:

 

     

 
fetch(r)
@@ -14892,13 +14924,13 @@ 
Parallel Computing - Multiple
 

 
 
-
Out[92]:

+
Out[85]:

 
 
 

 
2x2 Array{Float64,2}:
- 0.692386  0.947491
- 0.120261  0.170056

+ 0.25081   0.223139
+ 0.529448  0.892006

 

 
 

@@ -14909,7 +14941,7 @@ 
Parallel Computing - Multiple
 

 

 

-
In [93]:

+
In [ ]:

 

     

 
#addprocs(fill("ergophobie.molgen.mpg.de",10),dir="/home/arndt",exename="/usr/bin/julia")
@@ -14924,29 +14956,6 @@ 
Parallel Computing - Multiple
 

 

 
-

-

-
-
-

-

-
  4.478546 seconds (6.06 k allocations: 431.346 KB)
-

-

-

-
-
Out[93]:

-
-
-

-
1000002994

-

-
-

-
-

-

-
 

 

 

@@ -14959,7 +14968,7 @@ 
Graphics - Plots
 

-
In [94]:

+
In [86]:

 

     

 
using Plots
@@ -14978,15 +14987,13 @@ 
Graphics - Plots

 

-
INFO: Recompiling stale cache file /Users/arndt/.julia/lib/v0.4/PlotUtils.ji for module PlotUtils.
-INFO: Recompiling stale cache file /Users/arndt/.julia/lib/v0.4/Plots.ji for module Plots.
-WARNING: using Plots.scatter in module Main conflicts with an existing identifier.
+
WARNING: using Plots.scatter in module Main conflicts with an existing identifier.
 WARNING: using Plots.scatter3d in module Main conflicts with an existing identifier.
 

 

 

 
-
Out[94]:

+
Out[86]:

 
 
 

@@ -15001,7 +15008,7 @@ 
Graphics - Plots
 

-
In [95]:

+
In [87]:

 

     

 
Plots.plot(rand(10,5),w=4)
@@ -15022,7 +15029,7 @@ 
Graphics - Plots
Out[95]:

+
Out[87]:

 
 

 
@@ -15049,16 +15056,16 @@ 
Graphics - Plots
 
 
 
 Graphics - Plots
 
-0.2
+0.2
 
 
-0.4
+0.4
 
 
-0.6
+0.6
 
 
-0.8
+0.8
 
 
 
 2
@@ -15111,31 +15118,31 @@ 
Graphics - Plots
 
 
 
 
 
 
 
 f:
  •  f(x::AbstractString) at In[28]:2
  •  f(x::AbstractFloat) at In[28]:7
  •  f(x) at In[6]:1
"
-      ],
-      "text/plain": [
-       "# 3 methods for generic function \"f\":\n",
-       "f(x::AbstractString) at In[28]:2\n",
-       "f(x::AbstractFloat) at In[28]:7\n",
-       "f(x) at In[6]:1"
-      ]
-     },
-     "execution_count": 29,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "methods(f)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "now in f(x::AbstractFloat) with x=2.5 of type Float64\n",
-      "f(2.5) = 3.5\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "@show f(2.5);"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "now in f(x::AbstractFloat) with x=2.5 of type Float16\n",
-      "f(Float16(2.5)) = 3.5\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "@show f(Float16(2.5));"
+    "@show f( Float16(2.5) );"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "now in f(x::AbstractString) with x=abc of type ASCIIString\n",
-      "f(\"abc\") = \"Hello abc\"\n",
-      "\n",
-      "now in f(x::AbstractString) with x=αβγ of type UTF8String\n",
-      "f(\"αβγ\") = \"Hello αβγ\"\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "@show f(\"abc\")\n",
     "@show f(\"αβγ\");"
@@ -654,70 +345,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 38,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "18 methods for generic function print:"
-      ],
-      "text/plain": [
-       "# 18 methods for generic function \"print\":\n",
-       "print(io::IO, c::Char) at char.jl:47\n",
-       "print(io::IO, s::AbstractString) at strings/io.jl:46\n",
-       "print(io::IO, s::Symbol) at show.jl:5\n",
-       "print(io::IO, n::Unsigned) at show.jl:145\n",
-       "print(io::IO, ex::Union{Expr,GlobalRef,GotoNode,LabelNode,LineNumberNode,QuoteNode,SymbolNode,TopNode}) at show.jl:290\n",
-       "print(io::IO, ip::IPv4) at socket.jl:38\n",
-       "print(io::IO, ip::IPv6) at socket.jl:95\n",
-       "print{mime}(io::IO, ::MIME{mime}) at multimedia.jl:19\n",
-       "print(io::IO, x::Float32) at grisu.jl:121\n",
-       "print(io::IO, x::Float16) at grisu.jl:122\n",
-       "print(io::IO, v::VersionNumber) at version.jl:54\n",
-       "print(io::IO, b::BigFloat) at mpfr.jl:845\n",
-       "print(::IO, ::Base.WorkerState) at Enums.jl:89\n",
-       "print(io::IO, t::Text{Function}) at docs/utils.jl:72\n",
-       "print(io::IO, t::Text{T}) at docs/utils.jl:71\n",
-       "print(io::IO, x) at strings/io.jl:6\n",
-       "print(io::IO, xs...) at strings/io.jl:15\n",
-       "print(xs...) at strings/io.jl:27"
-      ]
-     },
-     "execution_count": 38,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
    "source": [
     "methods(print)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 36,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "2 methods for generic function println:"
-      ],
-      "text/plain": [
-       "# 2 methods for generic function \"println\":\n",
-       "println(io::IO, xs...) at strings/io.jl:25\n",
-       "println(xs...) at strings/io.jl:28"
-      ]
-     },
-     "execution_count": 36,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "methods(println)"
    ]
@@ -731,7 +374,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 39,
+   "execution_count": null,
    "metadata": {
     "collapsed": true
    },
@@ -746,47 +389,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 40,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "Point(2,3,\"Siegfried\")"
-      ]
-     },
-     "execution_count": 40,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "p = Point(2,3,\"Siegfried\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 41,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "g (generic function with 5 methods)"
-      ]
-     },
-     "execution_count": 41,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
-    "function g(p::Point)\n",
-    "    println(\"in g(p::Point)\")\n",
+    "function f(p::Point)\n",
+    "    println(\"\\nnow in f(x::Point) with p=$p of type $(typeof(p))\")\n",
     "    p.x = p.x + p.y\n",
     "    return p.name\n",
     "end"
@@ -794,107 +415,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 42,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "5 methods for generic function g:
  •  g(y::Int64) at In[29]:2
  •  g(y::AbstractString) at In[29]:7
  •  g(y::AbstractString, z) at In[29]:7
  •  g(p::Point) at In[41]:2
  •  g(y) at In[26]:2
"
-      ],
-      "text/plain": [
-       "# 5 methods for generic function \"g\":\n",
-       "g(y::Int64) at In[29]:2\n",
-       "g(y::AbstractString) at In[29]:7\n",
-       "g(y::AbstractString, z) at In[29]:7\n",
-       "g(p::Point) at In[41]:2\n",
-       "g(y) at In[26]:2"
-      ]
-     },
-     "execution_count": 42,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "methods(g)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 43,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "1-element Array{Method,1}:
  •  g(p::Point) at In[41]:2
"
-      ],
-      "text/plain": [
-       "1-element Array{Method,1}:\n",
-       " g(p::Point) at In[41]:2"
-      ]
-     },
-     "execution_count": 43,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
-    "methodswith(Point)"
+    "methods(f)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 44,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "in g(p::Point)\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "\"Siegfried\""
-      ]
-     },
-     "execution_count": 44,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
-    "g(p)"
+    "f(p)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 45,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "Point(5,3,\"Siegfried\")"
-      ]
-     },
-     "execution_count": 45,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "p"
    ]
@@ -908,7 +455,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 46,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
@@ -925,101 +472,49 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 47,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "Line{Int64}(23,3,4,44,\"Julia\")"
-      ]
-     },
-     "execution_count": 47,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "L1=Line(23,3,4,44,\"Julia\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 48,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "Line{Float64}(23.777,3.5,4.1,4.0,\"Rolf\")"
-      ]
-     },
-     "execution_count": 48,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "L2=Line(23.777,3.5,4.1,4.0,\"Rolf\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 49,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "g (generic function with 6 methods)"
-      ]
-     },
-     "execution_count": 49,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
-    "function g{T}(x::Line{T}) \n",
-    "    println(\"in g for $T\")\n",
+    "function f{T}(x::Line{T}) \n",
+    "    println(\"\\nnow in f(x::Line{T}) with x=$x of type $(typeof(x))\")\n",
     "    x.name\n",
     "end"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 50,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "in g for Int64\n",
-      "in g for Float64\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "(\"Julia\",\"Rolf\")"
-      ]
-     },
-     "execution_count": 50,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
-    "g(L1),g(L2)"
+    "f(L1),f(L2)"
    ]
   },
   {
@@ -1031,182 +526,88 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 37,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "3-element Array{Int64,1}:\n",
-       " 1\n",
-       " 2\n",
-       " 9"
-      ]
-     },
-     "execution_count": 37,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "A=[1,2,9]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 38,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "3-element Array{Float64,1}:\n",
-       "  3.1\n",
-       "  4.1\n",
-       " 11.1"
-      ]
-     },
-     "execution_count": 38,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
-    "A+2.1"
+    "A == 2"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 41,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "3-element BitArray{1}:\n",
-       " false\n",
-       "  true\n",
-       " false"
-      ]
-     },
-     "execution_count": 41,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "A .== 2"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 42,
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "A+2.1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "3x3 Array{Int64,2}:\n",
-       " 1  2  3\n",
-       " 6  7  4\n",
-       " 6  2  1"
-      ]
-     },
-     "execution_count": 42,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "B=[1 2 3; 6 7 4; 6 2 1]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 43,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "3x4 Array{Int64,2}:\n",
-       " 1  2  3   4\n",
-       " 2  4  6   8\n",
-       " 3  6  9  12"
-      ]
-     },
-     "execution_count": 43,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "C=[ i*j for i in 1:3, j in 1:4 ]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 56,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "3-element Array{Int64,1}:\n",
-       " 32\n",
-       " 56\n",
-       " 19"
-      ]
-     },
-     "execution_count": 56,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "B * A"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 57,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "  0.490006 seconds (285.75 k allocations: 12.694 MB, 1.31% gc time)\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "3-element Array{Float64,1}:\n",
-       " 10.6722 \n",
-       " -3.25534\n",
-       "  1.58311"
-      ]
-     },
-     "execution_count": 57,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "#B =rand(500,500)\n",
     "@time eigvals(B)"
@@ -1214,39 +615,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 58,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "  0.226167 seconds (114.64 k allocations: 5.078 MB, 2.76% gc time)\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "(\n",
-       "3x3 Array{Float64,2}:\n",
-       " -0.258442  -0.523252  -0.812044\n",
-       " -0.83751   -0.297569   0.45829 \n",
-       " -0.481441   0.798536  -0.361324,\n",
-       "\n",
-       "[11.912870002845768,3.5155113987276136,1.3132813486506532],\n",
-       "3x3 Array{Float64,2}:\n",
-       " -0.685993   0.70617   -0.175321\n",
-       " -0.616336  -0.435902   0.655835\n",
-       " -0.386708  -0.557955  -0.734264)"
-      ]
-     },
-     "execution_count": 58,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
    "source": [
     "@time svd(B)"
    ]
@@ -1260,66 +633,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 59,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "Dict{ASCIIString,Int64} with 2 entries:\n",
-       "  \"B\" => 20\n",
-       "  \"A\" => 6"
-      ]
-     },
-     "execution_count": 59,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "d = Dict( \"A\"=>6, \"B\"=> 20)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 60,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "6"
-      ]
-     },
-     "execution_count": 60,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "d[\"A\"]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 61,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "B ----> 20\n",
-      "A ----> 6\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "for (key,value) in d\n",
     "    print(\"$key ----> $value\\n\")\n",
@@ -1335,21 +675,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 62,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "ismatch(my_regex,\"Foo\") = false\n",
-      "my_regex(\"Bar\") = true\n",
-      "my_regex(\"boo\") = false\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "my_regex = r\"[ABC]\"\n",
     "\n",
@@ -1360,22 +690,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 63,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "RegexMatch(\"500g\", 1=\"500\")"
-      ]
-     },
-     "execution_count": 63,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "my_regex =r\"(\\d+)g\"\n",
     "match(my_regex,\"take 500g sugar\")"
@@ -1390,23 +709,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 64,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "1\n",
-      "2\n",
-      "3\n",
-      "4\n",
-      "5\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "for i in 1:5 \n",
     "    println(i)\n",
@@ -1415,21 +722,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 65,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "3\n",
-      "6\n",
-      "9\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "for i in 1:10\n",
     "    if i % 3 == 0\n",
@@ -1458,123 +755,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 66,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "21 required packages:\n",
-      " - ArgParse                      0.3.0\n",
-      " - Atom                          0.4.2+             julia-0.4\n",
-      " - Bio                           0.2.0+             master\n",
-      " - Bokeh                         0.2.0\n",
-      " - Cairo                         0.2.33\n",
-      " - DataFrames                    0.7.5              master\n",
-      " - DimensionalityReduction       0.1.1\n",
-      " - DistributedArrays             0.2.0\n",
-      " - GR                            0.13.0\n",
-      " - Gadfly                        0.4.2\n",
-      " - IJulia                        1.1.10\n",
-      " - Jewel                         1.0.8\n",
-      " - Optim                         0.5.0\n",
-      " - PlotlyJS                      0.3.1\n",
-      " - Plots                         0.8.0              master\n",
-      " - ProfileView                   0.1.3\n",
-      " - PyPlot                        2.2.0\n",
-      " - RCall                         0.5.0\n",
-      " - RDatasets                     0.1.3\n",
-      " - Rsvg                          0.0.2\n",
-      " - UnicodePlots                  0.1.3\n",
-      "82 additional packages:\n",
-      " - ArndtLabJulia                 0.0.0-             master (unregistered)\n",
-      " - ArrayViews                    0.6.4\n",
-      " - AutoHashEquals                0.0.9\n",
-      " - BinDeps                       0.3.21\n",
-      " - Blink                         0.3.4\n",
-      " - Blosc                         0.1.5\n",
-      " - BufferedStreams               0.1.5\n",
-      " - Calculus                      0.1.15\n",
-      " - Clustering                    0.5.0\n",
-      " - CodeTools                     0.3.0+             master\n",
-      " - Codecs                        0.1.5\n",
-      " - ColorTypes                    0.2.3\n",
-      " - Colors                        0.6.5\n",
-      " - Compat                        0.8.4\n",
-      " - Compose                       0.4.2\n",
-      " - Conda                         0.2.2\n",
-      " - Contour                       0.1.0\n",
-      " - DataArrays                    0.3.6              master\n",
-      " - DataStructures                0.4.4\n",
-      " - Dates                         0.4.4\n",
-      " - Distances                     0.3.1\n",
-      " - Distributions                 0.9.0\n",
-      " - Docile                        0.5.23\n",
-      " - DualNumbers                   0.2.2\n",
-      " - FactCheck                     0.4.3\n",
-      " - FileIO                        0.1.0\n",
-      " - FixedPointNumbers             0.1.3\n",
-      " - FixedSizeArrays               0.2.2\n",
-      " - GZip                          0.2.19\n",
-      " - Graphics                      0.1.3\n",
-      " - Grid                          0.4.0\n",
-      " - Gtk                           0.10.1\n",
-      " - GtkUtilities                  0.0.9\n",
-      " - HDF5                          0.6.3\n",
-      " - Hexagons                      0.0.4\n",
-      " - Hiccup                        0.0.2\n",
-      " - Homebrew                      0.3.1\n",
-      " - HttpCommon                    0.2.6\n",
-      " - HttpParser                    0.1.1\n",
-      " - HttpServer                    0.1.5\n",
-      " - IndexableBitVectors           0.1.1\n",
-      " - IntervalTrees                 0.0.5\n",
-      " - Iterators                     0.1.9\n",
-      " - JLD                           0.6.3\n",
-      " - JSON                          0.6.0\n",
-      " - JuliaParser                   0.6.4\n",
-      " - KernelDensity                 0.1.2\n",
-      " - LNR                           0.0.2\n",
-      " - LaTeXStrings                  0.1.6\n",
-      " - Lazy                          0.10.1\n",
-      " - LegacyStrings                 0.1.1\n",
-      " - Libz                          0.1.1\n",
-      " - LightGraphs                   0.5.5\n",
-      " - LightXML                      0.2.1\n",
-      " - Loess                         0.0.6\n",
-      " - MacroTools                    0.3.0\n",
-      " - MbedTLS                       0.2.4\n",
-      " - Measures                      0.0.2\n",
-      " - Media                         0.1.2\n",
-      " - Mustache                      0.0.15\n",
-      " - Mux                           0.2.0\n",
-      " - NaNMath                       0.2.1\n",
-      " - Nettle                        0.2.3\n",
-      " - PDMats                        0.4.2\n",
-      " - ParserCombinator              1.7.8\n",
-      " - PlotUtils                     0.0.3\n",
-      " - PositiveFactorizations        0.0.1\n",
-      " - PyCall                        1.6.3\n",
-      " - RecipesBase                   0.0.6\n",
-      " - Reexport                      0.0.3\n",
-      " - Requires                      0.2.2\n",
-      " - SHA                           0.1.2\n",
-      " - Showoff                       0.0.7\n",
-      " - SortingAlgorithms             0.0.6\n",
-      " - StatsBase                     0.8.3\n",
-      " - StatsFuns                     0.2.2\n",
-      " - SubstitutionModels            0.0.0-             master (unregistered)\n",
-      " - TextWrap                      0.1.5\n",
-      " - URIParser                     0.1.5\n",
-      " - WebSockets                    0.1.2\n",
-      " - WoodburyMatrices              0.1.5\n",
-      " - ZMQ                           0.3.2\n"
-     ]
-    }
-   ],
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
    "source": [
     "Pkg.status()"
    ]
@@ -1633,6 +818,17 @@
     "Pkg.checkout(\"DataFrames\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "#Pkg.generate(\"someName\")"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1642,37 +838,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 67,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "
xy
1210.04611913606157114
2220.8373635242857538
3230.9066330243929763
4240.29675648510293584
5250.026788088896794626
6260.5217667751899686
7270.9032616276257022
8280.20058000081954552
9290.784639890245026
10300.6536073175415043
"
-      ],
-      "text/plain": [
-       "10×2 DataFrames.DataFrame\n",
-       "│ Row │ x  │ y         │\n",
-       "├─────┼────┼───────────┤\n",
-       "│ 1   │ 21 │ 0.0461191 │\n",
-       "│ 2   │ 22 │ 0.837364  │\n",
-       "│ 3   │ 23 │ 0.906633  │\n",
-       "│ 4   │ 24 │ 0.296756  │\n",
-       "│ 5   │ 25 │ 0.0267881 │\n",
-       "│ 6   │ 26 │ 0.521767  │\n",
-       "│ 7   │ 27 │ 0.903262  │\n",
-       "│ 8   │ 28 │ 0.20058   │\n",
-       "│ 9   │ 29 │ 0.78464   │\n",
-       "│ 10  │ 30 │ 0.653607  │"
-      ]
-     },
-     "execution_count": 67,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
    "source": [
     "using DataFrames\n",
     "d = DataFrame(x = 21:30, y = rand(10))"
@@ -1680,44 +850,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 68,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "(25.5,0.5177515870161777)"
-      ]
-     },
-     "execution_count": 68,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "mean(d[:x]), mean(d[:y])"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 69,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "0.21569762172381235"
-      ]
-     },
-     "execution_count": 69,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "using StatsBase\n",
     "cov(d[:x], d[:y])"
@@ -1725,40 +873,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 70,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "size(iris) = (150,5)\n"
-     ]
-    },
-    {
-     "data": {
-      "text/html": [
-       "
SepalLengthSepalWidthPetalLengthPetalWidthSpecies
15.13.51.40.2setosa
24.93.01.40.2setosa
34.73.21.30.2setosa
44.63.11.50.2setosa
55.03.61.40.2setosa
65.43.91.70.4setosa
"
-      ],
-      "text/plain": [
-       "6×5 DataFrames.DataFrame\n",
-       "│ Row │ SepalLength │ SepalWidth │ PetalLength │ PetalWidth │ Species  │\n",
-       "├─────┼─────────────┼────────────┼─────────────┼────────────┼──────────┤\n",
-       "│ 1   │ 5.1         │ 3.5        │ 1.4         │ 0.2        │ \"setosa\" │\n",
-       "│ 2   │ 4.9         │ 3.0        │ 1.4         │ 0.2        │ \"setosa\" │\n",
-       "│ 3   │ 4.7         │ 3.2        │ 1.3         │ 0.2        │ \"setosa\" │\n",
-       "│ 4   │ 4.6         │ 3.1        │ 1.5         │ 0.2        │ \"setosa\" │\n",
-       "│ 5   │ 5.0         │ 3.6        │ 1.4         │ 0.2        │ \"setosa\" │\n",
-       "│ 6   │ 5.4         │ 3.9        │ 1.7         │ 0.4        │ \"setosa\" │"
-      ]
-     },
-     "execution_count": 70,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
    "source": [
     "using RDatasets\n",
     "iris = dataset(\"datasets\", \"iris\")\n",
@@ -1768,124 +887,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 73,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "
Speciesx1
1setosa(50,5)
2versicolor(50,5)
3virginica(50,5)
"
-      ],
-      "text/plain": [
-       "3×2 DataFrames.DataFrame\n",
-       "│ Row │ Species      │ x1     │\n",
-       "├─────┼──────────────┼────────┤\n",
-       "│ 1   │ \"setosa\"     │ (50,5) │\n",
-       "│ 2   │ \"versicolor\" │ (50,5) │\n",
-       "│ 3   │ \"virginica\"  │ (50,5) │"
-      ]
-     },
-     "execution_count": 73,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "by(iris, :Species, size)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 74,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "Rotation:\n",
-       "4x4 Array{Float64,2}:\n",
-       "  0.360172   -0.608141    0.731739   0.14552  \n",
-       " -0.0979983  -0.783089   -0.13081   -0.0362072\n",
-       "  0.855279   -0.0841303  -0.308115  -0.951556 \n",
-       "  0.359402   -0.0992901  -0.593727   0.268428 \n",
-       "\n",
-       "Scores:\n",
-       "150x4 Array{Float64,2}:\n",
-       " -2.25714   -0.478424    0.12728     0.0240875 \n",
-       " -2.07401    0.671883    0.233826    0.102663  \n",
-       " -2.35634    0.340766   -0.0440539   0.0282823 \n",
-       " -2.29171    0.5954     -0.0909853  -0.0657353 \n",
-       " -2.38186   -0.644676   -0.0156856  -0.0358029 \n",
-       " -2.0687    -1.48421    -0.0268782   0.00658612\n",
-       " -2.43587   -0.0474851  -0.33435    -0.0366528 \n",
-       " -2.22539   -0.222403    0.0883994  -0.0245299 \n",
-       " -2.32685    1.1116     -0.144592   -0.0267695 \n",
-       " -2.17703    0.467448    0.252918   -0.0397661 \n",
-       " -2.15908   -1.04021     0.267784    0.0166755 \n",
-       " -2.31836   -0.132634   -0.0934462  -0.133038  \n",
-       " -2.21104    0.726243    0.23014     0.00241694\n",
-       "  ⋮                                            \n",
-       "  0.921737  -0.0171656  -0.415434    0.00522092\n",
-       "  1.84586   -0.673871    0.0126298   0.194544  \n",
-       "  2.00808   -0.611836   -0.426903    0.246712  \n",
-       "  1.89543   -0.687273   -0.129641    0.468128  \n",
-       "  1.15402    0.696536   -0.52839    -0.0403855 \n",
-       "  2.03374   -0.864624   -0.337015    0.0450363 \n",
-       "  1.99148   -1.04567    -0.630302    0.213331  \n",
-       "  1.86426   -0.385674   -0.255418    0.387957  \n",
-       "  1.55936    0.893693    0.0262833   0.219457  \n",
-       "  1.51609   -0.268171   -0.179577    0.118773  \n",
-       "  1.3682    -1.00788    -0.930279    0.0260414 \n",
-       "  0.957448   0.0242504  -0.526485   -0.162534  \n",
-       "\n",
-       "Reconstruction:\n",
-       "150x4 Array{Float64,2}:\n",
-       " -0.42537     0.578323   -1.95237  -0.832823\n",
-       " -0.969562   -0.357198   -2.00012  -0.923388\n",
-       " -1.08404    -0.0311948  -2.05733  -0.84696 \n",
-       " -1.26364    -0.227386   -1.91956  -0.846387\n",
-       " -0.482515    0.741605   -1.94402  -0.792335\n",
-       "  0.138808    1.36827    -1.64244  -0.578403\n",
-       " -1.09845     0.32096    -1.94146  -0.682068\n",
-       " -0.605156    0.381571   -1.88852  -0.836799\n",
-       " -1.62378    -0.622574   -2.0136   -0.867983\n",
-       " -0.889098   -0.184352   -1.94139  -0.989683\n",
-       "  0.0533268   0.990527   -1.85748  -0.82721 \n",
-       " -0.842088    0.348101   -1.8163   -0.800286\n",
-       " -1.06926    -0.382227   -2.02537  -1.00276 \n",
-       "  ⋮                                         \n",
-       "  0.0391933  -0.0227324   0.91282   0.581035\n",
-       "  1.11219     0.338113    1.44641   0.775038\n",
-       "  0.818858    0.329244    1.66572   1.10215 \n",
-       "  1.0739      0.352455    1.27344   0.952093\n",
-       " -0.400468   -0.58796     1.12964   0.648476\n",
-       "  1.01826     0.520228    1.87315   1.02897 \n",
-       "  0.923014    0.698414    1.78245   1.25106 \n",
-       "  0.775554    0.138687    1.33644   0.9641  \n",
-       "  0.0693136  -0.864039    1.04157   0.515005\n",
-       "  0.59502     0.0806172   1.26155   0.710015\n",
-       "  0.428789    0.775924    1.51684   1.15113 \n",
-       " -0.0788028  -0.038064    1.13372   0.610661\n",
-       "\n",
-       "Standard Deviations:\n",
-       "[1.7026570894991693,0.9528572479608981,0.38180950276393044,0.14344593936077485]\n",
-       "\n",
-       "Proportion of Variance:\n",
-       "[0.7296244541329988,0.22850761786701754,0.03668921889282881,0.005178709107154805]\n",
-       "\n",
-       "Cumulative Variance:\n",
-       "[0.7296244541329988,0.9581320720000163,0.9948212908928451,1.0]"
-      ]
-     },
-     "execution_count": 74,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
    "source": [
     "using DimensionalityReduction\n",
     "iris_S = convert(Array,DataArray(iris[:,1:4]))\n",
@@ -1901,141 +918,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 75,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "\n",
-       " \n",
-       " 
Plotly javascript loaded.
\n",
-       " 
To load again call 
init_notebook()
\n",
-       " "
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
    "source": [
     "using PlotlyJS\n",
     "using Colors\n",
@@ -2047,31 +934,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 76,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "
\n",
-       "\n",
-       "\n"
-      ]
-     },
-     "execution_count": 76,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "nms = unique(iris[:Species])\n",
     "colors = [RGB(0.89, 0.1, 0.1), RGB(0.21, 0.50, 0.72), RGB(0.28, 0.68, 0.3)]\n",
@@ -2117,36 +984,16 @@
    },
    "outputs": [],
    "source": [
-    "PlotlyJS.savefig(p1, \"output_filename.pdf\")"
+    "#PlotlyJS.savefig(p1, \"output_filename.pdf\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 77,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "
\n",
-       "\n",
-       "\n"
-      ]
-     },
-     "execution_count": 77,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "function clustering_alpha_shapes()\n",
     "    @eval using DataFrames, RDatasets, Colors\n",
@@ -2203,7 +1050,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 78,
+   "execution_count": null,
    "metadata": {
     "collapsed": true
    },
@@ -2214,54 +1061,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 79,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "RCall.RObject{RCall.RealSxp}\n",
-       " [1] -0.2684685  0.5427448 -0.9213678  0.8288000 -0.3974171  1.8959922\n",
-       " [7]  0.6632521 -0.3106209  1.6267463  0.5812782\n"
-      ]
-     },
-     "execution_count": 79,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "R\"rnorm(10)\""
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 80,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "8-element Array{Float64,1}:\n",
-       " -0.0371922\n",
-       " -0.164406 \n",
-       "  1.83884  \n",
-       "  0.562734 \n",
-       "  1.63202  \n",
-       "  0.611594 \n",
-       "  2.38667  \n",
-       " -0.608195 "
-      ]
-     },
-     "execution_count": 80,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "L = 8\n",
     "@rput L\n",
@@ -2272,31 +1087,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 81,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "Dict{Symbol,Any} with 9 entries:\n",
-       "  :statistic           => 0.10332942684641923\n",
-       "  symbol(\"conf.int\")   => [-0.05921758561151922,0.06580056524544481]\n",
-       "  :alternative         => \"two.sided\"\n",
-       "  :parameter           => 999.0\n",
-       "  symbol(\"p.value\")    => 0.9177222598844713\n",
-       "  :method              => \"One Sample t-test\"\n",
-       "  symbol(\"data.name\")  => \"rnorm(1000)\"\n",
-       "  symbol(\"null.value\") => 0.0\n",
-       "  :estimate            => 0.0032914898169627916"
-      ]
-     },
-     "execution_count": 81,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "rcopy(R\"t.test(rnorm(1000))\")"
    ]
@@ -2313,22 +1108,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 82,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "68447842"
-      ]
-     },
-     "execution_count": 82,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     " ccall( (:clock, \"libc\"), Int32, ())"
    ]
@@ -2342,40 +1126,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 83,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Hello\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "run(`echo Hello`)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 84,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "#!/usr/bin/env julia\n",
-      "\n",
-      "println(\"Hello World!\")\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "file = \"HelloWorld.jl\"\n",
     "\n",
@@ -2392,23 +1158,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 85,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "6nt DNA Sequence:\n",
-       "ACGTTT"
-      ]
-     },
-     "execution_count": 85,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "using Bio.Seq\n",
     "\n",
@@ -2417,44 +1171,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 86,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "6nt DNA Sequence:\n",
-       "AAACGT"
-      ]
-     },
-     "execution_count": 86,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "reverse_complement(seq)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 87,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "approxsearch(seq,@dna_str(\"AGGG\"),0) = 0:-1\n",
-      "approxsearch(seq,@dna_str(\"AGGG\"),1) = 3:6\n",
-      "approxsearch(seq,@dna_str(\"AGGG\"),2) = 1:4\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "seq = dna\"ACAGCGTAGCT\";\n",
     "@show approxsearch(seq, dna\"AGGG\", 0)\n",
@@ -2471,21 +1203,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 88,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "  0.588814 seconds (8.57 k allocations: 763.363 MB, 24.01% gc time)\n",
-      "  0.209379 seconds (2.16 k allocations: 108.431 KB)\n",
-      "  0.187016 seconds (4.43 k allocations: 220.211 KB)\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "L = 100000000\n",
     "A = rand(1:1000,L)\n",
@@ -2526,52 +1248,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 89,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "3-element Array{Int64,1}:\n",
-       " 1\n",
-       " 2\n",
-       " 3"
-      ]
-     },
-     "execution_count": 89,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "procs()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 90,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "5-element Array{Int64,1}:\n",
-       " 1\n",
-       " 2\n",
-       " 3\n",
-       " 4\n",
-       " 5"
-      ]
-     },
-     "execution_count": 90,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "addprocs(2)\n",
     "procs()"
@@ -2579,75 +1271,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 91,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "RemoteRef{Channel{Any}}(2,1,33)"
-      ]
-     },
-     "execution_count": 91,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "r = remotecall(2, rand, 2, 2)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 92,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "2x2 Array{Float64,2}:\n",
-       " 0.692386  0.947491\n",
-       " 0.120261  0.170056"
-      ]
-     },
-     "execution_count": 92,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "fetch(r)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 93,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "  4.478546 seconds (6.06 k allocations: 431.346 KB)\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "1000002994"
-      ]
-     },
-     "execution_count": 93,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "#addprocs(fill(\"ergophobie.molgen.mpg.de\",10),dir=\"/home/arndt\",exename=\"/usr/bin/julia\")\n",
     "nheads() = @parallel (+) for i=1:2000000000\n",
@@ -2666,32 +1316,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 94,
+   "execution_count": null,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "INFO: Recompiling stale cache file /Users/arndt/.julia/lib/v0.4/PlotUtils.ji for module PlotUtils.\n",
-      "INFO: Recompiling stale cache file /Users/arndt/.julia/lib/v0.4/Plots.ji for module Plots.\n",
-      "WARNING: using Plots.scatter in module Main conflicts with an existing identifier.\n",
-      "WARNING: using Plots.scatter3d in module Main conflicts with an existing identifier.\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "Plots.GRBackend()"
-      ]
-     },
-     "execution_count": 94,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "using Plots\n",
     "#plotlyjs()\n",
@@ -2701,178 +1330,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 95,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "[Plots.jl] Initializing backend: gr\n"
-     ]
-    },
-    {
-     "data": {
-      "text/html": [
-       "\n",
-       "\n",
-       "\n",
-       "  \n",
-       "    \n",
-       "  \n",
-       "\n",
-       "\n",
-       "\n",
-       "  \n",
-       "    \n",
-       "  \n",
-       "\n",
-       "\n",
-       "\n",
-       "  \n",
-       "    \n",
-       "  \n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "0.2\n",
-       "\n",
-       "\n",
-       "0.4\n",
-       "\n",
-       "\n",
-       "0.6\n",
-       "\n",
-       "\n",
-       "0.8\n",
-       "\n",
-       "\n",
-       "\n",
-       "2\n",
-       "\n",
-       "\n",
-       "4\n",
-       "\n",
-       "\n",
-       "6\n",
-       "\n",
-       "\n",
-       "8\n",
-       "\n",
-       "\n",
-       "10\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "y1\n",
-       "\n",
-       "\n",
-       "\n",
-       "y2\n",
-       "\n",
-       "\n",
-       "\n",
-       "y3\n",
-       "\n",
-       "\n",
-       "\n",
-       "y4\n",
-       "\n",
-       "\n",
-       "\n",
-       "y5\n",
-       "\n",
-       "\n"
-      ]
-     },
-     "execution_count": 95,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
    "source": [
     "Plots.plot(rand(10,5),w=4)"
    ]