Matias Piipari from the Sanger Institute gave a short tutorial, aimed at a scientific audience, on using Apple's Cocoa framework for developing applications.

1. Cocoa for Scientists
Matias Piipari
Wellcome Trust Sanger Institute
Friday, 21 May 2010

2. iMotifs
Friday, 21 May 2010

3. Friday, 21 May 2010

4. Biomartify
Friday, 21 May 2010

5. Outline
Friday, 21 May 2010

6. Outline
1. What is Cocoa?
Friday, 21 May 2010

7. Outline
1. What is Cocoa?
2. What can I do with it?
Friday, 21 May 2010

8. Outline
1. What is Cocoa?
2. What can I do with it?
3. How can I learn more about it?
Friday, 21 May 2010

9. Outline
1. What is Cocoa?
2. What can I do with it?
3. How can I learn more about it?
BONUS: A GUI design tutorial
Friday, 21 May 2010

10. What is Cocoa?
Friday, 21 May 2010

11. What is Cocoa?
• High-level object oriented collection of APIs for Mac OS X
Friday, 21 May 2010

12. What is Cocoa?
• High-level object oriented collection of APIs for Mac OS X
• It is much more than a GUI framework
Friday, 21 May 2010

13. What is Cocoa?
• High-level object oriented collection of APIs for Mac OS X
• It is much more than a GUI framework
• Interprocess communication: UNIX pipes, distributed notifications
Friday, 21 May 2010

14. What is Cocoa?
• High-level object oriented collection of APIs for Mac OS X
• It is much more than a GUI framework
• Interprocess communication: UNIX pipes, distributed notifications
• Networking: sockets, HTTP, service auto discovery...
Friday, 21 May 2010

15. What is Cocoa?
• High-level object oriented collection of APIs for Mac OS X
• It is much more than a GUI framework
• Interprocess communication: UNIX pipes, distributed notifications
• Networking: sockets, HTTP, service auto discovery...
• Data modelling & persistence (Core Data)
Friday, 21 May 2010

16. What is Cocoa?
• High-level object oriented collection of APIs for Mac OS X
• It is much more than a GUI framework
• Interprocess communication: UNIX pipes, distributed notifications
• Networking: sockets, HTTP, service auto discovery...
• Data modelling & persistence (Core Data)
• Using multicore CPUs: multithreading, Grand Central Dispatch
Friday, 21 May 2010

17. What is Cocoa?
• High-level object oriented collection of APIs for Mac OS X
• It is much more than a GUI framework
• Interprocess communication: UNIX pipes, distributed notifications
• Networking: sockets, HTTP, service auto discovery...
• Data modelling & persistence (Core Data)
• Using multicore CPUs: multithreading, Grand Central Dispatch
• 2D drawing (Quartz)
Friday, 21 May 2010

18. What is Cocoa?
• High-level object oriented collection of APIs for Mac OS X
• It is much more than a GUI framework
• Interprocess communication: UNIX pipes, distributed notifications
• Networking: sockets, HTTP, service auto discovery...
• Data modelling & persistence (Core Data)
• Using multicore CPUs: multithreading, Grand Central Dispatch
• 2D drawing (Quartz)
• Image / video processing (Core Image, Core Video, Quartz Composer)
Friday, 21 May 2010

19. What is Cocoa?
• High-level object oriented collection of APIs for Mac OS X
• It is much more than a GUI framework
• Interprocess communication: UNIX pipes, distributed notifications
• Networking: sockets, HTTP, service auto discovery...
• Data modelling & persistence (Core Data)
• Using multicore CPUs: multithreading, Grand Central Dispatch
• 2D drawing (Quartz)
• Image / video processing (Core Image, Core Video, Quartz Composer)
• Scripting bridge: script your app in Python, Ruby, AppleScript
Friday, 21 May 2010

20. 1985
Friday, 21 May 2010

21. NeXSTEP
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22. NeXSTEP
Friday, 21 May 2010

23. NeXSTEP
Friday, 21 May 2010

24. NeXSTEP
Friday, 21 May 2010

25. NeXSTEP
Friday, 21 May 2010

26. NeXSTEP
Friday, 21 May 2010

27. NeXSTEP
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28. NeXSTEP
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29. NeXSTEP OPENSTEP
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30. NeXSTEP OPENSTEP Cocoa
Friday, 21 May 2010

31. GNUStep
NeXSTEP OPENSTEP Cocoa
Friday, 21 May 2010

32. Cocoa Touch
GNUStep (iPhone OS)
NeXSTEP OPENSTEP Cocoa
Friday, 21 May 2010

33. NeXTSTEP legacy is clear
• AppKit (AppKit.h)
• FoundationKit (Foundation.h)
• “NS” prefix in the Cocoa foundation
classes (NSObject, NSArray, ... )
• Bundles (.app, .pages, .keynote, etc)
• Interface Builder
Friday, 21 May 2010

34. The Objective-C language
Friday, 21 May 2010

35. The Objective-C language
• Object oriented language bolted onto ANSI C
Friday, 21 May 2010

36. The Objective-C language
• Object oriented language bolted onto ANSI C
• Dynamic language
Friday, 21 May 2010

37. The Objective-C language
• Object oriented language bolted onto ANSI C
• Dynamic language
• Class definitions can change (even during runtime)
Friday, 21 May 2010

38. The Objective-C language
• Object oriented language bolted onto ANSI C
• Dynamic language
• Class definitions can change (even during runtime)
• Late binding: methods looked up during runtime
Friday, 21 May 2010

39. The Objective-C language
• Object oriented language bolted onto ANSI C
• Dynamic language
• Class definitions can change (even during runtime)
• Late binding: methods looked up during runtime
• Add or swap (‘swizzle’) methods during runtime
Friday, 21 May 2010

40. The Objective-C language
• Object oriented language bolted onto ANSI C
• Dynamic language
• Class definitions can change (even during runtime)
• Late binding: methods looked up during runtime
• Add or swap (‘swizzle’) methods during runtime
• You need to manage your memory (GC exists, but it’s crap)
Friday, 21 May 2010

41. The Objective-C language
• Object oriented language bolted onto ANSI C
• Dynamic language
• Class definitions can change (even during runtime)
• Late binding: methods looked up during runtime
• Add or swap (‘swizzle’) methods during runtime
• You need to manage your memory (GC exists, but it’s crap)
• A language with some strong conventions
Friday, 21 May 2010

42. Cocoa design patterns
• Model-View-Controller
• Dependency Injection
• Target-Action
• Delegation
• Responder chain
• Facade
• Decorator
• Command
Friday, 21 May 2010

43. The APIs
Friday, 21 May 2010

44. Quartz: drawing
(DEMO)
Friday, 21 May 2010

45. Quartz: drawing API
Friday, 21 May 2010

46. Quartz: drawing API
• Identical API for drawing into...
• a window
• an off-screen bitmap buffer
• A PDF
Friday, 21 May 2010

47. Quartz: drawing API
• Identical API for drawing into...
• a window
• an off-screen bitmap buffer
• A PDF
• API available for C and Objective-C
(or supported scripting languages)
Friday, 21 May 2010

48. Quartz: drawing API
• Identical API for drawing into...
• a window
• an off-screen bitmap buffer
• A PDF
• API available for C and Objective-C
(or supported scripting languages)
• Toll free bridging between
C structs / Objective-C objects
Friday, 21 May 2010

49. Image / video processing
with Quartz Composer
Friday, 21 May 2010

50. Image / video processing
with Quartz Composer
• A visual programming language for image /
video processing
Friday, 21 May 2010

51. Image / video processing
with Quartz Composer
• A visual programming language for image /
video processing
• Embeddable into your own application
Friday, 21 May 2010

52. Image / video processing
with Quartz Composer
• A visual programming language for image /
video processing
• Embeddable into your own application
• New in Snow Leopard: OpenCL kernels
Friday, 21 May 2010

53. Image / video processing
with Quartz Composer
• A visual programming language for image /
video processing
• Embeddable into your own application
• New in Snow Leopard: OpenCL kernels
• It is powerful but documentation isn’t great
Friday, 21 May 2010

54. Image / video processing
with Quartz Composer
• A visual programming language for image /
video processing
• Embeddable into your own application
• New in Snow Leopard: OpenCL kernels
• It is powerful but documentation isn’t great
• (DEMO)
Friday, 21 May 2010

55. Child processes, UNIX pipes
stdout
GUI process motif inference process
(native Mac app) (crossplatform Java app)
Friday, 21 May 2010

56. Networking & web services
Friday, 21 May 2010

57. Networking & web services
• High-level API for streams & sockets
Friday, 21 May 2010

58. Networking & web services
• High-level API for streams & sockets
• HTTP client with asynchronous I/O
Friday, 21 May 2010

59. Networking & web services
• High-level API for streams & sockets
• HTTP client with asynchronous I/O
• XML handling
Friday, 21 May 2010

60. Networking & web services
• High-level API for streams & sockets
• HTTP client with asynchronous I/O
• XML handling
• Event based parsing
Friday, 21 May 2010

61. Networking & web services
• High-level API for streams & sockets
• HTTP client with asynchronous I/O
• XML handling
• Event based parsing
• DOM based parsing, XPath queries
Friday, 21 May 2010

62. Networking & web services
• High-level API for streams & sockets
• HTTP client with asynchronous I/O
• XML handling
• Event based parsing
• DOM based parsing, XPath queries
• SOAP OK
Friday, 21 May 2010

63. Networking & web services
• High-level API for streams & sockets
• HTTP client with asynchronous I/O
• XML handling
• Event based parsing
• DOM based parsing, XPath queries
• SOAP OK
• JSON OK
Friday, 21 May 2010

64. Networking & web services
Friday, 21 May 2010

65. Core Data
Friday, 21 May 2010

66. Core Data
Friday, 21 May 2010

67. Core Data
• Data modelling framework
Friday, 21 May 2010

68. Core Data
• Data modelling framework
• Serialise / deserialise data
Friday, 21 May 2010

69. Core Data
• Data modelling framework
• Serialise / deserialise data
• SQLite
Friday, 21 May 2010

70. Core Data
• Data modelling framework
• Serialise / deserialise data
• SQLite
• XML
Friday, 21 May 2010

71. Core Data
• Data modelling framework
• Serialise / deserialise data
• SQLite
• XML
• Auto-generate model classes
Friday, 21 May 2010

72. Core Data
• Data modelling framework
• Serialise / deserialise data
• SQLite
• XML
• Auto-generate model classes
• Query data
Friday, 21 May 2010

73. Core Data
• Data modelling framework
• Serialise / deserialise data
• SQLite
• XML
• Auto-generate model classes
• Query data
• Automatic undo / redo support
Friday, 21 May 2010

74. Multicore
Friday, 21 May 2010

75. Multicore
• NSOperation: high level multithreading API
Friday, 21 May 2010

76. Multicore
• NSOperation: high level multithreading API
• Grand Central Dispatch (10.6 only)
Friday, 21 May 2010

77. Multicore
• NSOperation: high level multithreading API
• Grand Central Dispatch (10.6 only)
• Use closures to represent independent work units
Friday, 21 May 2010

78. Multicore
• NSOperation: high level multithreading API
• Grand Central Dispatch (10.6 only)
• Use closures to represent independent work units
• Lighter memory footprint than threads
Friday, 21 May 2010

79. Multicore
• NSOperation: high level multithreading API
• Grand Central Dispatch (10.6 only)
• Use closures to represent independent work units
• Lighter memory footprint than threads
• Easy: worry less about resources, syncing, locking
Friday, 21 May 2010

80. Multicore
• NSOperation: high level multithreading API
• Grand Central Dispatch (10.6 only)
• Use closures to represent independent work units
• Lighter memory footprint than threads
• Easy: worry less about resources, syncing, locking
• POSIX threads
Friday, 21 May 2010

81. Multicore
• NSOperation: high level multithreading API
• Grand Central Dispatch (10.6 only)
• Use closures to represent independent work units
• Lighter memory footprint than threads
• Easy: worry less about resources, syncing, locking
• POSIX threads
• OpenCL: an extension to C for data-parallel computing
Friday, 21 May 2010

82. Scripting bridge
Friday, 21 May 2010

83. Scripting bridge
• Python - Objective-C bridge: PyObjC
Friday, 21 May 2010

84. Scripting bridge
• Python - Objective-C bridge: PyObjC
• Ruby - Objective-C bridge: RubyCocoa
Friday, 21 May 2010

85. Scripting bridge
• Python - Objective-C bridge: PyObjC
• Ruby - Objective-C bridge: RubyCocoa
• MacRuby: a ‘native’ Cocoa Ruby interpreter
Friday, 21 May 2010

86. Scripting bridge
• Python - Objective-C bridge: PyObjC
• Ruby - Objective-C bridge: RubyCocoa
• MacRuby: a ‘native’ Cocoa Ruby interpreter
• Ruby or Python can also be used as a
replacement for AppleScript
Friday, 21 May 2010

87. Scripting bridge
• Python - Objective-C bridge: PyObjC
• Ruby - Objective-C bridge: RubyCocoa
• MacRuby: a ‘native’ Cocoa Ruby interpreter
• Ruby or Python can also be used as a
replacement for AppleScript
• My advice: keep away until you’re
comfortable with Cocoa.
Friday, 21 May 2010

88. BioCocoa
Friday, 21 May 2010

89. BioCocoa
• Sequence I/O (DNA / RNA / protein)
Friday, 21 May 2010

90. BioCocoa
• Sequence I/O (DNA / RNA / protein)
• Annotations
Friday, 21 May 2010

91. BioCocoa
• Sequence I/O (DNA / RNA / protein)
• Annotations
• Sequence alignments
Friday, 21 May 2010

92. BioCocoa
• Sequence I/O (DNA / RNA / protein)
• Annotations
• Sequence alignments
• Nothing like Bioruby / Bioperl...
Friday, 21 May 2010

93. BioCocoa
• Sequence I/O (DNA / RNA / protein)
• Annotations
• Sequence alignments
• Nothing like Bioruby / Bioperl...
• Alternatives:
Friday, 21 May 2010

94. BioCocoa
• Sequence I/O (DNA / RNA / protein)
• Annotations
• Sequence alignments
• Nothing like Bioruby / Bioperl...
• Alternatives:
• scripting bridge + Bioruby / Biopython
Friday, 21 May 2010

95. BioCocoa
• Sequence I/O (DNA / RNA / protein)
• Annotations
• Sequence alignments
• Nothing like Bioruby / Bioperl...
• Alternatives:
• scripting bridge + Bioruby / Biopython
• pipe to a child process which does more
complex manipulations with biol data
Friday, 21 May 2010

96. Fine...
but it’s Mac only
Friday, 21 May 2010

97. ... or is it?
Friday, 21 May 2010

98. Cocotron
Friday, 21 May 2010

99. GNUStep
Friday, 21 May 2010

100. Learning resources
Aaron Hillegass: Stephen G. Kochan:
Cocoa Programming Programming in
for Mac OS X Objective-C 2.0
http://itunes.stanford.edu/
Stanford University iPhone SDK course
Friday, 21 May 2010

101. Learning resources
• http://mattgemmell.com/
• http://cocoawithlove.com/
• http://www.cocotron.org/blog/
• http://www.boyfarrell.com/tutorials/
• http://weblog.bignerdranch.com/
• http://abizern.org/
• http://cocoadev.com/
Friday, 21 May 2010

102. My experiences
Friday, 21 May 2010

103. My experiences
• It’s a lot of fun!
Friday, 21 May 2010

104. My experiences
• It’s a lot of fun!
• It is just C with added decoration
Friday, 21 May 2010

105. My experiences
• It’s a lot of fun!
• It is just C with added decoration
• Documentation is not always great
Friday, 21 May 2010

106. My experiences
• It’s a lot of fun!
• It is just C with added decoration
• Documentation is not always great
• ... but the community is:
Friday, 21 May 2010

107. My experiences
• It’s a lot of fun!
• It is just C with added decoration
• Documentation is not always great
• ... but the community is:
• blogs, forums
Friday, 21 May 2010

108. My experiences
• It’s a lot of fun!
• It is just C with added decoration
• Documentation is not always great
• ... but the community is:
• blogs, forums
• plenty of open source code
Friday, 21 May 2010

109. My experiences
• It’s a lot of fun!
• It is just C with added decoration
• Documentation is not always great
• ... but the community is:
• blogs, forums
• plenty of open source code
• #macdev,#iphonedev on IRC (freenode)
Friday, 21 May 2010

110. Interface Builder
Tutorial
Friday, 21 May 2010

111. Target - Action
Friday, 21 May 2010

112. Bindings
key-value observing
Friday, 21 May 2010

113. Controllers
Friday, 21 May 2010

114. Biomartify
Friday, 21 May 2010

115. Biomartify
• Goals
Friday, 21 May 2010

116. Biomartify
• Goals
• Browse the Biomart registry:
marts, their datasets
Friday, 21 May 2010

117. Biomartify
• Goals
• Browse the Biomart registry:
marts, their datasets
• Build a Biomart query: filters & attributes
Friday, 21 May 2010

118. Biomartify
• Goals
• Browse the Biomart registry:
marts, their datasets
• Build a Biomart query: filters & attributes
• Save the query on disk, edit it later
Friday, 21 May 2010

119. Biomartify
• Goals
• Browse the Biomart registry:
marts, their datasets
• Build a Biomart query: filters & attributes
• Save the query on disk, edit it later
• Submit the query
Friday, 21 May 2010

120. Biomartify
• Goals
• Browse the Biomart registry:
marts, their datasets
• Build a Biomart query: filters & attributes
• Save the query on disk, edit it later
• Submit the query
• ‘Migrate’ a query to a dataset
Friday, 21 May 2010