Cocoa for Scientists: An Introduction
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Matias Piipari from the Sanger Institute gave a short tutorial, aimed at a scientific audience, on using Apple's Cocoa framework for developing applications.
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Cocoa for Scientists: An Introduction
- 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 Friday, 21 May 2010
- 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 Friday, 21 May 2010
- 28. NeXSTEP Friday, 21 May 2010
- 29. NeXSTEP OPENSTEP Friday, 21 May 2010
- 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