{Code}forScience<br />Andrew Lenards<br />December 6, 2010<br />
slideshare.net/lenards<br />
Andrew Lenards<br />iPlant Collaborative<br />on Core S/W team<br />University of Arizona<br />CS Grad, 2001<br />Experien...
Andrew Lenards - Activities<br />Learning about:<br />Requirements, User Stories, etc. <br />S/W Design/Architecture, Patt...
Hybrid Vigor <br />
Computational ___________<br />
Computational _Thinking_<br />
Computational _Biology_<br />
Computational _Gardening_<br />
Computational _Gardening_<br />
Bio________<br />
Biofuels<br />
Biochemistry<br />
Biophysics<br />
Bioinformatics<br />
…<br />
What do you expectwhen you graduate? <br />
… for the computer sciencemajors <br />
Myth of the Lone Developer <br />
in-practice: lots of interaction w/ technical&non-technical people<br />
Take Away:<br />Communication is amajor challenge<br />
What might help?<br />
Software projects#fail.<br />
… quite often<br />
Why?<br />
P00R(0////U||1(4710||<br />
Speaking in tongues is not allowed<br />
Adaption<br />
{Code}for Science<br />
I wasn’t always interested in science/biology<br />
Biology is an interesting domain<br />
I know too much aboutAuto titling & international trucking fees<br />
I know knew too muchaboutAuto titling & international trucking fees<br />
Conclusion: Act I<br />
Miscellaneous Info<br />Contact Info<br />Traditional: <br />lenards@iplantcollaborative.org<br />lenards@email.arizona.ed...
… of the community,     by the community,    for the community <br />
Empowering the next generation of biologist<br />
Why?<br />
The world faces tough problems in the future<br />
Fuel/Energy<br />
Food<br />
Water Supply<br />
…<br />
Cyberinfrastructure<br />
“In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, compu...
Large systems designleads to diverse,interdisciplinary teams<br />
With the direction of Computational Biology & Bioinformatics… <br />
Software Development as aCollaborative Game<br />
Soft skills are important<br />
Speaking in tongues is not allowed<br />
Working in pairs, not just forpair-programming ordebugging<br />
Impromptu design discussions <br />(they often include more than just technical folks)<br />
Image Acknowledgements<br />“Mad Scientist Photo” of Andrew by Alex Yelich<br />http://www.flickr.com/photos/sskennel/4496...
The content of this work is licensed under a Creative Commons  <br />Attribution-NonCommercial-ShareAlike License.  Your u...
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Code for science (rev 2)

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  • Originally prepared for UBRP group session - http://ubrp.arizona.edu/
  • When people hear “hybrid” they usually think of cars, and likely the ToyotaPrius.http://www.flickr.com/photos/sskennel/4496534369/
  • Darwin studied hybrid vigorhttp://upload.wikimedia.org/wikipedia/commons/3/32/Charles_Darwin_by_Elliott_and_Fry.jpg
  • Major of corn grown worldwide is from hybridshttp://en.wikipedia.org/wiki/File:Koeh-283.jpg
  • Successful combinations
  • It seems like computer science and computational thinking are creating plenty of hybrid disciplines now
  • Okay – that was a bogus one. Computational Gardening is a horrible idea.
  • But computational approaches are not only ones creating new disciplines. Biology is have a major impact.
  • And the list goes on…. And on.
  • Games usually have some limiting factor so that user-controlled characters cannot specialize in everything. This is an example from Star Wars Galaxies and how they controlled user characters by imposing a skill tree.http://jitterypenguin.com/images01/SWG%20Screenshots/Zoee/Master%20Commando%20Skill%20Tree.jpg
  • What limits you? Time, attention, energy… http://www.flickr.com/photos/tonivc/2283676770/
  • No one person can be a master of all the skills needed to produce large, scalable systems to support biology, bioinformatics, or computational biologyhttp://www.flickr.com/photos/lorelei-ranveig/2294093649/
  • Douglas Rushkoff –&quot;Program or be Programmed: Ten Commands for a Digital Age”http://www.flickr.com/photos/designbyfront/3428784075
  • Photo taken at Startup School 2009 at UC Berkeley.Some rights reserved by Mathieu Thouvenin -&gt; http://www.flickr.com/photos/mathoov/4040824373/sizes/l/
  • http://www.flickr.com/photos/thatgrumguy/402041540/
  • http://www.flickr.com/photos/pkmousie/2652404430/
  • http://www.flickr.com/photos/sklathill/479528238/
  • If you’re dealing with non-technical, technical folks who are not familiar with your expertise then how do expect to be successful communicating?
  • Beyond patience and plain, approachable explanation – maybe a technical savvy implementation of the Babel fishhttp://commons.wikimedia.org/wiki/File:Babel_fish_badge.jpg
  • Why do many software project fail? Communication and misunderstandings.
  • Poor communication and misunderstandings.
  • Why do many software project fail? Communication and misunderstandings. Project need to adaption.
  • I previously worked in the motor vehicle domain on projects that involved proportioned registration for international trucking. http://www.flickr.com/photos/roadsidepictures/389828793/
  • “In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.” src: http://en.wikipedia.org/wiki/Cyberinfrastructure
  • “In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.” src: http://en.wikipedia.org/wiki/Cyberinfrastructure
  • “In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.” src: http://en.wikipedia.org/wiki/Cyberinfrastructure
  • “In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.” src: http://en.wikipedia.org/wiki/Cyberinfrastructure
  • “In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.” src: http://en.wikipedia.org/wiki/Cyberinfrastructure
  • “In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.” src: http://en.wikipedia.org/wiki/Cyberinfrastructure
  • “In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.” src: http://en.wikipedia.org/wiki/Cyberinfrastructure
  • “In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.” src: http://en.wikipedia.org/wiki/Cyberinfrastructure
  • “Ideas worth spreading” … the recent TEDxTucson centered around innovation in the area of green technology.
  • “In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.” src: http://en.wikipedia.org/wiki/Cyberinfrastructure
  • “In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.” src: http://en.wikipedia.org/wiki/Cyberinfrastructure
  • The knowledge of many is needed to solve the grand challenges facing biology and bioinformatics. http://www.flickr.com/photos/lorelei-ranveig/2294093649/
  • Code for science (rev 2)

    1. 1. {Code}forScience<br />Andrew Lenards<br />December 6, 2010<br />
    2. 2. slideshare.net/lenards<br />
    3. 3. Andrew Lenards<br />iPlant Collaborative<br />on Core S/W team<br />University of Arizona<br />CS Grad, 2001<br />Experienced developer, former consultant, instructor, & technical trainer<br />Domain experience:<br />Motor Vehicle Domain<br />Phylogenetics / Bioinformatics (sort of) <br />
    4. 4. Andrew Lenards - Activities<br />Learning about:<br />Requirements, User Stories, etc. <br />S/W Design/Architecture, Patterns, SOA<br />Molecular Biology, Phylogenetics, Phyloinformatics, Genetics, and Genomics<br />Active in:<br />Tucson Java Users Group<br />Semi-active in:<br />Tucson Startup Drinks<br />Ubuntu Arizona Local Community / TFUG<br />
    5. 5.
    6. 6.
    7. 7.
    8. 8. Hybrid Vigor <br />
    9. 9. Computational ___________<br />
    10. 10. Computational _Thinking_<br />
    11. 11. Computational _Biology_<br />
    12. 12. Computational _Gardening_<br />
    13. 13. Computational _Gardening_<br />
    14. 14. Bio________<br />
    15. 15. Biofuels<br />
    16. 16. Biochemistry<br />
    17. 17. Biophysics<br />
    18. 18. Bioinformatics<br />
    19. 19. …<br />
    20. 20.
    21. 21.
    22. 22.
    23. 23.
    24. 24.
    25. 25. What do you expectwhen you graduate? <br />
    26. 26. … for the computer sciencemajors <br />
    27. 27.
    28. 28.
    29. 29.
    30. 30. Myth of the Lone Developer <br />
    31. 31.
    32. 32. in-practice: lots of interaction w/ technical&non-technical people<br />
    33. 33. Take Away:<br />Communication is amajor challenge<br />
    34. 34. What might help?<br />
    35. 35.
    36. 36. Software projects#fail.<br />
    37. 37. … quite often<br />
    38. 38. Why?<br />
    39. 39. P00R(0////U||1(4710||<br />
    40. 40. Speaking in tongues is not allowed<br />
    41. 41. Adaption<br />
    42. 42.
    43. 43. {Code}for Science<br />
    44. 44. I wasn’t always interested in science/biology<br />
    45. 45. Biology is an interesting domain<br />
    46. 46.
    47. 47. I know too much aboutAuto titling & international trucking fees<br />
    48. 48. I know knew too muchaboutAuto titling & international trucking fees<br />
    49. 49. Conclusion: Act I<br />
    50. 50. Miscellaneous Info<br />Contact Info<br />Traditional: <br />lenards@iplantcollaborative.org<br />lenards@email.arizona.edu<br />Hipster:<br />@alenards<br />Slides are posted here:<br />http://www.slideshare.net/lenards<br />
    51. 51.
    52. 52. … of the community, by the community, for the community <br />
    53. 53. Empowering the next generation of biologist<br />
    54. 54. Why?<br />
    55. 55. The world faces tough problems in the future<br />
    56. 56. Fuel/Energy<br />
    57. 57. Food<br />
    58. 58. Water Supply<br />
    59. 59. …<br />
    60. 60.
    61. 61. Cyberinfrastructure<br />
    62. 62. “In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.” <br />
    63. 63. Large systems designleads to diverse,interdisciplinary teams<br />
    64. 64. With the direction of Computational Biology & Bioinformatics… <br />
    65. 65.
    66. 66. Software Development as aCollaborative Game<br />
    67. 67. Soft skills are important<br />
    68. 68. Speaking in tongues is not allowed<br />
    69. 69. Working in pairs, not just forpair-programming ordebugging<br />
    70. 70. Impromptu design discussions <br />(they often include more than just technical folks)<br />
    71. 71. Image Acknowledgements<br />“Mad Scientist Photo” of Andrew by Alex Yelich<br />http://www.flickr.com/photos/sskennel/4496534369/<br />http://upload.wikimedia.org/wikipedia/commons/3/32/Charles_Darwin_by_Elliott_and_Fry.jpg<br />http://en.wikipedia.org/wiki/File:Koeh-283.jpg<br />http://jitterypenguin.com/images01/SWG%20Screenshots/Zoee/Master%20Commando%20Skill%20Tree.jpg<br />http://www.flickr.com/photos/tonivc/2283676770/<br />http://www.flickr.com/photos/designbyfront/3428784075/<br />http://www.flickr.com/photos/lorelei-ranveig/2294093649/<br />http://www.flickr.com/photos/mathoov/4040824373/<br />http://www.flickr.com/photos/thatgrumguy/402041540/<br />http://www.flickr.com/photos/freya_gefn/2777209147/<br />http://www.flickr.com/photos/pkmousie/2652404430/<br />http://www.flickr.com/photos/sklathill/479528238/<br />http://commons.wikimedia.org/wiki/File:Babel_fish_badge.jpg<br />http://www.teachforamerica.org/assets/images/img/logo_tfa.gif<br />http://www.flickr.com/photos/roadsidepictures/389828793/<br />“Take Away” font: http://www.dafont.com/mailart-rubberstamp.font<br />
    72. 72. The content of this work is licensed under a Creative Commons <br />Attribution-NonCommercial-ShareAlike License. Your use of this material constitutes acceptance of that license and the conditions of use of materials on this site: <br />http://creativecommons.org/licenses/by-nc-sa/3.0/<br />

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