code for science (rev 1)
DESCRIPTION
Slides that accompanied a talk given to undergraduate biologists and computer scientists.TRANSCRIPT
Code forScience
Andrew LenardsJune 24, 2010
slideshare.net/lenards
Andrew Lenards • iPlant Collaborative– on Core S/W team
• University of Arizona– CS Grad, 2001
• Experienced developer, former consultant, instructor, & technical trainer
• Domain experience:– Motor Vehicle Domain– Phylogenetics / Bioinformatics (sort of)
Andrew Lenards - Activities• Learning about:
– Requirements, User Stories, etc. – S/W Design/Architecture, Patterns, SOA– Molecular Biology, Phylogenetics, Phyloinformatics, Genetics, and
Genomics
• Active in:– Tucson Java Users Group
• Semi-active in:– Tucson Startup Drinks– Ubuntu Arizona Local Community / TFUG
Hybrid Vigor
Computational ___________
Computational _Thinking_
Computational _Biology_
Computational _Gardening_
Computational _Gardening_
Bio________
Biofuels
Biochemistry
Biophysics
Bioinformatics
…
What do you expectwhen you graduate?
… for the computer sciencemajors
Myth of the Lone
Developer
in-practice: lots of interaction w/ technical& non-technical people
Communication is amajor challenge
Take Away:
What might help?
Software projects fail.
… quite often
Why?
Adaption
Adaption & Quality lead to success
Quality Researchrequires
Quality Software
“good enough” Softwarecan help produceQuality Research
Starts with understanding
purpose…
… and leadsto testing
"Testing is the engineering rigor of software development."
-- Neal Ford
Testing affects your design
Flexible design grows out of making code
“testable”
testing brings about higher quality
Take Away:
Code for Science
I wasn’t always interested in
science/biology
Biology is an interesting domain
I know too much aboutAuto titling & international trucking fees
Conclusion: Act I
Miscellaneous Info
• Contact Info– [email protected]– [email protected]
• Slides– Will be posted here:• http://www.slideshare.net/lenards
… of the community, by the community, for the community
Empowering the next generation of biologist
Why?
The world faces tough problems
in the future
Fuel/Energy
Food
Water Supply
…
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.”
Large systems designleads to diverse,
interdisciplinary teams
With the direction of Computational Biology &
Bioinformatics…
Software Development
as aCollaborative Game
Soft skills are important
Speaking in tongues is not allowed
Working in pairs, not just for
pair-programming ordebugging
Impromptu design discussions
(they often include more than just technical folks)
Conclusion: Act II
Small team
Varying backgrounds
(brilliant co-workers)
Diverse skill-sets
What’d I get out of it?
“Lone” Developer, Meet your team:
- PastYou-FutureMe
Systems grow & change in organic ways
(related topic: Entropy)
Learned importance of unit testing
“Safety net for refactoring”
Ruthless refactoringw/ extreme confidence
Automation keepsyou & your team
honest
(Continuous Integration)
Broken Window Theory
(Pragmatic Programmer)
Need an infectious attitude toward
testing…
Robust software is well-tested software
Good day for QA ==Bad day for Dev
Image Acknowledgements• “Mad Scientist Photo” of Andrew by Alex Yelich• http://www.flickr.com/photos/sskennel/4496534369/• http://upload.wikimedia.org/wikipedia/commons/3/32/Charles_Darwin_by_Elliott_and_Fry.jpg• http://en.wikipedia.org/wiki/File:Koeh-283.jpg• http://jitterypenguin.com/images01/SWG%20Screenshots/Zoee/Master%20Commando%20Skill%
20Tree.jpg• http://www.flickr.com/photos/tonivc/2283676770/• http://www.flickr.com/photos/lorelei-ranveig/2294093649/• http://www.flickr.com/photos/thatgrumguy/402041540/• http://www.flickr.com/photos/freya_gefn/2777209147/• http://www.flickr.com/photos/pkmousie/2652404430/• http://www.flickr.com/photos/sklathill/479528238/• http://commons.wikimedia.org/wiki/File:Babel_fish_badge.jpg• http://www.flickr.com/photos/lorelei-ranveig/2294093649/• http://www.flickr.com/photos/roadsidepictures/389828793/• http://www.teachforamerica.org/assets/images/img/logo_tfa.gif• “Take Away” font: http://www.dafont.com/mailart-rubberstamp.font
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