Loosely Coupled Thoughts

Loosely Coupled Thoughts

Andrew LenardsFeb. 12, 2010

Andrew Lenards • iPlant Collaborative– S/W Eng on Core S/W team

• University of Arizona– CS Grad, 2001

• Reformed .NET 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

What do you expectwhen you graduate?

The Myth of the Lone Developer

SRS -> * -> Code

(rarely talking to anyone else, if so only other devs)

in-practice: lots of interaction w/ technical& non-technical people

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

"Testing is the engineering rigor of software development."

-- Neal Ford

ExecutableDocumentation

Testing affects your design

TDD: Test-driven Development

TDD: Test-driven Design

Flexible design grows out of making code

“testable”

“Legacy Code”:any source w/o unit tests

… 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)

Code for Science

I wasn’t always interested in

science/biology

Confused looks are commonplace for me

YOU > me

Biology is an interesting domain

I know too much aboutAuto titling &

international trucking fees

Going forward…

Test, test, test

If not test-first, test-very-soon-after

Help a FOSS project(best place to start: testing)

[FOSS or F/OSS: Free or Open Source Software]

Practice communicating

• Join/start a FOSS project (as a group)• Writing / Blog / Whatever• Present @ User Groups– Toastmasters?

• UTA Program?

Design

• READ– Books, Blogs, Magazines, Publications

AND other people’s code• Code– Make mistakes and learn from them

Suggested Reading

• Pragmatic Programmer– Andy Hunt & Dave Thomas

• 97 Things Every Programmer Should Know• Productive Programmer– Neal Ford

• Read “Uncle Bob”• “The Humble Dialog Box”– Michael Feathers

Learn a new programming language

every year (or two)

Groovy, Python, Ruby,Perl, Icon, Scala, Lisp, Self, Scheme, Smalltalk, SML, …

Become familiar with popular FOSS projects…

What’s Inversion of Control?Don’t know?

Learn more about Spring or Guice

Interested in biologyor computational biology?

Fun Foundational Materials

• The Manga Guide to Molecular Biology• The Stuff of Life: the Graphic Guide to Genetics and DNA

• Cartoon Guide to Genetics• The Manga Guide to Statistics • Cartoon Guide to Statistics

Still interested?

Really?!?

More Materials

• Lawrence Hunter– Introduction to Molecular Biology for Computer

Scientists• http://compbio.uchsc.edu/Hunter/01-Hunter.pdf

– The Processes of Life: An Introduction to Molecular Biology

• A Computer Scientist’s Guide to Cell Biology• …

Miscellaneous Info

• Contact Info– [email protected]– [email protected]

• Slides– Will be posted here:• http://www.slideshare.net/lenards

Image Acknowledgements• http://www.flickr.com/photos/lenards/3955049100/• “Mad Scientist Photo” of Andrew by Alex Yelich• 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://www.flickr.com/photos/lorelei-ranveig/2294093649/• http://www.flickr.com/photos/roadsidepictures/389828793/• http://www.flickr.com/photos/graylight/72935997/• http://www2.genome.arizona.edu/images/bio5bldg.jpg• http://www.flickr.com/photos/7298460@N03/4335819270/• http://www.teachforamerica.org/assets/images/img/logo_tfa.gif

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