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GitHub for Science Arfon Smith @arfon Creative Commons Attribution 3.0 Unported License

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Three ideas we should steal from Open Source Arfon Smith @arfon Creative Commons Attribution 3.0 Unported License

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!

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What is a GitHub?

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GitHub

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0 3,000,000 6,000,000 9,000,000 2007 2008 2009 2010 2011 2012 2013 2014 Users

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4,000,000 8,000,000 12,000,000 16,000,000 20,000,000 2007 2008 2009 2010 2011 2012 2013 2014 Repositories

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Guess the language!

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1750 3500 5250 7000 2008 2009 2010 2011 2012 2013 2014

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1750 3500 5250 7000 2008 2009 2010 2011 2012 2013 2014 Fortran

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15000 30000 45000 60000 2008 2009 2010 2011 2012 2013 2014 LaTeX

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500 1000 1500 2000 2009 2010 2011 2012 2013 2014 IDL

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0 175,000 350,000 525,000 700,000 2008 2009 2010 2011 2012 2013 2014 C++

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350,000 700,000 1,050,000 1,400,000 2008 2009 2010 2011 2012 2013 2014 Python

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Why build a GitHub?

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Made writing code a social experience 1.

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Changed the collaborative model of open source 2.

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‘May I have access to your codes please?’

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From 653314448c7c6f6ec2f93de346896895f786773f Mon Sep 17 00:00:00 2001 From: Arfon Smith Date: Mon, 13 Oct 2014 16:37:46 -0500 Subject: [PATCH] Bust that cache --- lib/linguist/repository.rb | 14 ++++++++++++-- test/test_repository.rb | 12 ++++++++++++ 2 files changed, 24 insertions(+), 2 deletions(-) diff --git a/lib/linguist/repository.rb b/lib/linguist/repository.rb index 1f9e09c..9998ee6 100644 --- a/lib/linguist/repository.rb +++ b/lib/linguist/repository.rb @@ -1,6 +1,6 @@ require 'linguist/lazy_blob' require 'rugged' - +require 'pry' module Linguist # A Repository is an abstraction of a Grit::Repo or a basic file # system tree. It holds a list of paths pointing to Blobish objects. @@ -128,13 +128,23 @@ def current_tree protected def compute_stats(old_commit_oid, cache = nil) - file_map = cache ? cache.dup : {} old_tree = old_commit_oid && Rugged::Commit.lookup(repository,

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GitHub delivered on a theoretical promise of open source

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Open source collaborations Open Source: the right to modify

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Open source collaborations Open Source: the right to modify, not the right to contribute.

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"

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Open source collaborations Forking a project was done as a last resort

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Open source collaborations GitHub made forking the norm

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1. Open Collaborations

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Open source collaborations Open Source vs Open Collaborations

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Open source collaborations Open Source: the right to modify

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Open source collaborations Open Collaborations: a highly collaborative development process and are receptive to contributions of code, documentation, discussion, etc from anyone who shows competent interest.

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Open source collaborations Open Collaborations: a highly collaborative development process and are receptive to contributions of code, documentation, discussion, etc from anyone who shows competent interest. THIS

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How do 4000 people work together?

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The pull request

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discuss improve Code first, permission later

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Exposed process

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Every time this happens the community learns

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Academia makes the same promise

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Explain what you did

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So that others can repeat

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Everybody learns

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(doesn’t have to mean this) Open Public? =

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Open (within your team, department or institution)

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Electronic & Available

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Asynchronous, exposed process

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Asynchronous, exposed process

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Asynchronous, exposed process

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Lock-free

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Open, low friction collaborations

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Merged pull requests

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Culture of Reuse 2.

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A story from my life (~10 years ago)

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http://amandabauer.blogspot.com/

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130 130 1 2048 189 189 258 258 480 562 378 378 493 521 390 397 851 851 247 274 319 319 304 580 493 511 610 636 188 188 228 228 > cat bad_pix_mask.txt

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2 days work 3 observing runs/week 52 weeks in year 15 year detector lifetime 2*3*52*15 = 4680 days (13 years)

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A second story from my life (~6 months ago)

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Software composed of many components

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Your software is the thing that is different

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Open Source: Ubiquitous culture of reuse

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Verification 3.

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Robots doing work

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“open source is… reproducible by necessity” Fernando Perez http://blog.fperez.org/2013/11/an-ambitious-experiment-in-data-science.html

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Software is an unforgiving medium

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“open source is… reproducible by necessity” Fernando Perez http://blog.fperez.org/2013/11/an-ambitious-experiment-in-data-science.html

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GitHub for Science

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A product?

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Collaborative model?

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Credit system?

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Discoverability?

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Reproducibility?

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GitHub

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* Other vendors of version control software are available *

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Barriers are cultural, not technical

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Reproducibility Data intensive

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If we want to crib what Open Source does

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What’s required to make this behaviour the norm?

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Credit

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“Academic environments of today do not reward tool builders” Ed Lazowska, OSTP event http://lazowska.cs.washington.edu/MS/MS.OSTP.pdf

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“publishing a paper about code is basically just advertising” David Donoho http://www.stanford.edu/~vcs/Video.html

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How to derive meaningful metrics from open contributions?

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Trust

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Discoverability

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Starts with you

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Be more exact

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Try out some tools

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Focus most effort where your peers will most easily recognise value

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Share software, data and methods (and cite them too!)

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Where do communities form?

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Around a shared challenge?

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Around shared data?

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10 ? n Level 1 (continual) Level 2 (periodic)

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LSST is a project that is inherently open

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Supernovae Weak lensing Active Galactic Nuclei Solar System Galaxies Transients/variable stars Large-scale structure Stars, Milky Way Strong lensing Informatics and Statistics Dark Energy (DESC)

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Your software should be the thing that is different

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science too! Your software should be the thing that is different

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Barriers are cultural, not technical

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Next time you review, ask for methods, code and data

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Share (and license) your work

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Take a course (and send your students on one)

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Try versioning your work

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Open source has solved much of what academia needs

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The challenge is to adapt and evolve the academy in this new collaborative age

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Thanks. [email protected] @arfon #