Academia's Biggest Blind Spot

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ACADEMIA’S BIGGEST BLIND SPOT Arfon Smith (@arfon) Creative Commons Attribution 4.0 International License.

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Software datA?

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Software is important

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Software is everywhere

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Software turns a theoretical model into quantitative predictions; software controls an experiment; and software extracts from raw data evidence supporting or rejecting a theory. Gaël Varoquaux

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Software is important becoming increasingly ^

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deep intellectual contributions (Are) now encoded in software. Victoria Stodden

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Complex things numbers science! data science! science!

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Reproducibility Data intensive

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http://www.nature.com/news/2011/111005/full/478026a.html

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Complex things Unpacking the box Transparency Reproducibility Credit Trust

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Complex things Few incentives for the individual Transparency Reproducibility Credit Trust

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Software can be a competitive advantage

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Human Genome project 15 years 3 billion bases $3 billion

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Human Genome project 15 years 3 billion bases $3 billion

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Human Genome project 15 years 3 billion bases $3 billion 5000 perl modules

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Change was the only constant

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Continual change Flexible Web-based Service-oriented 1000s of projects

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Galaxy Zoo 1 million galaxies 300,000 people two postdocs & a student

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A1: Smooth A2: Features or disk A3: Star or artifact A1: Completely round A2: In between A3: Cigar shaped A1: Yes A2: No A1: 1 A2: 2 A3: 3 A4: 4 A5: More than 4 A6: Can't tell A1: Straight Line A2: Chain A3: Cluster A4: Spiral A1: Yes A2: No A1: Yes A2: No A1: Yes A2: No A1: Yes A2: No A1: Rounded A2: Boxy A3: No bulge A1: Bar A2: No bar A1: Spiral A2: No spiral A1: Tight A2: Medium A3: Loose A1: 1 A2: 2 A3: 3 A4: 4 A5: More than 4 A6: Can't tell T01: Is the galaxy simply smooth and rounded, with no sign of a disk? T07: How rounded is it? T12: Does the galaxy have a mostly clumpy appearance? T16: How many clumps are there? T15: Do the clumps appear in a straight line, a chain, a cluster, or a spiral pattern? T13: Is there one clump which is clearly brighter than the others? T14: Is the brightest clump central to the galaxy? T17: Does the galaxy appear symmetrical? T02: Could this be a disk viewed edge-on? T09: Does the galaxy have a bulge at its center? If so, what shape? T03: Is there a sign of a bar feature through the center of the galaxy? T04: Is there any sign of a spiral arm pattern? T10: How tightly wound do the spiral arms appear? T11: How many spiral arms are there?

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A1: Yes A2: No A1: Yes A2: No A1: Yes A2: No A1: Yes A2: No A1: Rounded A2: Boxy A3: No bulge A1: Spiral A2: No spiral A1: Tight A2: Medium A3: Loose A1: 1 A2: 2 A3: 3 A4: 4 A5: More than 4 A6: Can't tell A1: No bulge A2: Just noticeable A3: Obvious A4: Dominant A1: Yes A2: No A1: Ring A2: Lens or arc A3: Disturbed A4: Irregular A5: Other A6: Merger A7: Dust lane T13: Is there one clump which is clearly brighter than the others? T14: Is the brightest clump central to the galaxy? T17: Does the galaxy appear symmetrical? T18: Do the clumps appear to be embedded within a larger object? T09: Does the galaxy have a bulge at its center? If so, what shape? T04: Is there any sign of a spiral arm pattern? T10: How tightly wound do the spiral arms appear? T11: How many spiral arms are there? T05: How prominent is the central bulge, compared with the rest of the galaxy? T06: Is there anything odd? T08: Is the odd feature a ring, or is the galaxy disturbed or irregular? End 1st Tier Question 2nd Tier Question 3rd Tier Question 4th Tier Question 5th Tier Question

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Zooniverse Scalable/Fast Flexible domain model Highly available Cheap

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Software became our competitive advantage

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Both were special cases

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1000s of staff 100s of engineers (with some hope of a career)

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staffed by engineers who’d given up on a research career

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Software is important becoming increasingly ^

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What is required for these to not be special cases?

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How do we enable people who want to write software?

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the skills required to be a successful scientific researcher are increasingly indistinguishable from the skills required to be successful in industry. Jake VanderPlas

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Software currently isn’t a creditable research output

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We must find a way to legitimize software as a form of scholarship. Phil Bourne, Director for Data Science, NIH

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Software currently isn’t a creditable research output why?

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Challenge Technical Cultural How do you cite software? ✔ ❌ Software Citations aren’t allowed ❌ ✔ software isn’t citable ✔ ❌ Software citations aren’t indexed ✔ ✔ Software isn’t peer reviewed ❌ ✔ Software can’t cite other software ✔ ❌

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Possible solutions

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Three categories of solutions Self-service (individual) Self-service (groups) external (Ecosystem)

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Solution #1 Write Software papers

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We now have something to cite! Write Software papers

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BUT: It’s a ton of work… Write Software papers

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Not all journals accept them… Write Software papers

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And what about authorship? Write Software papers

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Many papers = citation dilution Write Software papers ☹

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Going beyond the software paper…

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Solution #2 Make it possible to cite software

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Why do we cite? To show we’ve done our research To credit the work of others To enrich the scholarly record To avoid plagiarism

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Why do we cite? To show we’ve done our research To credit the work of others To enrich the scholarly record To avoid plagiarism

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Solution #2 Make it possible to cite software Smith et al., My Awesome Codes, v1.0.0, http://github.com/arfon/awesome-codes

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Solution #2 Make it possible to cite software http://github.com/arfon/awesome-codes

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Cite software natively! Make it possible to cite software

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BUT: Many journals don’t allow it Make it possible to cite software

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And have citation limits… Make it possible to cite software

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And indexers don’t count them Make it possible to cite software

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Doesn’t help people’s careers ☹ Make it possible to cite software

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https://www.force11.org/software-citation-principles

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http://www.newslocker.com/en-uk/news/uk_news/family-struggle-to-force-giant-sofa-into-tiny-car/

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Already an incredible ecosystem around software

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What does (open source) software do especially well?

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Authorship

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Authorship isn’t static

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Metrics &Veriﬁcation

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Dependencies Citations?

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What if we tried to copy use some of these ideas?

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What if we built a better academic credit model?

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Solution #3 Go beyond the h-index

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Solution #3 Go beyond the h-index paper-centric ^

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Really hard. Probably. ☹ Go beyond the h-index

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Richer citations papers Datasets software Cite Anything EVERYTHING

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Smith et al WMAP astropy PLANK Jones et al Smith et al scikit-learn 0.3 0.1 0.1 0.1 0.2 0.2 Transitive Credit Dan Katz

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Smith et al WMAP astropy PLANK Jones et al Smith et al scikit-learn 0.3 0.1 0.1 0.1 0.2 0.2 whyte et al numpy scipy 0.5 0.25 0.25

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Hard because we have no control Go beyond the h-index paper-centric ^

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Solution #4 Elevating the role of software

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Individual actions Ask for authors to include software when reviewing papers

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Individual actions Include non-paper contributions when assessing candidates

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Individual actions Take a course (or send your student on one)

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Individual actions Share your software on GitHub :-)

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All the ﬁxes Write Software papers Make it possible to cite software Go beyond the h-index Elevating the role of software

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Thanks Arfon Smith (@arfon)