1. Open Software for (Open) Science http://dx. doi. org/10. 6084/m9
Open Software for (Open) Science e-IRG Workshop, 3 June 2015, Riga Neil Chue Hong Software Sustainability Institute ORCID: |
The Software Sustainability Institute is supported by EPSRC grants EP/H043160/1 and EP/N006410/1 (which includes funding from BBSRC and ESRC).
Additional projects have been funded by Jisc (Software Preservation Framework and Software Hub) and NERC (Advanced Short Courses).
Supported by
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Slides licensed under CC-BY where indicated:

2. Overview Open source: philosophy and practice Open source licenses
Other types of licenses
Pros/Cons of licenses
Case studies
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3. I Am Not A Lawyer For legal insight, I recommend: http://ifosslawbook
I Am Not A Lawyer For legal insight, I recommend: and for everything else:
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4. Open Source Software is Free...
Photo “free beer tap” by jakob fenger (CC-BY)
Photo “Speech”by Quinn Dombrowski (CC-BY)
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5. Free as in Puppy... Long term costs Needs love and attention
May lose charm after growing up
Occasional clean-ups required
Many left abandoned by their owners
Scott McNealy coined the phrase
Inspired by Scott McNealy
Photos of Great Pyrenees from Jen Schopf
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6. Free as in kittens... Can become snarling, clawing, aloof…
… but they will provide joy if you treat them well
Open source is very much in the spirit of open science and vice-versa
Photo “Kittens!”by James Wragg (CC-BY)
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7. Four essential freedoms
Freedom for anyone to run the program as they wish, for any purpose (non-discriminatory)
Freedom to study how the program works, and change it so it does your computing as you wish (source code available, modifications allowed)
Freedom to redistribute copies so you can help others (redistribution allowed)
Freedom to distribute copies of your modified versions to others to give them a chance to benefit from your changes (derivatives allowed)
From
Note that there are some differences between the open source movement (as led by the OSI) and the free software movement (led by GNU/FSF), the former is a development methodology, the latter a social movement.
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8. Open Source Definition (1)
Free redistribution
Author and others can sell or give away as part of an aggregation of software
Author cannot impose a royalty or fee on those redistributing
Source code available
Must include a way of accessing un-obfuscated source code at a reasonable reproduction code
Derived works allowed
Must allow modifications and derived works
Must allow distribution under same terms as license of original
Integrity of The Author's Source Code
License may restrict source-code from being distributed in modified form only if the license allows the distribution of "patch files" with the source code for the purpose of modifying the program at build time, but must explicitly permit distribution of software built from modified source code.
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9. Open Source Definition (2)
Non-discriminatory
Can’t restrict based on geography, person, group, field or type of organisation
Product and technology neutral
Not dependent on code being part of a particular product
Not predicated on any individual technology or interface
License must not restrict other software
License must not place restrictions on other software that is distributed along with the licensed software.
Distribution of license
Rights must apply to all to whom the program is redistributed without the need for execution of an additional license by those parties
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10. Open source, open science
Non-discriminatory
Research should not be restricted or siloed
Access to source code
Research should be transparent, robust, and accessible
Redistribution of software
Providing access to the widest possible community
Removing barriers to reuse
Research should encourage building on the work of others, and giving them credit
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11. Types of open source license
Permissive (“Use with attribution”)
Simple (e.g. Modified “3-clause” BSD, MIT)
Grant Patent Rights (e.g. Apache, Eclipse)
Copyleft (“Share modifications under same license”)
Strongly copyleft (e.g. GPL)
Weakly copyleft (e.g. LGPL, Mozilla, EUPL)
All OS licenses allow private and commercial use; modification; distribution; limit liability; retain copyright
More information
Permissive similar to CC-BY
Copyleft similar to CC-BY-SA
No concept of ND or NC restrictive clauses
Strongly copyleft means cannot be “bundled” – GPL license dominates
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12. Other common licenses Closed (“Proprietary”)
Restricted (“Academic” / “Non-commercial”)
Public domain / CC0
Informal license
No license
Also
Larger works comprising code with different licenses (“license compatibility”)
Software made available under more than one license (“dual licensing”)
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13. Licenses vs Governance
Open source software is more than the license
Some open licensed software is not produced openly
Some closed licensed software benefits from open source project principles and processes
Most open source contributors are paid to do so
Best practice identified from OSS projects useful for governance and project/product management of all types of software
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14. Pros and Cons of Open Source
Easier to evaluate
Harder to corner cut when shipping to deadline
No lock-in
Harder to gain income from selling the software
Easier to attract contributors and staff
But most sell services
Frictionless code sharing
Cannot restrict to non-commercial use only
Free advertising
Able to take with you
But what is non-commercial use?
Generally better modularisation
Once licensed, cannot revoke license
Reduced duplication
Can work together on common platforms
Though can relicense
Can increase competition
Copyrighting better than patenting for software (costs far less!)
Don’t open source anything that represents core business value
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15. Building out new functionality
Dropbox moved to Go from Python to benefit from better concurrency support and execution speed
Go did not have the depth of libraries that Dropbox needed to build larger systems
Dropbox team started to build its own libraries
connection management and memcache client
Open-sourced work to kickstart community and help create better production systems
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16. Building community
Spark started as academic project at Berkeley in 2009
Code released under BSD in 2010
Started Apache Incubator process in June 2013
Gained contributions from 120 developers in 25 organisations, including Intel, Yahoo!, Cloudera, Alibaba
Relicensed under Apache 2.0 license
Became full Apache project in February 2014
Most active Apache project in 2014
Source code on GitHub
Used globally by Alibaba, Amazon, IBM
Company formed to commercialise in Sep 2013
Based around hosting and consulting
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17. Creating widely used platforms
Git originally written and released by Linus Torvalds under GPL license
Git trademarks enforced for consistency
Easy for third parties to create services on top
GitHub contribute to Git and open source some of their own tools
Business model exploits paid hosting / support for enterprise installations
Gitlab go further and release their commercial EE edition under MIT license, but code must be requested
And GItLab ask nicely that you do not redistribute the EE edition if you want to help them
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18. Underpinning research
Basics: Website, mailing list, code repository, issue resolution
Remove barriers to participation, increase efficiency
1993: First public release; 2 devs
1995: Code open sourced; 3 devs
1996: r-testers list set up
1997: lists split: r-announce, r-help, r-devel; public CVS; 11 devs
2000: CRAN split and mirror
2001: BioConductor
2003: Namespaces
2005: I8n, L8n
2007: R-Forge
Today: BioConductor (33 core devs), R-Forge (532 projects, 1562 devs), CRAN (1400+ packages)
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19. Case studies in academia
OSS Watch have produced case studies of several open source software projects in academia
Koha: a case study in project ownership
Wookie: a case study in sustainability
ATutor LMS: a case study
TexGen: a case study
MediaWiki: a case study in sustainability
WebPA: the road to sustainability
Apache Cocoon: a case study in sustainability
Moodle: a case study in sustainability
Exim: a case study in sustainability
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20. “[T]here's been a stunning and irreversible trend in enterprise infrastructure. If you're operating a data center, you're almost certainly using an open source operating system, database, middleware and other plumbing. No dominant platform-level software infrastructure has emerged in the last ten years in closed-source, proprietary form.” - Mike Olsen, Cloudera founder

21. GPL vs Apache Software freedom vs developer freedom
Copyleft licenses have increased license management costs
Industry is generally more supportive of permissive licenses
Open source software no longer written as an alternative to closed, but as the platform to drive service provision
Software no longer the competitive differentiator, but the ability to operate it at scale
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22. Open licensing should be used for data and code
Software Infrastructure and Environments for Reproducible and Extensible Research
Open licensing should be used for data and code
Workflow tracking should be carried out during the research process
Data must be available and accessible
Code and methods must be available and accessible
All 3rd party data and software should be cited
Stodden V and Miguez S, (2014) Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research, DOI: /jors.ay

23. Open Source lets others benefit
Slide courtesy of Nancy Wilkins Diehr
“Arman Bilge, a 10th grader at Lexington High School in Massachusetts, was a newbie to phylogenetics when a science teacher there organized an after-school phylogenetic tree club. In the club, Bilge learned how to use a variety of software applications, including one well known to systematic biologists called BEAST.
That led Bilge to create a map and timeline that identified when the Human Immunodeficiency Virus (HIV) arrived in the Americas, and where and when it spread across North and South America.
“The BEAST is a beast,” Bilge said in a telephone interview from Lexington. He managed to tame it enough to create a detailed phylogenetic tree based on similarities and differences in the 3,000 nucleotide subunits of a gene for an envelope protein among 700 known HIV-1 strains.
“You ask the BEAST program to guess at a most likely family tree for all of them and the software scores each possible tree with a likelihood function,” Bilge said. “The number of possible phylogenetic trees for HIV-1 exceeds the number of protons in the universe, and only one of them is correct, so this is a big calculation.”
Bilge first tried to run the analysis on his home computer. “I ran it for three weeks, but I didn’t reach the accepted way of knowing that you came to the end,” he said. Bilge said his parameters and settings were impossible for any computer to analyze, but he learned from the experience. “I started multiple simultaneous runs on CIPRES and the geographic component of my project is the result of the concatenation of these analyses,” he said.
The phylogenetic tree Bilge published for his science fair project was the one that BEAST said was the most optimal, and Bilge said his conclusions supported the previously published results of HIV experts: “A single introduction of the virus in Haiti in the mid-1900s resulted in its dispersion across the American continent.”
While Bilge may not have been satisfied with his residual statistical uncertainty, the judges at the 2012 Massachusetts Science and Engineering Fair were – they awarded him first place in the biology category.”
Slide courtesy of Nancy Wilkins-Diehr
BEAST software licensed under LGPL

24. Summary Open source now de facto for infrastructure software
Open source encourages
Exploitation
Reproducibility and Robustness
Reuse
Open source helps support open science
“Publicly funded research […] is a public good, produced in the public interest, which should be made openly available” – RCUK
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