Eagle Bioinformatics Symposium: 3.Cameron Neylon: Network Ready Research: The Role of Open Source...

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The highest principle of network architecture design is interoperability. If Metcalfe's Law tells us that a network's value can scale as some exponent of the number of connections, then our job in building networks is to ensure that those connections are as numerous, as operational, and as easy to create as possible. Where we make it easy for anyone to wire in new connections, we maximize the ability of others to contribute to the value of our shared networks. Bioinformatics has, from time to time, been derided as "slidedecks full of hairballs," yet those hairballs and their ubiquity are emblematic of the fact that at its heart bioinformatics is a science of networks: networks of physical interactions, of genetic control, of degrees of similarity, or of ecological interactions among many others. Bioinformatics is also among the most networked of research communities and among the most open in the sharing of research papers, research data, tools, and even research in process in online conversations and writing. How can we apply the expertise we have on the study of networks to the creation of effective networks for research communication?

Transcript of Eagle Bioinformatics Symposium: 3.Cameron Neylon: Network Ready Research: The Role of Open Source...

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Network Ready Research The role of Open Source and Open Thinking

!

Eagle Symposium - Cambridge 27 March 2014 - Cameron Neylon

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Networks.

Torres-Sosa et al, doi:10.1371/journal.pcbi.1002669 Waters et al, doi:10.1371/journal.pone.0040337http://bit.ly/bosc-cn-fig1 http://bit.ly/bosc-cn-fig2

Torres-Sosa et al, doi:10.1371/journal.pcbi.1002669 Waters et al, doi:10.1371/journal.pone.0040337http://bit.ly/bosc-cn-fig1 http://bit.ly/bosc-cn-fig2

Torres-Sosa et al, doi:10.1371/journal.pcbi.1002669 Waters et al, doi:10.1371/journal.pone.0040337http://bit.ly/bosc-cn-fig1 http://bit.ly/bosc-cn-fig2

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ircuit_of_the_Globe,_1869.jpg

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Many networks

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What can we...

Here’s another...

Martínez-Delgado et al (http://www.cosmotography.com/images/lrg_ring_ngc5907.html)

Lang, Hogg et al (http://astrometry.net/svn/trunk/projects/rankorder/)

27 January 2009

http://gowers.wordpress.com/

27 January 2009

February 1 2009

http://gowers.wordpress.com/

“It is not the case that the aim of the project is [...to solve the problem...] I think that the chances of success even for this more modest aim are substantially less than 100%.” !Tim Gowers http://gowers.wordpress.com/2009/02/01/a-combinatorial-approach-to-density-hales-jewett/

27 January 2009

February 1 2009

March 10 2009

http://gowers.wordpress.com/

“It feels as though this is to normal research as driving is to pushing a car.” !Tim Gowers http://gowers.wordpress.com/2009/02/01/questions-of-procedure/#comment-1701

Successful open projects...

...exploit order-disorder transitions

...or...

...network transitions can be exploited...

...by adopting open approaches

“Open”isWhat

about anyway?

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“Open”doesWhat

mean?

http://www.flickr.com/photos/yourdon/3088582622

...sharing what we already create

The license must not restrict anyone from making use of the program in a specific field of endeavor. Open Source Definition - http://opensource.org/osd

The license must not discriminate against any person or group of persons.. Open Definition - http://opendefinition.org/okd

By Open Access we mean...permitting any users to read, download, copy, distribute,

print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or

technical barriers other than those inseparable from gaining access to the internet itself.

!

Budapest Open Access Initiativehttp://www.budapestopenaccessinitiative.org/read

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For any

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“Open”does beingWhat

mean?

My work can help someone...

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P = InterestFriction

x N (help someone)

P = InterestFriction

x N (help someone)

Proportion that could use your work

Usability of your work

Number of people you can

reach

Someone out there can help...

http://www.flickr.com/photos/mararie/3313582639/ CC-BY-SA

P = InterestFriction

x N (getting help)

P = InterestFriction

x N (getting help)

Proportion that create work you can use

Ease of contributing

Number of people you can

reach

P = InterestFriction

x N (getting help)

Fixed

P = InterestFriction

x N (getting help)

As small as possible...

P = InterestFriction

x N (getting help)

As small as possible...

As large as possible...

Being open is acting to reduce friction and to maximize N...

...for both outgoing and incoming information...

http://www.flickr.com/photos/nanagyei/6744708487 CC BY

Enable forking..

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...and merging

What tools...?

http://www.flickr.com/photos/booleansplit/3055314411 CC BY

Repositories...

...documentation.

...VMs...

...continuous integration...

...unit tests...

...issue trackers...

...cloud.

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http://www.software.ac.uk/blog/2013-07-09-recomputation-manifesto

http://ivory.idyll.org/blog/vms-considered-harmful.html

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Different audiences...

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Different audiences...

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...different supports.

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...different supports.

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But how do you support the

unexpected...?

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http://www.flickr.com/photos/robbie73/3387189144 CC-BY-SA

http://www.flickr.com/photos/mukumbura/4052671706 CC-BY-SA

If it’s near zero cost...

http://www.flickr.com/photos/gaelx/6340466785 CC BY-SA

...and reduces

...or increases

http://www.flickr.com/photos/jennycu/4527765710 CC BY

...then do it.

If it costs...

http://www.flickr.com/photos/pagedooley/5000489105 CC BY

...but helps a known audience

http://www.flickr.com/photos/gaelx/6340466785 CC BY-SA

...and reduces

...or increases

http://www.flickr.com/photos/jennycu/4527765710 CC BY

...for all...

...then do it.

Can move it upstream...

http://flickr.com/photos/jason_burmeister/2053139930 CC-BY

...use shared platforms

http://www.flickr.com/photos/37984062@N03/3495256118 CC-BY-SA

http://www.flickr.com/photos/mdpettitt/3455884055 CC-BY

...share the load

...then...

http://www.flickr.com/photos/mecklenburg/5026128169 CC BY-SA

Something is missing....

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No-one ever got...

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one of these...

...for infrastructure

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Hack the incentives system...?

More of the same...?

http://www.flickr.com/photos/levork/5026708729 CC BY-SA

http://www.flickr.com/photos/yakobusan/2436481628 CC-BY

Community architecture...

...open in the foundations

http://www.flickr.com/photos/56380734@N05/7852142720 CC-BY-SA

Reduce friction...

http://www.flickr.com/photos/g_kat26/3535474947 CC-BY-SA

...and support sharing...

http://www.flickr.com/photos/cogdog/5910598311 CC BY-SA

http://www.flickr.com/photos/dno1967b/6295812307 CC BY

...but also merging

Where are the opportunities?

Points of nucleation?

http://www.flickr.com/photos/vitroids/1527109907 CC BY

Where are we close to a phase transition?

http://www.flickr.com/photos/mararie/2185487355 CC BY-SA

That’d be a problem for people who know networks...

@cameronneylon http://cameronneylon.net