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
http://www.flickr.com/photos/small_realm/6898449633 CC BY
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
http://commons.wikimedia.org/wiki/File:Arpanet_logical_map,_march_1977.png
http://commons.wikimedia.org/wiki/File:Map_Showing_the_Telegraph_Lines_In_Operation,_Under_Contract,_and_Contemplated_to_Complete_the_C
ircuit_of_the_Globe,_1869.jpg
http://commons.wikimedia.org/wiki/File:Post_und_Reisecarte_der_Wege_durch_Frankreich_1703.PNG
Many networks
http://www.flickr.com/photos/47691521@N07/6082519811/ CC BY-SA
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/)
“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?
http://www.flickr.com/photos/tawheedmanzoor/2309847575 CC BY
“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
http://www.flickr.com/photos/mrsdkrebs/6522929727 CC BY
http://www.flickr.com/photos/leesean/5114553800 CC BY-SA
For any
http://www.flickr.com/photos/fontplaydotcom/2636754594 CC BY
“Open”does beingWhat
mean?
My work can help someone...
http://www.flickr.com/photos/mararie/3313582639/ CC-BY-SA
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..
http://www.flickr.com/photos/dno1967b/8531643597 CC BY
...and merging
What tools...?
http://www.flickr.com/photos/booleansplit/3055314411 CC BY
Repositories...
...documentation.
...VMs...
...continuous integration...
...unit tests...
...issue trackers...
...cloud.
http://www.flickr.com/photos/drachmann/327122302 CC-BY-SA
http://www.flickr.com/photos/robbie73/3387189144 CC-BY-SA
http://www.flickr.com/photos/mukumbura/4052671706 CC-BY-SA
http://www.software.ac.uk/blog/2013-07-09-recomputation-manifesto
http://ivory.idyll.org/blog/vms-considered-harmful.html
http://www.flickr.com/photos/marfis75/2459534903 CC BY-SA
Different audiences...
http://www.flickr.com/photos/pagedooley/5000489105 CC BY
Different audiences...
http://www.flickr.com/photos/9610484@N05/1120115961
...different supports.
http://www.flickr.com/photos/soldiersmediacenter/4311667534 CC BY
...different supports.
http://www.flickr.com/photos/celebdu/291322346 CC BY
But how do you support the
unexpected...?
http://www.flickr.com/photos/drachmann/327122302 CC-BY-SA
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....
http://www.flickr.com/photos/beccapeterson/5338013478 CC BY-ND
No-one ever got...
http://www.flickr.com/photos/natematias/310642831 CC-BY-SA
one of these...
...for infrastructure
http://www.flickr.com/photos/joshwept/5689555989/ CC BY
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