Digitize Me, Visualize Me, Search Me: Open Science and its Discontents

edited by Gary Hall

Introduction: White Noise (coming soon...)

Open Science

It’s An Open (Science), Open (Access), Open (Source), Open (Notebook) World

<a href="http://usefulchem.wikispaces.com/">Open Notebook Science </a>

Patrick O. Brown, Michael B. Eisen, Harold Varmus

<a href="http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0000036">Why PLoS Became a Publisher</a>

Sally Murray, Stephen Choi, John Hoey, Claire Kendall, James Maskalyk, and Anita Palepu

<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091592/pdf/OpenMed-02-e1.pdf??tool=pmcentrez">Open Science, Open Access and Open Source Software at Open Medicine</a>

Community Science

<a href="http://www.psfk.com/2010/09/biocurious-a-community-lab-for-biotechnology.html">BioCurious: A Community Lab for Biotechnology</a>

Richard Stallman

<a href="http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.0020047">Free Community Science and the Free Development of Science</a>

‘This Revolution Will Be Digitized’: Online Tools for Open Science

<a href="http://biogang.openwetware.org/">Biogang</a>

Bill Hooker

<a href="http://3quarksdaily.blogs.com/3quarksdaily/2007/01/the_future_of_s.html">The Future of Science is Open, Part 3: An Open Science World</a>

Chris Patil and Vivian Siegel

<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675795/">This Revolution Will Be Digitized: Online Tools for Radical Collaboration</a>

Open Science Publishing

Philip E. Bourne

<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877727/?tool=pmcentrez#pcbi.1000787-Hey1">What Do I Want from the Publisher of the Future?</a>

Cameron Neylon

<a href="http://pirsa.org/08090038/">Science in the Open/or/How I Learned to Stop Worrying and Love My Blog</a>

Open Knowledge

Open Access to Knowledge

Gaelle Krikorian and Amy Kapczynski, eds,

<a href="http://www.soros.org/initiatives/information/focus/access/articles_publications/publications/age-of-intellectual-property-20101110/age-of-intellectual-property-20101110.pdf">Access to Knowledge In the Age of Intellectual Property</a>

<a href="http://okfn.org/">Open Knowledge Foundation</a>

New Models for Open Sharing and Open Research
Anne H. Margulies<a href="http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0020200">
</a>

<a href="http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0020200">A New Model for Open Sharing</a>

Thomas B. Kepler, Marc A. Marti-Renom, Stephen M. Maurer, Arti K. Rai, Ginger Taylor, Matthew H. Todd

<a href="http://www.publish.csiro.au/nid/51/paper/CH06095.htm">Open Source Research - The Power of Us</a>

Open Knowledge and its Discontents

JJ King

<a href="http://www.metamute.org/proudtobeflesh">The Packet Gang: Openness and its Discontents</a>

Michael Gurstein

<a href="http://gurstein.wordpress.com/2011/07/03/are-the-open-data-warriors-fighting-for-robin-hood-or-the-sheriff-some-reflections-on-okcon-2011-and-the-emerging-data-divide/">Are the Open Data Warriors Fighting for Robin Hood or the Sheriff?: Some Reflections on OKCon 2011 and the Emerging Data Divide</a>

Open Data

Data-Intensive Science
Vincent S. Smith

<a href="http://www.biomedcentral.com/1756-0500/2/113">Data Publication: Towards a Database of Everything</a>

Tony Hey, Stewart Tansley, Kristen Tolle, eds

<a href="http://research.microsoft.com/en-us/collaboration/fourthparadigm/4th_paradigm_book_part4_complete.pdf">Scholarly Communication, The Fourth Paradigm: Data-Intensive Scientific Discovery</a>

World of Data

Simon Rogers

<a href="http://www.guardian.co.uk/news/datablog/2010/nov/09/canada-open-data">How Canada Became an Open Data and Data Journalism Powerhouse</a>

We Can Know It For You

Daniel Chandramohan, Kenji Shibuya, Philip Setel, Sandy Cairncross, Alan D. Lopez, Christopher J. L. Murray, Basia Żaba, Robert W. Snow, Fred Binka

<a href="http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.0050057">Should Data from Demographic Surveillance Systems Be Made More Widely Available to Researchers?</a>

Gary Hall

<a href="http://scm-rime.tees.ac.uk/VLE/DATA/CSEARCH/MODULES/CS/2010/05/0757/_.doc">We Can Know It For You: The Secret Life of Metadata</a>

Digitize Me

Encode Me/Decode Me
<a href="http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml">Human Genome Project</a>

The ENCODE Project Consortium

<a href="http://pubmedcentralcanada.ca/picrender.cgi?accid=PMC3079585&blobtype=pdf&tool=pmcentrez">A User's Guide to the Encyclopaedia of DNA Elements (ENCODE) </a>

<a href="http://www.decodeme.com/about-decodeme">deCODEme</a>

Life-Tracking
<a href="http://quantifiedself.com">Quantified Self</a>

Gary Wolf

<a href="http://xrl.us/bh3d4g">The Data-Driven Life</a>

Aiden R. Doherty and Alan F. Smeaton

<a href="http://doras.dcu.ie/15300/1/Sensors-03-154-Doherty-ie-edited.pdf">Automatically Augmenting Lifelog Events Using Pervasively Generated Content from Millions of People
</a>Jennifer S. Beaudin, Stephen S. Intille, and Margaret E. Morris

<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794006/?tool=pmcentrez#ref1">To Track or Not to Track: User Reactions to Concepts in Longitudinal Health Monitoring</a>

The Neurological Turn: or, ‘How the Internet Gets Inside Us’

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N. Katherine Hayles

<a href="http://www.sciy.org/2010/11/24/hyper-and-deep-attention-the-generational-divide-in-cognitive-modes-by-n-katherine-hayles/">Hyper and Deep Attention: The Generation Divide in Cognitive Modes</a>

Adam Gopnik

<a href="http://www.newyorker.com/arts/critics/atlarge/2011/02/14/110214crat_atlarge_gopnik">The Information: How the Internet Gets Inside Us</a>

Visualize Me

What is Visualization?
Lev Manovich

What is Visualization?

Nathan Yau

<a href="http://flowingdata.com/2011/02/23/data-visualization-meets-game-design-to-explore-your-digital-life/">Data Visualization Meets Game Design to Explore your Digital Life</a>

<a href="http://bloom.io/">Bloom</a>

Mood-mapping

Celeste Biever

<a href="http://www.newscientist.com/article/dn19200-twitter-mood-maps-reveal-emotional-states-of-america.html">Twitter Mood Maps Reveal Emotional States of America</a>

<a href="http://www.newscientist.com/articlevideo/dn19200/221111468001-twitter-mood-maps-reveal-emotional-states-of-america.html">Twitter mood video</a>

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<a href="http://www.moodscope.com/">Moodscope</a>

<a href="http://www.mappiness.org.uk">Mappiness</a>

The Visualized Human

Nicholas Felton

<a href="http://feltron.com/">The Annual Felton Report</a>

Anya Kamenetz

<a href="http://www.fastcompany.com/1733627/mit-scientist-captures-his-sons-first-90000-hours-on-video">MIT Scientist Captures 90,000 Hours of Video of His Son’s First Words, Graphs It</a>

Johanna Drucker

<a href="http://mitworld.mit.edu/video/796">Humanistic Approaches to the Graphical Expression of Interpretation</a>

Search Me

Search-Engine Science

Emily H. Chan, Vikram Sahai, Corrie Conrad, and John S. Brownstein

<a href="http://pubmedcentralcanada.ca/articlerender.cgi?accid=PMC3104029&tool=pmcentrez">Using Web Search Query Data to Monitor Dengue Epidemics: A New Model for Neglected Tropical Disease Surveillance</a>

Annie Y.S. Lau, Enrico Coiera, Tatjana Zrimec, and Paul Compton

<a href="http://pubmedcentralcanada.ca/articlerender.cgi?accid=PMC2956236&tool=pmcentrez">Clinician Search Behaviors May Be Influenced by Search Engine Design</a>

The Science of Control

Alession Signorini Alberto Maria Segre, Philip M. Polgreen

<a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019467">The Use of Twitter to Track Levels of Disease Activity and Public Concern in the U.S. During the Influenza A H1N1 Pandemic</a>

David Parry

<a href="http://www.livingbooksaboutlife.org/books/Surveillance">Surveilling Health, Surveillance </a>

Felix Stalder and Christine Mayer

<a href="http://felix.openflows.com/node/113">The Second Index: Search Engines, Personalization and Surveillance (Deep Search)</a>

Deep Search

Michael K. Bergman

<a href="http://quod.lib.umich.edu/cgi/t/text/text-idx?c=jep;view=text;rgn=main;idno=3336451.0007.104">The Deep Web: Surfacing Hidden Value</a>

Clare Birchall

The Invisible Web, <a href="http://www.livingbooksaboutlife.org/books/The_in/visible">The In/Visible</a>

White Noise

<a href="http://www.suicidemachine.org/">Web 2.0 Suicide Machine</a>

<a href="http://www.freedomboxfoundation.org/">Freedom Box Foundation</a>

<a href="http://navasse.net/traceblog/about.html">Traceblog</a>

<a href="http://turbulence.org/Works/JJPS/extension">The JJPS Firefox Extension</a>

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Appendix

Karl Popper, The Open Society and its Enemies

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