Digitize Me, Visualize Me, Search Me: Difference between revisions
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[http://www.psfk.com/2010/09/biocurious-a-community-lab-for-biotechnology.html BioCurious: A Community Lab for Biotechnology] | [http://www.psfk.com/2010/09/biocurious-a-community-lab-for-biotechnology.html BioCurious: A Community Lab for Biotechnology] | ||
Richard Stallman | ; Richard Stallman : [http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.0020047 Free Community Science and the Free Development of Science] | ||
[http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.0020047 Free Community Science and the Free Development of Science] | |||
=== 'This Revolution Will Be Digitized’: Online Tools for Open Science === | === 'This Revolution Will Be Digitized’: Online Tools for Open Science === | ||
| Line 30: | Line 28: | ||
[http://biogang.openwetware.org/ Biogang] | [http://biogang.openwetware.org/ Biogang] | ||
Bill Hooker | ; Bill Hooker : [http://3quarksdaily.blogs.com/3quarksdaily/2007/01/the_future_of_s.html The Future of Science is Open, Part 3: An Open Science World] | ||
[http://3quarksdaily.blogs.com/3quarksdaily/2007/01/the_future_of_s.html The Future of Science is Open, Part 3: An Open Science World] | |||
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675795/ This Revolution Will Be Digitized: Online Tools for Radical Collaboration] | ; Chris Patil and Vivian Siegel : [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675795/ This Revolution Will Be Digitized: Online Tools for Radical Collaboration] | ||
=== Open Science Publishing === | === Open Science Publishing === | ||
Philip E. Bourne | ; Philip E. Bourne : [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877727/?tool=pmcentrez#pcbi.1000787-Hey1 What Do I Want from the Publisher of the Future?] | ||
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877727/?tool=pmcentrez#pcbi.1000787-Hey1 What Do I Want from the Publisher of the Future?] | |||
[http://pirsa.org/08090038/ Science in the Open/or/How I Learned to Stop Worrying and Love My Blog] | ; Cameron Neylon : [http://pirsa.org/08090038/ Science in the Open/or/How I Learned to Stop Worrying and Love My Blog] | ||
== Open Knowledge == | == Open Knowledge == | ||
| Line 54: | Line 44: | ||
[http://okfn.org/ Open Knowledge Foundation] | [http://okfn.org/ Open Knowledge Foundation] | ||
Gaelle Krikorian and Amy Kapczynski, eds | ; Gaelle Krikorian and Amy Kapczynski, eds : [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''] | ||
[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''] | |||
=== New Models for Open Sharing and Open Research === | === New Models for Open Sharing and Open Research === | ||
Anne H. Margulies | ; Anne H. Margulies : [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0020200 A New Model for Open Sharing] | ||
[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0020200 A New Model for Open Sharing] | |||
[http://www.publish.csiro.au/nid/51/paper/CH06095.htm Open Source Research - The Power of Us] | ; Thomas B. Kepler, Marc A. Marti-Renom, Stephen M. Maurer, Arti K. Rai, Ginger Taylor, Matthew H. Todd : [http://www.publish.csiro.au/nid/51/paper/CH06095.htm Open Source Research - The Power of Us] | ||
=== Open Knowledge and its Discontents === | === Open Knowledge and its Discontents === | ||
J.J. King | ; J.J. King : [http://www.metamute.org/proudtobeflesh The Packet Gang: Openness and its Discontents] | ||
[http://www.metamute.org/proudtobeflesh The Packet Gang: Openness and its Discontents] | |||
[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] | ; Michael Gurstein : [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] | ||
== Open Data == | == Open Data == | ||
| Line 82: | Line 62: | ||
=== Data-Intensive Science === | === Data-Intensive Science === | ||
Vincent S. Smith | ; Vincent S. Smith : [http://www.biomedcentral.com/1756-0500/2/113 Data Publication: Towards a Database of Everything] | ||
[http://www.biomedcentral.com/1756-0500/2/113 Data Publication: Towards a Database of Everything] | |||
[http://research.microsoft.com/en-us/collaboration/fourthparadigm/4th_paradigm_book_part4_complete.pdf Scholarly Communication, ''The Fourth Paradigm: Data-Intensive Scientific Discovery''] | ; Tony Hey, Stewart Tansley, Kristen Tolle, eds : [http://research.microsoft.com/en-us/collaboration/fourthparadigm/4th_paradigm_book_part4_complete.pdf Scholarly Communication, ''The Fourth Paradigm: Data-Intensive Scientific Discovery''] | ||
=== World of Data === | === World of Data === | ||
| Line 94: | Line 70: | ||
[http://www.freeourdata.org.uk/ Free Our Data] | [http://www.freeourdata.org.uk/ Free Our Data] | ||
Simon Rogers | ; Simon Rogers : [http://www.guardian.co.uk/news/datablog/2010/nov/09/canada-open-data How Canada Became an Open Data and Data Journalism Powerhouse] | ||
[http://www.guardian.co.uk/news/datablog/2010/nov/09/canada-open-data How Canada Became an Open Data and Data Journalism Powerhouse] | |||
=== We Can Know It For You === | === We Can Know It For You === | ||
Omer Tene | ; Omer Tene : [http://epubs.utah.edu/index.php/ulr/article/viewArticle/136 What Google Knows: Privacy and Internet Search Engines] | ||
[http://epubs.utah.edu/index.php/ulr/article/viewArticle/136 What Google Knows: Privacy and Internet Search Engines] | |||
[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?] | ; Daniel Chandramohan, Kenji Shibuya, Philip Setel, Sandy Cairncross, Alan D. Lopez, Christopher J. L. Murray, Basia Żaba, Robert W. Snow, Fred Binka : [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?] | ||
== '''Digitize Me''' == | == '''Digitize Me''' == | ||
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[http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml Human Genome Project] | [http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml Human Genome Project] | ||
The ENCODE Project Consortium | ; The ENCODE Project Consortium : [http://pubmedcentralcanada.ca/picrender.cgi?accid=PMC3079585&blobtype=pdf&tool=pmcentrez A User's Guide to the Encyclopaedia of DNA Elements (ENCODE) ] | ||
[http://pubmedcentralcanada.ca/picrender.cgi?accid=PMC3079585&blobtype=pdf&tool=pmcentrez A User's Guide to the Encyclopaedia of DNA Elements (ENCODE) ] | |||
[http://www.decodeme.com/about-decodeme deCODEme] | [http://www.decodeme.com/about-decodeme deCODEme] | ||
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[http://quantifiedself.com Quantified Self] | [http://quantifiedself.com Quantified Self] | ||
Gary Wolf | ; Gary Wolf : [http://xrl.us/bh3d4g The Data-Driven Life] | ||
[http://xrl.us/bh3d4g The Data-Driven Life | |||
; Aiden R. Doherty and Alan F. Smeaton : [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] | |||
[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] | ; Jennifer S. Beaudin, Stephen S. Intille, and Margaret E. Morris : [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] | ||
=== The Neurological Turn: or, ‘How the Internet Gets Inside Us' === | === The Neurological Turn: or, ‘How the Internet Gets Inside Us' === | ||
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<youtube>NhLnoZFCDBM</youtube> | <youtube>NhLnoZFCDBM</youtube> | ||
Adam Gopnik | ; Adam Gopnik : [http://www.newyorker.com/arts/critics/atlarge/2011/02/14/110214crat_atlarge_gopnik The Information: How the Internet Gets Inside Us] | ||
[http://www.newyorker.com/arts/critics/atlarge/2011/02/14/110214crat_atlarge_gopnik The Information: How the Internet Gets Inside Us] | |||
[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] | ; N. Katherine Hayles : [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] | ||
== '''Visualize Me''' == | == '''Visualize Me''' == | ||
=== What is Visualization? === | === What is Visualization? === | ||
; Lev Manovich : [http://manovich.net/blog/wp-content/uploads/2010/10/manovich_visualization_2010.doc What is Visualization?] | |||
[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] | ; Nathan Yau : [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] | ||
[http://bloom.io/ Bloom] | [http://bloom.io/ Bloom] | ||
=== Mood-mapping === | === Mood-mapping === | ||
[http://www.newscientist.com/article/dn19200-twitter-mood-maps-reveal-emotional-states-of-america.html Twitter Mood Maps Reveal Emotional States of America] | ; Celeste Biever : [http://www.newscientist.com/article/dn19200-twitter-mood-maps-reveal-emotional-states-of-america.html Twitter Mood Maps Reveal Emotional States of America] | ||
[http://www.newscientist.com/articlevideo/dn19200/221111468001-twitter-mood-maps-reveal-emotional-states-of-america.html Twitter mood video] | [http://www.newscientist.com/articlevideo/dn19200/221111468001-twitter-mood-maps-reveal-emotional-states-of-america.html Twitter mood video] | ||
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=== The Visualized Human (or, The Human As Spectacle) === | === The Visualized Human (or, The Human As Spectacle) === | ||
[http://feltron.com/ The Annual Felton Report] | ; Nicholas Felton : [http://feltron.com/ The Annual Felton Report] | ||
<youtube>RE4ce4mexrU</youtube> | <youtube>RE4ce4mexrU</youtube> | ||
Deb Roy | ; Deb Roy : [http://www.youtube.com/watch?v=RE4ce4mexrU&feature=youtu.be The Birth of a Word] | ||
[http://www.youtube.com/watch?v=RE4ce4mexrU&feature=youtu.be The Birth of a Word] | |||
{{#widget:Drucker Video}} | {{#widget:Drucker Video}} | ||
Johanna Drucker | ; Johanna Drucker : [http://mitworld.mit.edu/video/796 Humanistic Approaches to the Graphical Expression of Interpretation] | ||
[http://mitworld.mit.edu/video/796 Humanistic Approaches to the Graphical Expression of Interpretation] | |||
== Search Me == | == Search Me == | ||
| Line 196: | Line 145: | ||
=== Search-Engine Science === | === Search-Engine Science === | ||
Emily H. Chan, Vikram Sahai, Corrie Conrad, and John S. Brownstein | ; Emily H. Chan, Vikram Sahai, Corrie Conrad, and John S. Brownstein : [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] | ||
[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] | |||
[http://pubmedcentralcanada.ca/articlerender.cgi?accid=PMC2956236&tool=pmcentrez Clinician Search Behaviors May Be Influenced by Search Engine Design] | ; Annie Y.S. Lau, Enrico Coiera, Tatjana Zrimec, and Paul Compton : [http://pubmedcentralcanada.ca/articlerender.cgi?accid=PMC2956236&tool=pmcentrez Clinician Search Behaviors May Be Influenced by Search Engine Design] | ||
=== The Science of Control === | === The Science of Control === | ||
Alession Signorini Alberto Maria Segre, Philip M. Polgreen | ; Alession Signorini Alberto Maria Segre, Philip M. Polgreen : [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] | ||
[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 | |||
; David Parry : [http://www.livingbooksaboutlife.org/books/Surveillance ''Surveillance'' ] | |||
[http://felix.openflows.com/node/113 The Second Index: Search Engines, Personalization and Surveillance (Deep Search)] | ; Felix Stalder and Christine Mayer : [http://felix.openflows.com/node/113 The Second Index: Search Engines, Personalization and Surveillance (Deep Search)] | ||
=== Deep Search === | === Deep Search === | ||
{{#widget:Vimeo|id=13456992}} | {{#widget:Vimeo|id=13456992}} | ||
Michael K. Bergman | ; Michael K. Bergman : [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] | ||
[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] | |||
[http://www.livingbooksaboutlife.org/books/The_in/visible The Invisible Web, ''The In/Visible''] | ; Clare Birchall : [http://www.livingbooksaboutlife.org/books/The_in/visible The Invisible Web, ''The In/Visible''] | ||
== Media Gifts? == | == Media Gifts? == | ||
| Line 244: | Line 179: | ||
<youtube>ukNkx45Ua0Y</youtube> | <youtube>ukNkx45Ua0Y</youtube> | ||
Karl Popper, The Open Society and its Enemies | ; Karl Popper, The Open Society and its Enemies : [http://www.livingbooksaboutlife.org/books/Open_science/Attributions Attributions] | ||
[http://www.livingbooksaboutlife.org/books/Open_science/Attributions Attributions] | |||
Revision as of 14:07, 30 September 2011
Open Science and its Discontents
edited by Gary Hall
Introduction: White Noise: On the Limits of Openness (Living Book Mix)
One of the aims of the Living Books About Life series is to provide a 'bridge' or point of connection, translation, even interrogation and contestation, between the humanities and the sciences. Accordingly, this introduction to Digitize Me, Visualize Me, Search Me, a book in the series on open science, takes as its starting point the so-called ‘computational turn’ to data-intensive scholarship in the humanities.
The phrase ‘the computational turn’ has been adopted to refer to the process whereby techniques and methodologies drawn from computer science and related fields – including science visualization, interactive information visualization, image processing, network analysis, statistical data analysis, and the management, manipulation and mining of data – are being increasingly used to produce new ways of approaching and understanding texts in the humanities - what is sometimes thought of as 'the digital humanities'. (more...)
Open Science
It’s An Open (Science), Open (Access), Open (Source), Open (Notebook) World
- Patrick O. Brown, Michael B. Eisen, Harold Varmus
- Why PLoS Became a Publisher
- Sally Murray, Stephen Choi, John Hoey, Claire Kendall, James Maskalyk, and Anita Palepu
- Open Science, Open Access and Open Source Software at Open Medicine
Community Science
BioCurious: A Community Lab for Biotechnology
- Richard Stallman
- Free Community Science and the Free Development of Science
'This Revolution Will Be Digitized’: Online Tools for Open Science
- Chris Patil and Vivian Siegel
- This Revolution Will Be Digitized: Online Tools for Radical Collaboration
Open Science Publishing
- Philip E. Bourne
- What Do I Want from the Publisher of the Future?
Open Knowledge
Access to Knowledge
- Gaelle Krikorian and Amy Kapczynski, eds
- Access to Knowledge In the Age of Intellectual Property
New Models for Open Sharing and Open Research
- Anne H. Margulies
- A New Model for Open Sharing
- Thomas B. Kepler, Marc A. Marti-Renom, Stephen M. Maurer, Arti K. Rai, Ginger Taylor, Matthew H. Todd
- Open Source Research - The Power of Us
Open Knowledge and its Discontents
- Michael Gurstein
- Are the Open Data Warriors Fighting for Robin Hood or the Sheriff?: Some Reflections on OKCon 2011 and the Emerging Data Divide
Open Data
Data-Intensive Science
- Vincent S. Smith
- Data Publication: Towards a Database of Everything
- Tony Hey, Stewart Tansley, Kristen Tolle, eds
- Scholarly Communication, The Fourth Paradigm: Data-Intensive Scientific Discovery
World of Data
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
- Should Data from Demographic Surveillance Systems Be Made More Widely Available to Researchers?
Digitize Me
Encode Me/Decode Me
- The ENCODE Project Consortium
- A User's Guide to the Encyclopaedia of DNA Elements (ENCODE)
Life-Tracking
- Gary Wolf
- The Data-Driven Life
- Aiden R. Doherty and Alan F. Smeaton
- Automatically Augmenting Lifelog Events Using Pervasively Generated Content from Millions of People
- Jennifer S. Beaudin, Stephen S. Intille, and Margaret E. Morris
- To Track or Not to Track: User Reactions to Concepts in Longitudinal Health Monitoring
The Neurological Turn: or, ‘How the Internet Gets Inside Us'
- Adam Gopnik
- The Information: How the Internet Gets Inside Us
- N. Katherine Hayles
- Hyper and Deep Attention: The Generation Divide in Cognitive Modes
Visualize Me
What is Visualization?
- Lev Manovich
- What is Visualization?
Mood-mapping
- Celeste Biever
- Twitter Mood Maps Reveal Emotional States of America
The Visualized Human (or, The Human As Spectacle)
- Nicholas Felton
- The Annual Felton Report
- Deb Roy
- The Birth of a Word
Search Me
Search-Engine Science
- Emily H. Chan, Vikram Sahai, Corrie Conrad, and John S. Brownstein
- Using Web Search Query Data to Monitor Dengue Epidemics: A New Model for Neglected Tropical Disease Surveillance
- Annie Y.S. Lau, Enrico Coiera, Tatjana Zrimec, and Paul Compton
- Clinician Search Behaviors May Be Influenced by Search Engine Design
The Science of Control
- Alession Signorini Alberto Maria Segre, Philip M. Polgreen
- The Use of Twitter to Track Levels of Disease Activity and Public Concern in the U.S. During the Influenza A H1N1 Pandemic
- David Parry
- Surveillance
- Felix Stalder and Christine Mayer
- The Second Index: Search Engines, Personalization and Surveillance (Deep Search)
Deep Search
- Michael K. Bergman
- The Deep Web: Surfacing Hidden Value
- Clare Birchall
- The Invisible Web, The In/Visible
Media Gifts?
Appendix
- Karl Popper, The Open Society and its Enemies
- Attributions