LIB 100, Information Literacy
Wake Forest University
November 18, 2010
and
Jeffery Loo
jeff@jeffloo.com
University of California, Berkeley Wake Forest University
Sharing research information
Letting others
• see your research work
• use it
• build upon it
WE WILL DISCUSS
1. The research practice of sharing
research information
2. A model of research sharing known
as Open Acce...
Part 1
“Genome Race”
To determine the order of the
chemical “letters” that
make up our DNA.
Chemical “letters”
A, T, G, and C
automated DNA sequencing
technology
Benefits of genome sequencing
Medical contributions
• detecting genes that lead to
diseases
• may lead to “personalized
me...
The Genome Race
PUBLIC EFFORT PRIVATE COMPANY
First to identify the sequence of the human genome?
International Human Geno...
The public effort
began in 1990
1.
carefully divided
the human
genome into large
fragments
2.
the DNA
fragments were
allot...
Celera’s approach
started in 1999
whole genome shotgun sequencing
1.
human genome
randomly
broken into
small pieces
2.
seq...
Pace of sequencing (overall)
Sharing genome sequence data
Public effort
Loaded results into the
publicly accessible database,
GenBank
Celera
Private ap...
According to Dr. Craig Venter, Celera used public data
“How can you ‘beat’ the runner who hands you the baton?”
Who won the genome sequencing race?
June 26, 2000
It was a tie!
Dr. Craig Venter
Celera Genomics
Dr. Francis Collins
Natio...
February 2001, published drafts
April 2003, complete genome identified
Public effort Celera
What happened in the end?
2005
Celera Genomics made data available in public database
What does
this case highlight?
1. different approaches to scientific research -
collaborate or not
2. different ways of sh...
Different approaches
Celera
individual effort
powerful computer systems to
facilitate this massive project
Public effort
d...
Different management of results
Public effort
deposited data in a publicly
accessible database
Celera
was seeking to paten...
Part 2.
Open access publishing
Publishing of scholarly works that is:
Digital and
online
Free of charge to
the reader
Free...
How is it free?
In traditional publishing,
readers or libraries pay a fee for access
Free for the reader
Author finds fund...
Sample open access publications
PLoS One
PLoS Biology
PLoS Medicine
Find OA articles
in the life and health sciences via:
...
Sample open access resources
http://www.doaj.org/
open access databases of research data
NCBI Entrez
PubChem (small molecu...
Value of open access publishing
1. greater audience / more publicity
2. authors retain ownership and control
3. advance kn...
Part 3. Synthesis skills
How do we cope with increasing volume of shared information?
 Howard Gardner’s Five Minds for th...
Kinds of synthesis
Narratives
Taxonomies
Complex concepts
Rules and aphorisms
Powerful metaphors, images, and themes
Embod...
Taxonomies
Categorizing items in terms of salient characteristics
Periodic table of
elements
Linnaean classification of
pl...
Powerful metaphors, images, and
themes
Invoking metaphors to bring concepts to life
combining digital works to create a new work
PadMapper = Google Maps + apartment rental listings
http://www.padmapper.com/...
visual representations of information, data, or knowledge
http://www.infographicsshowcase.com/
Information graphics
Embodiments without words
works of art that capture a lot of ideas
Picasso's Guernica expresses the horror of the Spanish ...
Cultivating synthesis skills
1. Digest new information
(i.e., recognize, learn, and
understand)
2. Organize it.
3. Apply t...
Examples
For professionals:
Recognize new knowledge
or skills.
Learn and apply.
For college students:
In assignments, coll...
Summary Open access publishing
is a model for sharing
research information
With greater sharing,
there will be a larger
vo...
References
Please review the transcript at:
http://www.jeffloo.com/stuff/2010/sharing-transcript.pdf
Upcoming SlideShare
Loading in …5
×

Research information sharing and information synthesis

765 views
674 views

Published on

Guest lecture for LIB 100, Wake Forest University
November 18, 2010

Published in: Education, Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
765
On SlideShare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
6
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide
  • http://www.google.com/imgres?imgurl=http://www.scq.ubc.ca/wp-content/uploads/2006/08/molecular-machine.gif&imgrefurl=http://www.scq.ubc.ca/the-human-genome-project-the-impact-of-genome-sequencing-technology-on-human-health/&usg=__Ha2UI1_jl-FPBzqfi_scUhczgH4=&h=407&w=356&sz=15&hl=en&start=0&sig2=AsoOO3VYpLoIla13f3yM1A&zoom=1&tbnid=QORbxnUIjyjgAM:&tbnh=146&tbnw=128&ei=J2fhTNSYKIHGsAOX4JSwCg&prev=/images%3Fq%3Dcelera%2Bhuman%2Bgenome%2Bsequencing%26um%3D1%26hl%3Den%26safe%3Dactive%26sa%3DN%26biw%3D1280%26bih%3D681%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=446&vpy=164&dur=2459&hovh=240&hovw=210&tx=78&ty=262&oei=J2fhTNSYKIHGsAOX4JSwCg&esq=1&page=1&ndsp=20&ved=1t:429,r:2,s:0
  • http://www.time.com/time/covers/0,16641,20000703,00.html
  • Research information sharing and information synthesis

    1. 1. LIB 100, Information Literacy Wake Forest University November 18, 2010 and Jeffery Loo jeff@jeffloo.com
    2. 2. University of California, Berkeley Wake Forest University
    3. 3. Sharing research information Letting others • see your research work • use it • build upon it
    4. 4. WE WILL DISCUSS 1. The research practice of sharing research information 2. A model of research sharing known as Open Access publishing 3. Developing synthesis skills to deal with the increasing volume of shared information RELEVANCE Know where to find quality research works at no cost Information synthesis skills that may be helpful for your future career
    5. 5. Part 1 “Genome Race” To determine the order of the chemical “letters” that make up our DNA.
    6. 6. Chemical “letters” A, T, G, and C automated DNA sequencing technology
    7. 7. Benefits of genome sequencing Medical contributions • detecting genes that lead to diseases • may lead to “personalized medicine” • may lead to gene therapy Human biology contributions • facilitate comparative genomics • identify “model organisms”
    8. 8. The Genome Race PUBLIC EFFORT PRIVATE COMPANY First to identify the sequence of the human genome? International Human Genome Sequencing Consortium (IHGSC)
    9. 9. The public effort began in 1990 1. carefully divided the human genome into large fragments 2. the DNA fragments were allotted to an international consortium of laboratories 3. each lab to sequence the fragments
    10. 10. Celera’s approach started in 1999 whole genome shotgun sequencing 1. human genome randomly broken into small pieces 2. sequenced the little random pieces 3. used computers to find overlaps between the pieces and then link together Fragment # 1 Fragment # 2 Reconstruction yellow indicates overlap
    11. 11. Pace of sequencing (overall)
    12. 12. Sharing genome sequence data Public effort Loaded results into the publicly accessible database, GenBank Celera Private approach In process of seeking patent protection on some genes Entrez GenBank
    13. 13. According to Dr. Craig Venter, Celera used public data “How can you ‘beat’ the runner who hands you the baton?”
    14. 14. Who won the genome sequencing race? June 26, 2000 It was a tie! Dr. Craig Venter Celera Genomics Dr. Francis Collins National Institutes of Health
    15. 15. February 2001, published drafts April 2003, complete genome identified Public effort Celera
    16. 16. What happened in the end? 2005 Celera Genomics made data available in public database
    17. 17. What does this case highlight? 1. different approaches to scientific research - collaborate or not 2. different ways of sharing research results - publicly share or not 3. information technology has a powerful impact on research approach and sharing
    18. 18. Different approaches Celera individual effort powerful computer systems to facilitate this massive project Public effort divided the work internationally computer systems to coordinate and merge results
    19. 19. Different management of results Public effort deposited data in a publicly accessible database Celera was seeking to patent some genes
    20. 20. Part 2. Open access publishing Publishing of scholarly works that is: Digital and online Free of charge to the reader Free of most traditional copyright and licensing restrictions (e.g., permission for users to re-distribute, remix, and reuse the content)
    21. 21. How is it free? In traditional publishing, readers or libraries pay a fee for access Free for the reader Author finds funding to pay for publication
    22. 22. Sample open access publications PLoS One PLoS Biology PLoS Medicine Find OA articles in the life and health sciences via: PubMed Central BioMed Central
    23. 23. Sample open access resources http://www.doaj.org/ open access databases of research data NCBI Entrez PubChem (small molecule and bioactivity)
    24. 24. Value of open access publishing 1. greater audience / more publicity 2. authors retain ownership and control 3. advance knowledge because publications and ideas are shared 4. meeting obligations to share research work NIH Public Access Policy, http://publicaccess.nih.gov/ Open access policy of the Wellcome Trust
    25. 25. Part 3. Synthesis skills How do we cope with increasing volume of shared information?  Howard Gardner’s Five Minds for the Future Synthesizing is: taking information from disparate sources, understanding and evaluating that information objectively, and putting it together in ways that make sense
    26. 26. Kinds of synthesis Narratives Taxonomies Complex concepts Rules and aphorisms Powerful metaphors, images, and themes Embodiments without words Theories Metatheory See handout, page 4.
    27. 27. Taxonomies Categorizing items in terms of salient characteristics Periodic table of elements Linnaean classification of plants and animals
    28. 28. Powerful metaphors, images, and themes Invoking metaphors to bring concepts to life
    29. 29. combining digital works to create a new work PadMapper = Google Maps + apartment rental listings http://www.padmapper.com/ Mashups
    30. 30. visual representations of information, data, or knowledge http://www.infographicsshowcase.com/ Information graphics
    31. 31. Embodiments without words works of art that capture a lot of ideas Picasso's Guernica expresses the horror of the Spanish Civil War
    32. 32. Cultivating synthesis skills 1. Digest new information (i.e., recognize, learn, and understand) 2. Organize it. 3. Apply the new knowledge. See handout, page 4.
    33. 33. Examples For professionals: Recognize new knowledge or skills. Learn and apply. For college students: In assignments, collect different types of information, and then organize them in a helpful manner. Experiment with visuals, layout, and organization.
    34. 34. Summary Open access publishing is a model for sharing research information With greater sharing, there will be a larger volume of information In response, develop synthesis skills for digesting, organizing, and applying new knowledge Sharing information and collaboration are important research practices
    35. 35. References Please review the transcript at: http://www.jeffloo.com/stuff/2010/sharing-transcript.pdf

    ×