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Guest lecture for LIB 100, Wake Forest University November 18, 2010
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LIB 100, Information LiteracyWake Forest University
November 18, 2010
Research information sharing
and
Jeffery [email protected]
information synthesis
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 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
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
medicine”• may lead to gene therapy
Human biology contributions• facilitate comparative genomics• identify “model organisms”
The Genome Race
PUBLIC EFFORT PRIVATE COMPANYFirst to identify the sequence of the human genome?
International Human Genome Sequencing Consortium (IHGSC)
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
Celera’s approachstarted in 1999whole 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
Pace of sequencing (overall)
Sharing genome sequence data
Public effortLoaded results into the publicly accessible database, GenBank
Celera Private approachIn process of seeking patent protection on some genes
EntrezGenBank
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 CollinsNational Institutes of Health
February 2001, published drafts
April 2003, complete genome identified
Public effort Celera
What happened in the end?
2005Celera 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 sharing research results - publicly share or not
3. information technology has a powerful impact on research approach and sharing
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
Different management of results
Public effort deposited data in a publicly accessible database
Celera was seeking to patent some genes
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)
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
Sample open access publications
PLoS OnePLoS BiologyPLoS Medicine
Find OA articles in the life and health sciences via:
PubMed CentralBioMed Central
Sample open access resources
http://www.doaj.org/
open access databases of research data NCBI EntrezPubChem (small molecule and bioactivity)
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 workNIH Public Access Policy, http://publicaccess.nih.gov/ Open access policy of the Wellcome Trust
Part 3. Synthesis skillsHow 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
Kinds of synthesisNarrativesTaxonomiesComplex concepts Rules and aphorisms Powerful metaphors, images, and themes Embodiments without wordsTheoriesMetatheory
See handout, page 4.
TaxonomiesCategorizing items in terms of salient characteristics
Periodic table of elements
Linnaean classification of plants and animals
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 listingshttp://www.padmapper.com/
Mashups
visual representations of information, data, or knowledgehttp://www.infographicsshowcase.com/
Information graphics
Embodiments without wordsworks of art that capture a lot of ideas
Picasso's Guernica expresses the horror of the Spanish Civil War
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.
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.
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
References
Please review the transcript at: http://www.jeffloo.com/stuff/2010/sharing-transcript.pdf