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Research information sharing and information synthesis

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Guest lecture for LIB 100, Wake Forest University

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

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  • 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
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Research information sharing and information synthesis Research information sharing and information synthesis Presentation Transcript

  • Research information sharing
    and
    information synthesis
    LIB 100, Information Literacy
    Wake Forest University
    November 18, 2010
    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
    The research practice of sharingresearch information
    A model of research sharing known as Open Access publishing
    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
    Human biology contributions
    detecting genes that lead to diseases
    may lead to “personalized medicine”
    may lead to gene therapy
    facilitate comparative genomics
    identify “model organisms”
  • The Genome Race
    First to identify the sequence of the human genome?
    PUBLIC EFFORT
    PRIVATE COMPANY
    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 approach
    started in 1999
    whole genome shotgun sequencing
    1.
    human genome randomly broken into small pieces
    2.
    sequenced the little random pieces
    yellow
    indicates
    overlap
    3.
    used computers to find overlaps between the pieces and then link together
    Fragment # 1
    Fragment # 2
    Reconstruction
  • Pace of sequencing (overall)
  • 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
  • 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?
    It was a tie!
    June 26, 2000
    Dr. Craig Venter
    Celera Genomics
    Dr. Francis Collins
    National Institutes of Health
  • 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?
    different approaches to scientific research - collaborate or not
    different ways of sharing research results - publicly share or not
    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?
    Free for the reader
    Author finds funding to pay for publication
    In traditional publishing,
    readers or libraries pay a fee for access
  • Sample open access publications
    PLoS One
    PLoS Biology
    PLoS Medicine
    Find OA articles
    in the life and health sciences via:
    PubMed Central
    BioMed Central
  • Sample open access resources
    http://www.doaj.org/
    open access databases of research data  
    NCBI Entrez
    PubChem (small molecule and bioactivity)
  • Value of open access publishing
    greater audience / more publicity
    authors retain ownership and control
    advance knowledge because publications and ideas are shared
    meeting obligations to share research work
    NIH Public Access Policy, http://publicaccess.nih.gov/  
    Open access policy of the Wellcome Trust
  • 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, understandingand evaluatingthat information objectively, and
    putting it together in ways that make sense
  • Kinds of synthesis
    Narratives
    Taxonomies
    Complex concepts
    Rules and aphorisms
    Powerful metaphors, images, and themes
    Embodiments without words
    Theories
    Metatheory
    See handout, page 4.
  • Taxonomies
    Categorizing 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 listings
    http://www.padmapper.com/
    Mashups
  • 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 Civil War
  • Cultivating synthesis skills
    Digest new information (i.e., recognize, learn, and understand)
    Organize it.
    Apply the new knowledge.See handout, page 4.
  • Examples
    For college students:
    In assignments, collect different types of information, and then organize them in a helpful manner.  
    Experiment with visuals, layout, and organization.
    For professionals:
    Recognize new knowledge or skills.  
    Learn and apply.
  • Summary
    Open access publishing is a model for sharing research information
    Sharing information and collaboration are important research practices
    In response, develop synthesis skills for digesting, organizing, and applying new knowledge
    With greater sharing, there will be a larger volume of information
  • References
    Please review transcript at:
    http://www.jeffloo.com/stuff/2010/sharing-transcript.pdf