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Research information sharing and information synthesis

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

Published in: Education, Technology
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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

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