Explorations in bioinformatics


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Library of Congress presentation on working with translational research teams, or learning how to embrace your inner geek

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Explorations in bioinformatics

  1. 1. Explorations in bioinformatics: Working with translational research teams, or learning how to embrace your inner g ee k Douglas James Joubert, MLIS Biomedical Informationist National Institutes of Health Library October 10, 2005
  2. 2. Outline <ul><li>Bioinformatics </li></ul><ul><li>Translational Research </li></ul><ul><li>Collaborative Research within CIT </li></ul><ul><li>Informationist Model and Traditional Library Services </li></ul><ul><li>Project Example </li></ul>
  3. 3. Bioinformatics - A Definition in Flux
  4. 4. Bioinformatics – My Approach
  5. 5. Bioinformatics – My Approach <ul><li>Formal and informal educational opportunities </li></ul><ul><li>MS in bioinformatics </li></ul><ul><li>NIH SIGs </li></ul><ul><li>ACM SIGs </li></ul><ul><li>ACM book/journal clubs </li></ul><ul><li>AMIA Working Groups </li></ul>
  6. 6. Translational Research <ul><li>“Transformation of scientific laboratory research into applications that benefit patient health and medical care * ” </li></ul><ul><li>Bench to bedside </li></ul><ul><li>Adopted by NIH in 1953 </li></ul><ul><li>Historically, clinics were in close proximity to research laboratories </li></ul>*National Institutes of Health. NIH CC: CRC – Overview. from http://www.cc.nih.gov/ccc/crc/
  7. 7. Collaborative Research @ CIT Division of Computational Bioscience Center for Molecular Modeling Computational Bioscience and Engineering Laboratory Imaging Sciences Laboratory Mathematical and Statistical Computing Laboratory
  8. 8. Informationist Model and Traditional Library Services <ul><li>MLA coined the phrase Information Specialist in Context (ISIC), in 2002 </li></ul><ul><li>Informationists Bibliography - http://www.mlanet.org/research/informationist/reading.html </li></ul><ul><li>NIH informationists concept modeled from Eskind Biomedical Library (EBL), Vanderbilt University </li></ul><ul><ul><li>Primarily clinical </li></ul></ul><ul><ul><li>Basic researchers now being targeted </li></ul></ul>
  9. 9. What is Unique About MSCL – Informationist Collaboration <ul><li>MSCL does not use “library resources” in the traditional sense of the word </li></ul><ul><li>50% work commitment in lab </li></ul><ul><li>Office space @ DCB, access to the NIH mainframe through HELIX </li></ul><ul><li>MSCL collaborative efforts are intermittent, and project bound </li></ul><ul><li>MSCL has been working with some core groups for 5+ years </li></ul>
  10. 10. What is “Familiar” About MSCL – Informationist Collaboration <ul><li>Primary role is data and text mining </li></ul><ul><li>Evaluate resources - resources typically text mining tools and database interfaces </li></ul><ul><li>Conduct searches, subject terms are gene sets and microarray probe IDs; methods of database access are unique </li></ul>
  11. 11. Balancing Roles
  12. 12. Balancing Roles <ul><li>Library Branding </li></ul><ul><li>Communication of roles/responsibilities </li></ul><ul><li>Project Management </li></ul><ul><li>Think box Think </li></ul>
  13. 13. Balancing Roles - Library Branding <ul><li>Important that informationist groups realize that value-added services are provided by the library </li></ul><ul><li>Examples of branding opportunities </li></ul><ul><ul><li>Packaging of reports </li></ul></ul><ul><ul><li>Instructional packets </li></ul></ul><ul><ul><li>Web-based informational resources </li></ul></ul>
  14. 14. Balancing Roles - Communication <ul><li>Because work is project-based, communication is vital </li></ul><ul><ul><li>Everyone brings their own agenda </li></ul></ul><ul><ul><ul><li>Clinical vs. research vs. information technology </li></ul></ul></ul><ul><ul><li>Each team has an individual component </li></ul></ul><ul><ul><li>Scheduling meetings with three different research teams is a challenge </li></ul></ul><ul><li>Biologblog </li></ul>
  15. 15. Balancing Roles - Project Management <ul><li>Keep a written record of all activities </li></ul><ul><ul><li>Lab book for daily activities </li></ul></ul><ul><ul><li>Project workbook for specific projects </li></ul></ul><ul><li>More of a software development model </li></ul><ul><ul><li>Non-linear </li></ul></ul><ul><ul><li>Internal and external specifications </li></ul></ul><ul><ul><li>Any interface (design) issues </li></ul></ul><ul><ul><li>Deliverable - does it work, and does it work well? </li></ul></ul>
  16. 16. Balancing Roles - Think box Think MSCL LINUX/UNIX 70% Mac/LINUX 25% WIN 5%
  17. 17. Balancing Roles - Think box Think <ul><li>Moving from a GUI world to the command line world </li></ul>
  18. 20. Project Example - Pheo Group Probe data from researcher
  19. 21. Project Example - Pheo Group Data Mining
  20. 22. Project Example - Pheo Group A B
  21. 23. Project Example - Pheo Group A B C
  22. 25. Project Example - Pheo Group N-myc downstream regulated gene 1 NDRG1 10397 vascular endothelial growth factor VEGF 7422 insulin-like growth factor binding protein 7 IGFBP7 3490 collagen, type I, alpha 2 COL1A2 1278 aquaporin 1 (channel-forming integral protein, 28kDa) AQP1 358 Gene description Gene GeneID
  23. 26. Project Example - Pheo Group
  24. 28. Project Example - Pheo Group
  25. 29. Project Example - Pheo Group A B C EASE : the E xpression A nalysis S ystematic E xplorer
  26. 30. Contact Information <ul><li>Douglas J. Joubert, MLIS </li></ul><ul><li>Biomedical Informationist </li></ul><ul><li>National Institutes of Health Library </li></ul><ul><li>Bldg. 10, Room 1L09A </li></ul><ul><li>Bethesda, MD 20906-1150 </li></ul><ul><li>Phone: 301.594.6282 </li></ul><ul><li>E-mail: joubertd@ors.od.nih.gov </li></ul><ul><li>E-mail: joubertd@helix.nih.gov </li></ul>