Explorations in bioinformatics
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The document discusses the role of bioinformatics in translational research and collaborative efforts at the NIH, emphasizing the informationist model in supporting researchers. It describes various projects and educational opportunities, highlighting the importance of data and text mining, communication, and project management within collaborative teams. The document also outlines examples of past projects and the challenges faced by informationists in balancing roles and branding within research settings.
Explorations in bioinformatics
- 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. Outline Bioinformatics Translational Research Collaborative Research within CIT Informationist Model and Traditional Library Services Project Example
- 3. Bioinformatics - A Definition in Flux
- 4. Bioinformatics – My Approach
- 5. Bioinformatics – My Approach Formal and informal educational opportunities MS in bioinformatics NIH SIGs ACM SIGs ACM book/journal clubs AMIA Working Groups
- 6. Translational Research “Transformation of scientific laboratory research into applications that benefit patient health and medical care * ” Bench to bedside Adopted by NIH in 1953 Historically, clinics were in close proximity to research laboratories *National Institutes of Health. NIH CC: CRC – Overview. from http://www.cc.nih.gov/ccc/crc/
- 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. Informationist Model and Traditional Library Services MLA coined the phrase Information Specialist in Context (ISIC), in 2002 Informationists Bibliography - http://www.mlanet.org/research/informationist/reading.html NIH informationists concept modeled from Eskind Biomedical Library (EBL), Vanderbilt University Primarily clinical Basic researchers now being targeted
- 9. What is Unique About MSCL – Informationist Collaboration MSCL does not use “library resources” in the traditional sense of the word 50% work commitment in lab Office space @ DCB, access to the NIH mainframe through HELIX MSCL collaborative efforts are intermittent, and project bound MSCL has been working with some core groups for 5+ years
- 10. What is “Familiar” About MSCL – Informationist Collaboration Primary role is data and text mining Evaluate resources - resources typically text mining tools and database interfaces Conduct searches, subject terms are gene sets and microarray probe IDs; methods of database access are unique
- 11. Balancing Roles
- 12. Balancing Roles Library Branding Communication of roles/responsibilities Project Management Think box Think
- 13. Balancing Roles - Library Branding Important that informationist groups realize that value-added services are provided by the library Examples of branding opportunities Packaging of reports Instructional packets Web-based informational resources
- 14. Balancing Roles - Communication Because work is project-based, communication is vital Everyone brings their own agenda Clinical vs. research vs. information technology Each team has an individual component Scheduling meetings with three different research teams is a challenge Biologblog
- 15. Balancing Roles - Project Management Keep a written record of all activities Lab book for daily activities Project workbook for specific projects More of a software development model Non-linear Internal and external specifications Any interface (design) issues Deliverable - does it work, and does it work well?
- 16. Balancing Roles - Think box Think MSCL LINUX/UNIX 70% Mac/LINUX 25% WIN 5%
- 17. Balancing Roles - Think box Think Moving from a GUI world to the command line world
- 20. Project Example - Pheo Group Probe data from researcher
- 21. Project Example - Pheo Group Data Mining
- 22. Project Example - Pheo Group A B
- 23. Project Example - Pheo Group A B C
- 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
- 26. Project Example - Pheo Group
- 28. Project Example - Pheo Group
- 29. Project Example - Pheo Group A B C EASE : the E xpression A nalysis S ystematic E xplorer
- 30. Contact Information Douglas J. Joubert, MLIS Biomedical Informationist National Institutes of Health Library Bldg. 10, Room 1L09A Bethesda, MD 20906-1150 Phone: 301.594.6282 E-mail: joubertd@ors.od.nih.gov E-mail: joubertd@helix.nih.gov