Post on 09-Dec-2014
description
Explorations in bioinformatics:Working with translational research teams, or
learning how to embrace your inner geek
Douglas James Joubert, MLISBiomedical InformationistNational Institutes of Health Library
October 10, 2005
EXPLORATIONS IN BIOINFORMATICS
Outline
Bioinformatics Translational Research Collaborative Research within CIT Informationist Model and Traditional Library
Services Project Example
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Bioinformatics - A Definition in Flux
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Bioinformatics – My Approach
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Bioinformatics – My Approach
Formal and informal educational opportunities
MS in bioinformatics NIH SIGs
ACM SIGs ACM book/journal clubs AMIA Working Groups
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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/
Division of Computational Bioscience
Center for Molecular ModelingComputational Bioscience
and Engineering Laboratory
Imaging Sciences Laboratory
Mathematical and Statistical Computing Laboratory
Collaborative Research @ CIT
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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
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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
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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
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Balancing Roles
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Balancing Roles
Library Branding Communication of
roles/responsibilities Project Management Think box Think
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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
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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
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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?
Balancing Roles - Think box Think
LINUX/UNIX70%
Mac/LINUX25%
WIN5%
MSCL
Balancing Roles - Think box Think
Moving from a GUI world to the command line world
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Probe data from researcher
Project Example -Pheo Group
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Data Mining
Project Example -Pheo Group
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Project Example - Pheo GroupA
B
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Project Example - Pheo Group
A
B C
Project Example - Pheo Group
GeneID Gene Gene description
358 AQP1 aquaporin 1 (channel-forming integral protein, 28kDa)
1278 COL1A2 collagen, type I, alpha 2
3490 IGFBP7 insulin-like growth factor binding protein 7
7422 VEGF vascular endothelial growth factor
10397 NDRG1 N-myc downstream regulated gene 1
Project Example - Pheo Group
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Project Example - Pheo Group
Project Example - Pheo Group
A
B
C
EASE: the Expression Analysis Systematic Explorer
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Contact Information
Douglas J. Joubert, MLISBiomedical InformationistNational Institutes of Health LibraryBldg. 10, Room 1L09ABethesda, MD 20906-1150Phone: 301.594.6282E-mail: joubertd@ors.od.nih.govE-mail: joubertd@helix.nih.gov