Development of an Information Service Program in Molecular Biology and Genetics

1
Development of an Information Service Program in
Molecular Biology and Genetics

• Ansuman Chattopadhyay, PhD
• Information Specialist in Molecular Biology and
  Genetics
• Barbara A. Epstein, MSLS, AHIP
• Associate Director, Health Sciences Library
  System
• Patricia C. Mickelson, MLS
• Director , Health Sciences Library System
• Nancy H. Tannery, MLS
• Assistant Director, Information Services
• Health Sciences Library System
• University of Pittsburgh
• Pittsburgh

2
Background

• Recognition that a rapidly growing research
• component is focused on molecular biology
• and genetics
• HSLS hosted NCBI workshops
• HSLS invited Stuart Yarfitz , Ph.D. from
• U. of Washington as a consultant to give
• presentation on the U. of Washington
• Bioinformatics Services Program and meet
• with key administrators and faculty

3
Background

• HSLS convened a planning group of interested
• individuals from several relevant units to help
• define information needs in molecular biology
• and genetics
• Center for Human Genetics
• Center for Computational Biology
• Center for Biomedical Informatics
• Office of Research
• Dept of Molecular Genetics and Biochemistry
• Pittsburgh Supercomputing Center
• With input from planning group, HSLS drafted a
  proposed Program Plan for a Specialized
  Information Service in Molecular Biology and
  Genetics and a position description for an
  Information Specialist

4
Background

• Senior Vice Chancellor for Health Sciences
  agreed to
• fund the Information Specialist position and
  contribute
• funding for resources
• School of Medicine alumnus donated 100,000 to
  subsidize molecular biology / genetics databases
• Recruitment for Information Specialist initiated
  in
• fall 2001.
• Position advertised in Cell, Nature, Science,
  
• The Scientist and Nature Structural Biology
  and numerous list-servs.
• Ansuman Chattopadhyay, PhD, hired in spring 2002

5
Ansuman Chattopadhyay, Ph.D. ansuman_at_pitt.edu

• 1990-1996
• University of Nebraska-Lincoln
• PhD. in Biochemistry
• Protein synthesis initiation in eukaryotic system

• 1997-2001
• Vanderbilt University School of Medicine
• Research Fellow
• Epidermal Growth Factor (EGF) mediated signal
  transduction

• 2001-2002
• Cellomics Inc., Pittsburgh
• Knowledge Engineer,
• Literature retrieval software

• 2002- Present
• Information Specialist in Molecular Biology and
  Genetics
• HSLS, University of Pittsburgh

6
Molecular Biology and Genetics Information
Service

• Development of a web-based portal
• for molecular biology and genetics
• information
• Development of training workshops
• on the use of bioinformatics tools
• Consultation service to access biological
• information resources

7
Modern day life science research a
multi-step process
Proteome BioKnowledge Library
Vector NTI
BLAST Search
Research Link
Nucleic Acid Sequence Analysis Software
PubMed Search
NCBI-LocusLink
Current Protocols Online
GeneLynx
GeneCards
Protein Sequence and StructureAnalysis
CellSpace Knowledge Miner
Commercial Free to academic users
Protein Interaction Databases
Starting Point
Knowledge Mining
Nucleic Acid / Protein analysis
Lab Work
8
HSLS Online-Molecular Biology web site A
Portal for Molecular Biology and Genetics
http//www.hsls.pitt.edu/guides/genetics
9
http//www.hsls.pitt.edu/guides/genetics
10
Workshop 1
Workshop 2
Workshop 3
Proteome BioKnowledge Library
Research Link
BLAST Search
Vector NTI
Nucleic Acid Sequence Analysis Software
Current Protocols Online
PubMed Search
NCBI-LocusLink
GeneLynx
GeneCards
Protein Sequence and StructureAnalysis
Commercial Free to academic users
CellSpace Knowledge Miner
Protein Interaction Databases
Starting Point
Knowledge Mining
Nucleic Acid/ Protein analysis
Lab Work
11
http//www.hsls.pitt.edu/guides/genetics
12
(No Transcript)
13
http//www.hsls.pitt.edu/guides/genetics
A task specific hierarchical list of hyperlinks
to bioinformatics software and databases
14
(No Transcript)
15
(No Transcript)
16
(No Transcript)
17
http//www.hsls.pitt.edu/guides/genetics
restriction digestion
18
(No Transcript)
19
Health Sciences Library Bioinformatics
Traineeship
Part of Pittsburgh Biomedical Informatics
Training Program funded by NLM Previously
traineeship was only a one year certificate
program in Health Sciences Library and
Bioinformatics Joint program between HSLS and
Center for Biomedical Informatics
20
Library Bioinformatics Traineeship

• Traineeship now includes option of two year
• degree program
• Designed for trainees with background in
• biological sciences (molecular biology
• and genetics)
• Courses lead to a master degree in
  Bioinformatics
• Trainee gains experience in providing
  specialized
• Molecular Biology / Genetics Information
  Services
• in the Health Sciences Library
• First trainee in two year program started in
  2003

21
Future Plan

• Introduce HSLS Molecular Biology portal via
• departmental seminars
• Offer workshops on
• Genomic Resources
• Structural Biology
• Licensed Resources
• Vector NTI CellSpace

22
..only half of biomedical researchers using
genome databases are familiar with the tools that
can be used to actually access the data. ..
all scientists on the planet must be empowered to
use these powerful databases to unravel
longstanding scientific mysteries. atabases to
unravel longstanding scientifi c
Andreas D. Baxevanis Francis S. Collins
Nature Genetics, September 2002,
Vol 32