Transcript Bioinformatics and the Engineering Library

Bioinformatics and the
Engineering Library
ASEE 2008
Amy Stout
What is bioinformatics?
• Using computers to solve biological
problems, usually on a molecular level
• “This represents a new phase in genomics
– making biological discoveries sitting not
at the lab bench, but at the computer
terminal.” – Manolis Kellis, MIT researcher
Examples of bioinformatics
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Sequence alignment: figuring out
sequences that are similar in structure or
function
Evolutionary biology: figuring out how an
organism evolved
Genome annotation: attaching biological
information to genes
Extremely data intensive
• Not only finding 1:1 relationships between
diseases and genes
• Mining data for combinations of genes that
result in disease
• Using complex algorithms with multiple
variables and multiple correlations
Examples of bioinformatics @ MIT
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Synthetic biology: The design and construction
of new biological entities such as enzymes,
genetic circuits, and cells, or the redesign of
existing biological systems
Microbial sequencing center at the Broad
Institute: they sequence microbes
Computational neuroanatomy at Brain and
Cognitive Sciences: to create automated
systems that will take a sample of brain tissue
as input and generate its "circuit diagram," a
list of all its neurons and their synaptic
connections
Why should libraries be involved?
• To support researchers and students
• Data is quickly coming under the purview
of academic libraries
• These are databases, like any other
• The tools require more specialized
knowledge
Bioinformatics @ the MIT Libraries
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We hired Courtney Crummet, a
bioinformatics specialist who spent last
year at MIT as a National Library of
Medicine (NLM) Fellow
Web site and collection development
Online tutorials and “Bioinformatics for
Beginners” class: teaches introductory
use of National Center for Biotechnology
Information (NCBI) databases and tools
Bioinformatics @ MIT, cont’d.
• Louisa Rogers collaborated with outside
instructors to provide:
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NCBI mini-courses for scientists
EMSEMBL workshops
Mouse Genome Informatics training
GenePattern software training
Biobase database training
Gene sequencing and protein analysis
BLAST
Microarray data
Bioinformatics
libraries.mit.edu/bioinformatics
NCBI demonstration
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Entrez with GABRA1: the name of a
gene implicated in schizophrenia
Pubmed
Gene
CoreNucleotide
BLAST
PubMed
CoreNucleotide
BLAST
GABRA1 in human RIFs
What have we learned?
1. Where the human equivalent of GABRA1
in the mouse is
2. Some functions associated with
GABRA1 in the human
3. Scholarly work that backs up #2
4. All of these discoveries were made using
a computer, not in the laboratory!
Questions?