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

• 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

• 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

• 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:– 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

• 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?