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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

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Bioinformatics and the Engineering Library

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  1. Bioinformatics and the Engineering Library ASEE 2008 Amy Stout

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. libraries.mit.edu/bioinformatics

  10. NCBI demonstration • Entrez with GABRA1: the name of a gene implicated in schizophrenia • Pubmed • Gene • CoreNucleotide • BLAST

  11. PubMed

  12. CoreNucleotide

  13. BLAST

  14. GABRA1 in human RIFs

  15. What have we learned? • Where the human equivalent of GABRA1 in the mouse is • Some functions associated with GABRA1 in the human • Scholarly work that backs up #2 • All of these discoveries were made using a computer, not in the laboratory!

  16. Questions?

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