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Bioinformatics and the Engineering Library ASEE 2008 Amy Stout.

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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


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


12 PubMed

13 CoreNucleotide








21 GABRA1 in human RIFs


23 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!

24 Questions?

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