bioinformatics and the engineering library
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Bioinformatics and the Engineering Library. ASEE 2008 Amy Stout. What is bioinformatics?. Using computers to solve biological problems, usually on a molecular level - PowerPoint PPT PresentationTRANSCRIPT
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Bioinformatics and the Engineering Library
ASEE 2008Amy Stout
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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
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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
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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
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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
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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
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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
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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
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libraries.mit.edu/bioinformatics
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NCBI demonstration
• Entrez with GABRA1: the name of a gene implicated in schizophrenia
• Pubmed• Gene• CoreNucleotide• BLAST
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PubMed
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CoreNucleotide
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BLAST
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GABRA1 in human RIFs
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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 #24. All of these discoveries were made using
a computer, not in the laboratory!
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Questions?