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Protein Bioinformatics (260.841)
Provides students with an overview of protein bioinformatics including computational and experimental approaches. The course will introduce amino acid and protein physical properties as well as the alignment and evolution of protein sequences. Protein structure and methods of structure determination will be presented as well as the use of protein databases and software for visualizing proteins. Methods for secondary and tertiary protein structure prediction will be discussed as well as methods for modeling small/molecule-protein interactions and protein-protein interactions. The course will also cover mass spectrometry and the analysis of high-throughput mass spectrometry data. A survey of mass spectrometry ionization techniques and instrument types will be followed by an overview of data analysis techniques for protein identification, de novo protein sequencing, and the analysis of post-translational modifications. Finally, students will be introduced to experimental and computational aspects of mapping protein interaction networks.
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Biological Databases and Distributed Computing (140.637)
Provides students with the principles and skills required to implement biological databases and their web-based interfaces. Presents essential notions of distributed computing on the world-wide-web. This includes the fundamentals of TCP/IP, client-server model, http protocol, server-side and client-side scripting with CGI and PHP and Javascript. The course will present the principals of biological database design using relational and object-oriented database models and management systems, e.g. MySQL. Topics to be covered include SQL, database design, normalization, optimization and ER modeling. We will discuss biological database interoperability, with e.g. XML, XML schema, and ontologies (i.e. GO). Guest lectures will provide insights into significant biological database projects such as the Human Protein Reference Database (HPRD) and DRAGON. As a final project, students will develop and publish a database-driven web-based application for a biological application.
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Bioinformatics (M.E:800.707)
The use of computers has revolutionized biological research. This BCMB core course provides an introduction to bioinformatics, the combined field of biology and informatics (information science and technology). The course focuses on the analysis of proteins, genes, and genomes.
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