Introduction to Systems Biology

This is a graduate course I taught in the College of Life Sciences at Jeju National University. The main goal of this course is to present some basic ideas of the relatively new field called “Systems Biology”, and how it involves the use of computer modeling and visualization techniques in order to describe complex metabolic, regulatory and transcription networks functioning inside the living cells. One reason for the development of these techniques was to handle and analyze the large amounts of data resulting from high-throughput genomic and proteomic experiments, so an overview of different online biological databases currently available is also presented.

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Convergence / Divergence

Two data visualizations I did in 2010 using the output of folding simulations of protein molecules. These renderings were created by combining thousands of protein models generated by the computer across several simulations for the protein ubiquitin. The simulated folding process progresses from the initial, unfolded, random coil ensamble of the molecule, ultimately converging into a more localized set of conformations that resemble the biologically functional state of the protein.

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Molecular visualization

During the time I did research in the protein folding problem, also started to develop some software to generate 3D representations of biological molecules, mainly proteins. The original code used OpenGL for rendering, and the interface was done with Borland Delphi. The software was called YapView (Yet Another Protein Viewer), and is still available for download here (including the source code), although I’m not maintaining any longer.

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Protein Folding

As a postdoctoral researcher at the University of Chicago from 2002 to 2005, I studied the protein folding problem. This problem consists in predicting the three dimensional structure of a protein molecule given the only information of its linear sequence of amino acids. This research was conducted in a multidisciplinary environment, with experts from molecular biology, computer science, and physical chemistry.

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