Resources
BioGrapher
Author(s): Rama Viswanathan1, Han Lai1, Hlaing Lin1, Khalid Qumsieh1, John Jungck1
Beloit College
634 total view(s), 50 download(s)
BIOGRAPHER-DIST_MAY21_2021.zip(ZIP | 20 MB)- Graphviz
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Overview
BioGrapher: Graph Theoretical Properties and Visualization of Biological Interactions
BioGrapher is an Excel front-end for the AT&T GraphViz graphical visualization and layout package (http://www.graphviz.org/). BioGrapher is unique in that it (1) allows users to enter data into an Excel spreadsheet in one of three ways: adjacency matrices, nodal lists, and Newick format for phylogenetic trees; (2) displays graphs in four different layouts: radial, circular, hierarchical, and tree; (3) properties of graphs, e.g., diameter, connectedness, and average clustering can be computed and displayed; (4) data can be read from standard comma separated value (CSV) text files. A VBA custom menu interface for the Windows and Mac OS X versions of GraphViz has been programmed and added to the standard Excel menu bar so that the user can easily invoke the graphical layout and computation routines.
Our front-end is a modest effort to provide undergraduates with fairly sophisticated access to graphical visualization without a steep learning curve, in keeping with the ESTEEM philosophy. BioGrapher is a work in progress, and we have made no attempt to optimize our libraries and routines. In fact, the approach used is true brute-force and consists mainly of assembling the input file for the AT&T GraphViz package, calling the package using Excel shell, and then parsing the output file and drawing the graph using Excel drawing tools.
Citation
Researchers should cite this work as follows:
- Viswanathan, R., Lai, H., Lin, H., Qumsieh, K., Jungck, J. (2024). BioGrapher. ESTEEM, QUBES Educational Resources. doi:10.25334/6G0Y-4W47
Fundamental Mathematical Concepts
Developed By
The professional life of Professor F.R. "Buck" McMorris began in 1969 when he was awarded a Ph.D. in mathematics (abstract algebra) from the University of Wisconsin-Milwaukee. Earlier, he received a Bachelor of Science in mathematics from Beloit College and a Master of Arts in mathematics from the University of California, Riverside.
In 1971, he accepted a two-year National Institutes of Health post-doctoral fellowship in biomathematics at North Carolina State University. Since then, he has worked primarily in the area of applied mathematics, using discrete mathematics to solve problems in biology, data analysis, voting theory and location theory. He has published more than 120 research papers and four books while obtaining significant grant funds from the Office of Naval Research.
McMorris spent 15 years at the University of Louisville, where he was assistant vice president for research, a Distinguished University Scholar, and professor of mathematics. He led a university initiative to create a high-profile interdisciplinary Logistics and Distribution Institute, for which he served as acting director for one year. He also held an associate appointment in the Department of Industrial Engineering. During the 1980s, he served as chair of the Department of Mathematics at the University of Louisville, and as Scientific Officer for discrete mathematics at the Office of Naval Research.
In 1999, he joined IIT as chair of the Applied Mathematics Department, where he developed new applied mathematics degree programs and increased the departmentís research activities. He was named dean of the College of Science and Letters in 2003.
Early in his career, McMorris was a mathematics professor at Bowling Green State University. He also held visiting appointments at Rutgers University, Clemson University, University of South Carolina, University of Central Florida, and Erasmus University Rotterdam.