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BioGrapher

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 ATT GraphViz package, calling the package using Excel shell, and then parsing the output file and drawing the graph using Excel drawing tools.

Source

Author(s):
Rama Viswanathan, Beloit College
Han Lai, Beloit College
Hlaing Lin, Beloit College
Khalid Qumsieh, Beloit College
John R. Jungck, Beloit College

Published by: BioQUEST Curriculum Consortium

OS: New version coming soon (03/2014)

User Manuals and Curricular Materials

BioGRAPHER Software Manual

BioGRAPHER Installation Instructions

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Citation
Viswanathan Rama , Lai Han , Lin Hlaing , Qumsieh Khalid , Jungck John R. () BioGrapher. A module of the Biological ESTEEM Collection, published by the BioQUEST Curriculum Consortium. URL: http://bioquest.org/esteem/esteem_details.php?product_id=6509