Citing the GARLI Web Service

Here is an example of how the GARLI Web Service can be cited in a publication:

"To complete the phylogenetic analyses we used GARLI (Genetic Algorithm for Rapid Likelihood Inference; Zwickl 2006) and Grid computing (Cummings and Huskamp 2005) through The Lattice Project (Bazinet and Cummings 2008), which includes clusters and desktops in one encompassing system (Myers et al. 2008). A Grid service for GARLI was developed using a special programming library and associated tools (Bazinet et al. 2007). Following the general computational model of a previous phylogenetics study (Cummings et al. 2003), which used an earlier Grid computing system (Myers and Cummings 2003), we distributed required files among hundreds of computers where the analyses were conducted asynchronously in parallel."

List of publications:

Bazinet, A. L., and M. P. Cummings. 2008. The Lattice Project: a grid research and production environment combining multiple grid computing models. Pages 2-13. In Weber, M. H. W. (Ed.) Distributed & Grid Computing - Science Made Transparent for Everyone. Principles, Applications and Supporting Communities. Rechenkraft.net, Marburg.

Bazinet, A. L., D. S. Myers, J. Fuetsch, and M. P. Cummings. 2007. Grid services base library: a high-level, procedural application program interface for writing Globus-based Grid services. Future Generation Computer Systems 23:517.

Cummings, M. P., and J. C. Huskamp. 2005. Grid computing. Educause Review 40:116-117.

Cummings, M. P., S. A. Handley, D. S. Myers, D. L. Reed, A. Rokas, and K. Winka. 2003. Comparing bootstrap and posterior probability values in the four-taxon case. Systematic Biology 52:477-487.

Myers, D. S., A. L. Bazinet and M. P. Cummings. 2008. Expanding the reach of Grid computing: combining Globus- and BOINC-based systems. Pages 71-85. In Talbi, E.-G. and A. Zomaya (Eds.) Grids for Bioinformatics and Computational Biology, Wiley Book Series on Parallel and Distributed Computing. John Wiley & Sons, New York.

Myers, D. S., and M. P. Cummings. 2003. Necessity is the mother of invention: a simple grid computing system using commodity tools. Journal of Parallel and Distributed Computing 63:578-589.

Zwickl, D. J. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas at Austin.