Skip to Main Content

NIMBioS.



|  Announcements  |  Calendars  |  VisitorInfo  |  Sitemap  |  Blog  |  Contact  |     RSS icon. NIMBioSNews Twitter icon Facebook LinkedIn icon. YouTube icon. Flickr icon. Storify icon.

Scientific Description Participants Agenda Products

Fast, Free Phylogenies: HPC for Phylogenetics Tutorial

Group photo.

Topic: High Performance Computing for Phylogenetics

Meeting dates: October 13-15, 2010

Location: NIMBioS at the University of Tennessee, Knoxville

Co-sponsors: NIMBioS, iPlant, and National Institute for Computational Sciences

Tutorial leaders: Eric Carr (NIMBioS); Jim Ferguson (NICS UTK/ORNL); Susan Holmes (Statistics, Stanford); Brian O’Meara (Ecology & Evolutionary Biology, UTK); Sheldon McKay (iPlant); Alexis Stamatakis (Computer & Communication Sciences, Tech. Univ. of Munich); Dan Stanzione (Adv. Computing Ctr/iPlant, Texas); Robert Thomson (Center for Population Biology, UC Davis); James Wilgenbusch (Scientific Computing, Florida State Univ.)

Agenda (PDF) Participants Evaluation report (PDF)

Objectives: This tutorial focused on how to use TeraGrid, the CIPRES Portal, the iPlant Discovery environment, university clusters, and other typically free HPC resources for phylogenetic analysis. The tutorial was geared primarily toward biologists (including students, postdocs and faculty) who were at least moderately experienced with phylogenetic analysis and who had datasets to run but were typically running analyses on their own desktops, though other researchers, such as statisticians or mathematicians working in phylogenetics, were encouraged to apply. Participants were encouraged to apply as teams (such as a pairing of a biologist and a statistician who collaborate in their work). Participants had the option of receiving instruction in basic Unix usage via webinar and self-paced online resources before the actual workshop, so lack of experience in this area was not a barrier to participation.

Products

Publications

Bonito G, Reynolds H, Robeson MS, Nelson J, Hodkinson BP, Tuskan G, Schadt CW, Vilgalys R. 2014. Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Molecular Ecology, 23(13): 3356-3370. [Online]

Gong Z, Matzke NJ, Ermentrout B, Song D, Vendetti JE, Slatkin M, Oster G. 2012. Evolution of patterns on Conus shells. Proceedings of the National Academy of Sciences, 109(5): E234-E241. [Online]

Hodkinson BP, Lendemer JC. 2012. Phylogeny and taxonomy of an enigmatic sterile lichen. Systematic Botany, 37(4): 865-844. [Online]

Yang Y, Ricarda R, Morawetz JJ, Haevermans T, Aubriot X, Berry PE. 2012. Molecular phylogenetics and classification of Euphorbia subgenus Chamaesyce (Euphorbiaceae). Taxon, 61(4): 764-789(26). [Online]

Barnosky AD, Matzke N, Tomiya S, Wogan GOU, Swartz B, Quental TB, Marshall C, McGuire JL, Lindsey EL, Maguire KC, Mersey B, and Ferrer EA. 2011. Has the Earth's sixth mass extinction already arrived? Nature 471(7336): 51-57. [Online]

Media Coverage

Drake N. 2011. Scientists try to determine whether life on Earth is quickly heading toward extinction. San Jose Mercury News. San Jose, CA. [Online]

Gibbons A. 2011. Are We in the Middle of a Sixth Mass Extinction? ScienceNOW [Online]

Karlamangla S. 2011. Mass Extinction May Occur in 300 Years, Scientists Say. The Daily Californian. Berkeley, CA. [Online]

NSF Press release. 2 March 2011. Earth's Sixth Mass Extinction: Is It Almost Here? [Online]

Pappas S. 2011. 6th mass extinction looms but preventable, study says. LiveScience, MSNBC. [Online]

Redell B. 2011. Interview of Nick Matzke. NBC Bay Area Morning Show. Bay Area: 2 hours.

Sanders R. 2011. "Has the Earth's sixth mass extinction already arrived?" Retrieved March 2, 2011. [Online]

Welch K. 2011. Interview of Nick Matzke. Saturday Morning Talkies, KPFA radio. Berkeley, CA: 1 hour. [Online]

Zimmer C. 2011. Outlook: Warm, Grim, Cloudy: My story on global warming and extinctions in tomorrow's NY Tiimes [sic]. The Loom. Retrieved 4/4/2011, 2011. [Online]

Zimmer C. 2011. Multitude of Species Face Climate Threat. New York Times. New York, New York Times: D1. [Online]



A goal of NIMBioS is to enhance the cadre of researchers capable of interdisciplinary efforts across mathematics and biology. As part of this goal, NIMBioS is committed to promoting diversity in all its activities. Diversity is considered in all its aspects, social and scientific, including gender, ethnicity, scientific field, career stage, geography and type of home institution. Questions regarding diversity issues should be directed to Dr. Ernest Brothers, the NIMBioS Associate Director for Diversity Enhancement (diversity@nimbios.org). You can read more about our Diversity Plan on our NIMBioS Policies web page. The NIMBioS building is fully handicapped accessible.