Esta semana inició el curso de métodos filogenéticos de la WHS en Xalapa

Este Lunes 23 de Mayo inicio el taller de la WHS en el INECOL, Xalapa.
El curso despertó mucho interés y asisten 25 participantes de varios países: EUA, Mexico, Costa Rica, Colombia, Perú, Brasil, Argentina y España!
Varias fotos del grupo están en la Galería en el sito web del curso aquí.

En la foto arriba, John Wenzel a cargo de las clases el Lunes. Entre él y Kevin Nixon (foto abajo) impartieron las clases y prácticas del Lunes y Martes.



La tarde del Martes fuimos a un restaurant local para cenar como grupo. Disfrutamos de buena comida mexicana y un ambiente muy agradable con viejos y nuevos amigos. Para algunos la noche terminó en un karaoke muy revelador de habilidades vocales y musicales!



El taller sigue esta semana hasta el viernes. Miércoles y Jueves Ward Wheeler y Viernes con Chris Randle.

Junio 6, PD: Me informan que el viernes por la noche también hubo karaoke! Sin duda, todo un exito el taller!

La Galeria del curso esta en:
http://www.filogenetica.org/cursos/WHSphotos/Gallery/

Computational phyloinformatics workshop. Kyoto

Computational Phyloinformatics is an 11-day intensive summer workshop co-sponsored by the Bioinformatics Center of Kyoto University, DBCLS/JST and NESCent, and will take place at the Bioinformatics Center in Kyoto, Japan following the SMBE 2011 meeting.

The workshop aims to give biologists practical knowledge and hands-on programming skills in phyloinformatics.

Instructors and Course Organizers

• Christian Zmasek (Sanford-Burnham Medical Research Institute; Functional Genomics with BioRuby)
• Karen Cranston (NESCent Training Coordinator)
• Rutger A. Vos (University of Reading; Phyloinformatics with BioPerl and Bio::Phylo)
• Susumu Goto (Bioinformatics Center, KEGG laboratory)
• Toshiaki Katayama (Human Genome Center, University of Tokyo)
• William H. Piel (Yale Peabody Museum; Phyloinformatics with SQL)

MORE INFORMATION >>>

Faster exact maximum parsimony search with XMP

W. Timothy J. White1, and Barbara R. Holland. 2011. Faster exact maximum parsimony search with XMP. Bioinformatics (2011) 27 (10): 1359-1367. doi: 10.1093/bioinformatics/btr147 First published online: March 27, 2011


Abstract

Motivation: Despite trends towards maximum likelihood and Bayesian criteria, maximum parsimony (MP) remains an important criterion for evaluating phylogenetic trees. Because exact MP search is NP-complete, the computational effort needed to find provably optimal trees skyrockets with increasing numbers of taxa, limiting analyses to around 25–30 taxa. This is, in part, because currently available programs fail to take advantage of parallelism.

Results: We present XMP, a new program for finding exact MP trees that comes in both serial and parallel versions. The serial version is faster in nearly all tests than existing software. The parallel version uses a work-stealing algorithm to scale to hundreds of CPUs on a distributed-memory multiprocessor with high efficiency. An optimized SSE2 inner loop provides additional speedup for Pentium 4 and later CPUs.

Availability: C source code and several binary versions are freely available from http://www.massey.ac.nz/~wtwhite/xmp.
The parallel version requires an MPI implementation, such as the freely available MPICH2.