Invitación: Quiclear para ampliar
Conferencias
1. Jueves 24 de junio, 17:00 hrs. Introducción a la computación cuántica. Dr. Salvador Venegas Andraca. Auditorio del CITI, Mérida, Yucatán.
2. Viernes 25 de junio, 17:00 hrs. Algoritmos cuánticos adiabáticos aplicados en el plegado de proteínas. Dr. Salvador Venegas Andraca. Auditorio del CITI, Mérida, Yucatán
Informes en bioinf.curso2009@gmail.com
Comité organizador
Dr. Ernesto Pérez Rueda. IBT@UNAM - eprueda@gmail.com - Instructor
Dr. Alberto Muñoz Ubando. Universidad del Mayab - luis.munoz@unimayab.edu.mx
Dra. Leticia Arena. UMDI@UNAM - arena.leticia@gmail.com
Biól. Javier Apodaca. UMDI@UNAM - javier.apodaca@gmail.com
This year, Computational Phyloinformatics will be traveling to the Instituto Gulbenkian de Ciência, near Lisbon, Portugal. The IGC is one of Portugal's top research institutes that focuses on the genetic basis of development and evolution of complex systems. Please consult the main IGC GTPB course page here.
The course will provide a hands-on instruction in phyloinformatics using Perl (BioPerl and Bio::Phylo) and SQL (Postgres and BioSQL).
Phylogenetics is key to studying evolution, systematics, comparative genomics, and bioinformatics — phylogenies are now ubiquitous in the biological literature. However, with the growth in computational power and DNA sequencing, and with ever more complex substitution models and analytical methods, it is less and less practical to run simple, one-shot analyses on a personal computer with an off-the-shelf program. As a result, we increasingly rely on custom-scripted analyses or custom-designed computational pipelines, and often on large compute machines or clusters. While books and courses on phylogenetics are common, it is harder to find information on how to script large-scale and complex analyses, or how to write your own scripts and programs.
This course aims to address this gap by introducing these skills in a practical, hands-on setting at the Instituto Gulbenkian de Ciência, near the mouth of the Tagus river in Oeiras, Portugal. This year's course will focus on hands-on training in Perl and SQL and will be structured to accommodate students with less prior programming experience.
La exploración de la biodiversidad, la clasificación filogenética y la identificación de muestras son las tres tareas fundamentales de la sistemática. Los obstáculos y dificultades en cada área son diversos, pero como biólogos todos sabemos lo difícil que es identificar taxonómicamente una colección de muestras, sean de plantas, animales, hongos, etc. Ademas de la muestra en buen estado y claves de identificación, frecuentemente se necesita el "ojo experto" del taxónomo especialista.
Darwin 2009: 150 Years of Evolutionary Biology Category: Genetics
Posted on: May 12, 2009 9:01 AM, by Razib
La población mexicana actual resulta ser un mosaico de diferentes grupos genéticos. El gradiente va desde poblaciones con un genoma mayormente zapoteca (el único grupo indígena examinado) a poblaciones mestizas (seis regiones geográficamente distantes) con diferentes mezclas de genomas prehispánicos y europeos.
GenBank, the standard database for genetic information maintained by National Center for Biotechnology Information, has been accumulating DNA sequences for some three decades now. Since its creation in the late 1980s, it has become the de facto repository for genetic information– genetic data must now be submitted to GenBank for a paper to be accepted for publication. Most sequence data accumulated is the result of the sum of many “local” taxonomic studies, that have targeted a particular group of organism for a relatively small, but well-known collection of genes. It contents now span over hundreds of genes across all of life’s domains. So, what would happen if you were to take all the sequence information contained in GenBank and analyze it phylogenetically all together in a single, one-step study? Well, that is what Pablo A. Goloboff and coworkers just did, the results of which were published in last week’s online early edition of Cladistics, the international journal of the Willi Hennig Society.
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blog por Roberto KellerEsto si que es difícil de creer: el análisis cladístico de una matriz "super gigante" de 73060 entidades. Así es, no es error de dedo, más de 73 mil unidades terminales! Este análisis portentoso fue efectuado por un equipo basado en Tucumán (Argentina) liderado por Pablo Goloboff. La referencia del artículo, por ahora solo disponible en linea, es:Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groupsAntes de este logro, la idea de matriz "grande" andaba en los 500-1000 unidades terminales (Uts), y los más ambiciosos se esforzaban por ensamblar y analizar matrices de 1500 a 2000 unidades. Obviamente las dificultades para realizar análisis filogenéticos crecen desmesuradamente con cada unidad agregada a la matriz. Los intentos de exploración del enorme espacio de los arboles con estrategias y software convencional (como PAUP) no permitían ni siquiera ver la posibilidad de intentar el análisis de matrices gigantes. Entonces, Goloboff et al (2009) como lo lograron?
Pablo A. Goloboff, Santiago A. Catalano, J. Marcos Mirande, Claudia A. Szumik, J. Salvador Arias, Mari Källersjö and James S. Farris.
Cladistics
http://dx.doi.org/10.1111/j.1096-0031.2009.00255.x
ABSTRACT
Obtaining a well supported schema of phylogenetic relationships among the major groups of living organisms requires considering as much taxonomic diversity as possible, but the computational cost of calculating large phylogenies has so far been a major obstacle. We show here that the parsimony algorithms implemented in TNT can successfully process the largest phylogenetic data set ever analysed, consisting of molecular sequences and morphology for 73 060 eukaryotic taxa. The trees resulting from molecules alone display a high degree of congruence with the major taxonomic groups, with a small proportion of misplaced species; the combined data set retrieves these groups with even higher congruence. This shows that tree-calculation algorithms effectively retrieve phylogenetic history for very large data sets, and at the same time provides strong corroboration for the major eukaryotic lineages long recognized by taxonomists.
There is a skirmish going on at Dechronization blog right now. This is a coauthored blog about phylogenetics. I like this blog (its right there on my blogroll —->). There are surprisingly very few blogs about phylogenetic methods these days, despite the wide use that phylogenies currently have in evolutionary biology and beyond (e.g., linguistics). I will complain that, for nine authors, they post little, sometimes not a single post during a month.
The hot post in question is a mocking of an announcement about a (to be honest, very successful) workshop in phylogenetic methods cosponsored by the Willi Hennig Society and so far held in different continents.
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"Archetype, Ant reconstruction one homology at a time"
Question: What are the most exciting recent developments in systematics?
I think there are three. First, there are second-order statistical analyses that can now be applied across a sample of trees from a Bayesian posterior distribution. These include biogeography, comparative methods, and macroevolutionary tests. We used to have to rely on a single tree for our analyses; now we can do the same analyses accounting for phylogenetic uncertainty by sampling from the posterior distribution of trees.
Second, the explicit accommodation of incongruence in analyses of multilocus data through the use of the coalescent. I think it will be really cool when we can use these approaches to differentiate between incongruence caused by coalescent stochasticity from that caused by nonvertical transmission such as horizontal gene transfer or hybridization.
Third, the development of phylogenomics. I remember a symposium debate at the Evolution meetings when I was a graduate student in the early 1990s. The debate was about total evidence approaches versus other methods. During the debate, someone raised the question of, “If we could sequence every single nucleotide in the genome, would we then get the best possible estimate of the phylogeny?” I think that emerging datasets demonstrate that the answer to this question might be, “not necessarily.”
Actividad se llevo a cabo en la Universidad Austral de Chile en el marco de un proyecto Fondecyt de Incentivo a la Colaboración Internacional.
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Entre el 13 y el 17 de enero, 2009 se realizó en la sala Universia de la Universidad Austral de Chile el Curso-Taller "Análisis Filogenético de Secuencias del ADN", dictado por el Dr. Marcos Pérez Losada, académico de la Universidad Brigham Young, de Utah, USA.
Este curso, que se impartió a 25 estudiantes de pre y postgrado de la UACh y otras universidades del país, fue organizado por los Dres. Milton Gallardo y José Núñez, en el contexto del Proyecto Fondecyt de Incentivo a la Colaboración Internacional. Contó además, con el auspicio de la DID-UACh y el Decanato de la Facultad de Ciencias.
Durante las 60 horas del taller, los alumnos aprendieron el manejo de bases de datos de Genbank, edición de secuencias, selección de modelos de sustitución nucleotídica, reconstrucción filogenética, edición de los árboles filogenéticos y estimación del tiempo de divergencia entre taxones. La actividad finalizó con la entrega de certificados de asistencia.
Edición: Universia / PV
Lord Sutherland of Houndwood, Chairman of the Lords Science and Technology Sub-Committee on Systematics and Taxonomy, opened the debate on 25 March in the Grand Committee of the House of Lords, on the report by the Committee and the Government's response to the report.
Lords Select Committee reports are generally discussed either on the floor of the House (in the Chamber) or in Grand Committee. Any Member of the Lords can take part and a minister responds for the Government. The debate usually takes place once the Government has formally responded to the committee's recommendations.
