Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009.

An efficient method is given to reconstruct the current profile parameters, the plasma shape, and a current profile consistent with the magnetohydrodynamic equilibrium constraint from external magnetic measurements, based on a Picard iteration approach which approximately conserves the measurements. Computational efforts are reduced by parametrizing the current profile linearly in terms of a number of physical parameters. Results of detailed comparative calculations and a sensitivity study are described. Illustrative calculations to reconstruct the current profiles and plasma shapes in ohmically and auxiliarily heated Doublet III plasmas are given which show many interesting features of the current profiles.

Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer “core” genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.

Integral relations for the average poloidal beta J3 p and the plasma internal inductance 8j are derived from the magnetohydrodynamic (MHD) equilibrium equation for an axisymmetric torus. The volumedependent parameters that appear depend only weakly on the actual current density distribution inside the plasma and can be evaluated approximately, given the plasma shape and boundary poloidal magnetic field. In practice, these can be accurately and efficiently obtained for both diverted and limited plasmas from measured external poloidal magnetic field and flux values by approximating the plasma current distribution using a few filaments or distributed sources. For a tokamak plasma with a non-circular cross-section of sufficient elongation, J3 p and 8j can then be approximately determined separately. This is demonstrated for analytic equilibria of known shape as well as for actual Doublet III (D-III) plasmas for which /3 p and Z{ have been determined by using other methods. Results of a sensitivity study are described.