TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata

Motivation: Microbial community profiling is a highly active area of research, but tools that facilitate visualization of phylogenetic trees and associated environmental data have not kept up with the increasing quantity of data generated in these studies

Stable divisorial gonality is in NP

Divisorial gonality and stable divisorial gonality are graph parameters, which have an origin in algebraic geometry. Divisorial gonality of a connected graph $G$ can be defined with help of a chip firing game on $G$. The stable divisorial gonality of $G$ is the minimum divisorial gonality over all subdivisions of edges of $G$. In this paper we prove that deciding whether a given connected graph has stable divisorial gonality at most a given integer $k$ belongs to the class NP. Combined with the result that (stable) divisorial gonality is NP-hard by Gijswijt, we obtain that stable divisorial gonality is NP-complete. The proof consist of a partial certificate that can be verified by solving an Integer Linear Programming instance. As a corollary, we have that the number of subdivisions needed for minimum stable divisorial gonality of a graph with $n$ vertices is bounded by $2^{p(n)}$ for a polynomial $p$

Level-rank duality of the U(N) WZW model, Chern-Simons theory, and 2d qYM theory

We study the WZW, Chern-Simons, and 2d qYM theories with gauge group U(N). The U(N) WZW model is only well-defined for odd level K, and this model is shown to exhibit level-rank duality in a much simpler form than that for SU(N). The U(N) Chern-Simons theory on Seifert manifolds exhibits a similar duality, distinct from the level-rank duality of SU(N) Chern-Simons theory on S^3. When q = e^{2 pi i/(N+K)}, the observables of the 2d U(N) qYM theory can be expressed as a sum over a finite subset of U(N) representations. When N and K are odd, the qYM theory exhibits N K duality, provided q = e^{2 pi i/(N+K)} and theta = 0 mod 2 pi /(N+K).Comment: 19 pages; v2: minor typo corrected, 1 paragraph added, published versio

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.

Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at http://caporaso-lab.github.io/mockrobiota/. The materials contained in mockrobiota include data set and sample metadata, expected composition data (taxonomy or gene annotations or reference sequences for mock community members), and links to raw data (e.g., raw sequence data) for each mock community data set. mockrobiota does not supply physical sample materials directly, but the data set metadata included for each mock community indicate whether physical sample materials are available. At the time of this writing, mockrobiota contains 11 mock community data sets with known species compositions, including bacterial, archaeal, and eukaryotic mock communities, analyzed by high-throughput marker gene sequencing. IMPORTANCE The availability of standard and public mock community data will facilitate ongoing method optimizations, comparisons across studies that share source data, and greater transparency and access and eliminate redundancy. These are also valuable resources for bioinformatics teaching and training. This dynamic resource is intended to expand and evolve to meet the changing needs of the omics community

Designs for a high power superconducting delay line

Potential designs for a high power superconducting delay line of approximately 10 microsecs duration are described. The transmitted signal should have low dispersion and little attenuation to recapture the original signal. Such demands cannot be met using conventional metal conductors. This paper outlines a proposal for a new transmission line design using low temperature superconducting material which meets system specifications. The 25 omega line is designed to carry pulsed signals with an approximate rise time of 8 nsec and a maximum voltage magnitude of 25 kV. Predicted electrical design and performance of the line will be presented

Coupled-Bunch Beam Breakup due to Resistive-Wall Wake

The coupled-bunch beam breakup problem excited by the resistive wall wake is formulated. An approximate analytic method of finding the asymptotic behavior of the transverse bunch displacement is developed and solved.Comment: 8 page