The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.

The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.

An ab initio calculation of the 12 C elastic form factor, and sum rules of longitudinal and transverse response functions measured in inclusive (e, e ) scattering, is reported, based on realistic nuclear potentials and electromagnetic currents. The longitudinal elastic form factor and sum rule are found to be in satisfactory agreement with available experimental data. A direct comparison between theory and experiment is difficult for the transverse sum rule. However, it is shown that the calculated one has large contributions from two-body currents, indicating that these mechanisms lead to a significant enhancement of the quasi-elastic transverse response. This fact may have implications for the anomaly observed in recent neutrino quasi-elastic charge-changing scattering data off 12 C. The current picture of the nucleus as a system of protons and neutrons interacting among themselves via two-and three-body forces and with external electroweak probes via one-and two-body currents-a dynamical framework we will refer to below as the standard nuclear physics approach (SNPA)-has been shown to reproduce satisfactorily a variety of empirical properties of light nuclei with mass number A ≤ 12, including energy spectra [1][2][3][4][5][6][7], static properties [1,3,4,8,9] of low-lying states, such as charge radii, and magnetic and quadrupole moments, and longitudinal electron scattering [10,11]. However, it has yet to be established conclusively whether such a picture quantitatively and successfully accounts for the observed electroweak structure and response of these systems, at least those with A > 4, in a wide range of energy and momentum transfers. This issue has acquired new and pressing relevance in view of the anomaly seen in recent neutrino quasielastic charge-changing scattering data on 12 C [12], i.e., the excess, at relatively low energy, of measured cross section relative to theoretical calculations. Analyses based on these calculations have led to speculations that our present understanding of the nuclear response to chargechanging weak probes may be incomplete [13], and, in particular, that the momentum-transfer dependence of the axial form factor of the nucleon may be quite different from that obtained from analyses of pion electroproduction data [14] and measurements of neutrino and anti-neutrino reactions on protons and deuterons [15][16][17][18]. However, it should be emphasized that the calculations on which these analyses are based use rather crude models of nuclear structure-Fermi gas or local density approximations of the nuclear matter spectral function-as well as simplistic treatments of the reaction mechanism, and do not fit the picture outlined above. Conclusions based on them should therefore be viewed with caution.The present work provides the first step towards a comprehensive study, within the SNPA, of the quasi-elastic electroweak response functions of light nuclei. We report an exact quantum Monte Carlo (QMC) calculation of the elastic form factor and sum rules associated with the longitudi...

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Abstract.W-e present a process management system for parallel programs such as those written using MP1. .* primary goal of the system, which we call MPD (for multipurpose daemon), is to be scalable. By this we mean that startup of interactive parallel jobs comprising a thousand processes is quick, that signals can be quickly deIivered to processes, and that stdin, stdout, and stderr are managed intuitively. Our primary target is parallel machines made up of clusters of SNIPS, but the system is also useful in more tightly inteawated environments. We describe how MPD enables much faster startup and better runtime management of MPICH jobs. We show how close controi of stdio can support the easy implementation of a number of convenient system utilities, even a parallel debugger. MPD is implemented and freely distributed with NIPICH.

Parallel jobs are different from sequential jobs and require a different type of process management. We present here a process management system for parallel programs such as those written using MPI. A primary goal of the system, which we call MPD (for multipurpose daemon), is to be scalable. By this we mean that startup of interactive parallel jobs comprising thousands of processes is quick, that signals can be quickly delivered to processes, and that stdin, stdout, and stderr are managed intuitively. Our primary target is parallel machines made up of clusters of SMPs, but the system is also useful in more tightly integrated environments. We describe how MPD enables much faster startup and better runtime management of parallel jobs. We show how close control of stdio can support the easy implementation of a number of convenient system utilities, even a parallel debugger. We describe a simple but general interface that can be used to separate any process manager from a parallel library, which we use to keep MPD separate from MPICH.

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