Comprehensive data infrastructure for plant bioinformatics

The iPlant Collaborative is a 5-year, National Science Foundation-funded effort to develop cyberinfrastructure to address a series of grand challenges in plant science. The second of these grand challenges is the Genotype-to- Phenotype project, which seeks to provide tools, in the form of a web-based Discovery Environment, for understanding the developmental process from DNA to a full-grown plant. Addressing this challenge requires the integration of multiple data types that may be stored in multiple formats, with varying levels of standardization. Providing for reproducibility requires that detailed information documenting the experimental provenance of data, and the computational transformations applied to data once it is brought into the iPlant environment. Handling the large quantities of data involved in high-throughput sequencing and other experimental sources of bioinformatics data requires a robust infrastructure for storing and reusing large data objects. We describe the currently planned workflows to be developed for the Genotype-to-Phenotype discovery environment, the data types and formats that must be imported and manipulated within the environment, and we describe the data model that has been developed to express and exchange data within the Discovery Environment, along with the provenance model defined for capturing experimental source and digital transformation descriptions. Capabilities for interaction with reference databases are addressed, focusing not just on the ability to retrieve data from such data sources, but on the ability to use the iPlant Discovery Environment to further populate these important resources. Future activities and the challenges they will present to the data infrastructure of the iPlant Collaborative are also described. © 2010 IEEE

Trilogy on Computing Maximal Eigenpair

The eigenpair here means the twins consist of eigenvalue and its eigenvector. This paper introduces the three steps of our study on computing the maximal eigenpair. In the first two steps, we construct efficient initials for a known but dangerous algorithm, first for tridiagonal matrices and then for irreducible matrices, having nonnegative off-diagonal elements. In the third step, we present two global algorithms which are still efficient and work well for a quite large class of matrices, even complex for instance.Comment: Updated versio

The High Time Resolution Universe Pulsar Survey IV: Discovery and polarimetry of millisecond pulsars

We present the discovery of six millisecond pulsars (MSPs) in the High Time Resolution Universe (HTRU) survey for pulsars and fast transients carried out with the Parkes radio telescope. All six are in binary systems with approximately circular orbits and are likely to have white dwarf companions. PSR J1017-7156 has a high flux density and a narrow pulse width, making it ideal for precision timing experiments. PSRs J1446-4701 and J1125-5825 are coincident with gamma-ray sources, and folding the high-energy photons with the radio timing ephemeris shows evidence of pulsed gamma-ray emission. PSR J1502-6752 has a spin period of 26.7 ms, and its low period derivative implies that it is a recycled pulsar. The orbital parameters indicate it has a very low mass function, and therefore a companion mass much lower than usually expected for such a mildly recycled pulsar. In addition we present polarisation profiles for all 12 MSPs discovered in the HTRU survey to date. Similar to previous observations of MSPs, we find that many have large widths and a wide range of linear and circular polarisation fractions. Their polarisation profiles can be highly complex, and although the observed position angles often do not obey the rotating vector model, we present several examples of those that do. We speculate that the emission heights of MSPs are a substantial fraction of the light cylinder radius in order to explain broad emission profiles, which then naturally leads to a large number of cases where emission from both poles is observed.Comment: Update to correct affiliation for CAASTRO. 16 pages, 18 figures. Accepted for publication in MNRA

Modelling the Galactic distribution of free electrons

In this paper we test 8 models of the free electron distribution in the Milky Way that have been published previously, and we introduce 4 additional models that explore the parameter space of possible models further. These new models consist of a simple exponential thick disk model, and updated versions of the models by Taylor & Cordes and Cordes & Lazio with more extended thick disks. The final model we introduce uses the observed H-alpha intensity as a proxy for the total electron column density, also known as the dispersion measure (DM). We use the latest available data sets of pulsars with accurate distances (through parallax measurements or association with globular clusters) to optimise the parameters in these models. In the process of fitting a new scale height for the thick disk in the model by Cordes & Lazio we discuss why this thick disk cannot be replaced by the thick disk that Gaensler et al. advocated in a recent paper. In the second part of our paper we test how well the different models can predict the DMs of these pulsars at known distances. Almost all models perform well, in that they predict DMs within a factor of 1.5-2 of the observed DMs for about 75% of the lines of sight. This is somewhat surprising since the models we tested range from very simple models that only contain a single exponential thick disk to very complex models like the model by Cordes & Lazio. We show that the model by Taylor & Cordes that we updated with a more extended thick disk consistently performs better than the other models we tested. Finally, we analyse which sightlines have DMs that prove difficult to predict by most models, which indicates the presence of local features in the ISM between us and the pulsar. (abridged)Comment: 16 pages, 10 figures, 5 tables. Accepted for publication in the Monthly Notices of the RAS by the Royal Astronomical Society and Blackwell Publishin

Rotation measure variations for 20 millisecond pulsars

We report on variations in the mean position angle of the 20 millisecond pulsars being observed as part of the Parkes Pulsar Timing Array (PPTA) project. It is found that the observed variations are dominated by changes in the Faraday rotation occurring in the Earth's ionosphere. Two ionospheric models are used to correct for the ionospheric contribution and it is found that one based on the International Reference Ionosphere gave the best results. Little or no significant long-term variation in interstellar RM was found with limits typically about 0.1 rad m$^{-2}$ yr$^{-1}$ in absolute value. In a few cases, apparently significant RM variations over timescales of a few 100 days or more were seen. These are unlikely to be due to localised magnetised regions crossing the line of sight since the implied magnetic fields are too high. Most probably they are statistical fluctuations due to random spatial and temporal variations in the interstellar electron density and magnetic field along the line of sight.Comment: Accepted for publication in Astrophysics & Space Scienc

Pulsed Gamma Rays from the Original Millisecond and Black Widow Pulsars: a case for Caustic Radio Emission?

We report the detection of pulsed gamma-ray emission from the fast millisecond pulsars (MSPs) B1937+21 (also known as J1939+2134) and B1957+20 (J1959+2048) using 18 months of survey data recorded by the \emph{Fermi} Large Area Telescope (LAT) and timing solutions based on radio observations conducted at the Westerbork and Nan\c{c}ay radio telescopes. In addition, we analyzed archival \emph{RXTE} and \emph{XMM-Newton} X-ray data for the two MSPs, confirming the X-ray emission properties of PSR B1937+21 and finding evidence ($\sim 4\sigma$) for pulsed emission from PSR B1957+20 for the first time. In both cases the gamma-ray emission profile is characterized by two peaks separated by half a rotation and are in close alignment with components observed in radio and X-rays. These two pulsars join PSRs J0034-0534 and J2214+3000 to form an emerging class of gamma-ray MSPs with phase-aligned peaks in different energy bands. The modeling of the radio and gamma-ray emission profiles suggests co-located emission regions in the outer magnetosphere.Comment: Accepted for publication in the Astrophysical Journa

Discovery of Pulsed γ\gamma-rays from PSR J0034-0534 with the Fermi LAT: A Case for Co-located Radio and γ\gamma-ray Emission Regions

Millisecond pulsars (MSPs) have been firmly established as a class of gamma-ray emitters via the detection of pulsations above 0.1 GeV from eight MSPs by the Fermi Large Area Telescope (LAT). Using thirteen months of LAT data significant gamma-ray pulsations at the radio period have been detected from the MSP PSR J0034-0534, making it the ninth clear MSP detection by the LAT. The gamma-ray light curve shows two peaks separated by 0.274$\pm$0.015 in phase which are very nearly aligned with the radio peaks, a phenomenon seen only in the Crab pulsar until now. The $\geq$0.1 GeV spectrum of this pulsar is well fit by an exponentially cutoff power law with a cutoff energy of 1.8$\pm 0.6\pm$0.1 GeV and a photon index of 1.5$\pm 0.2\pm$0.1, first errors are statistical and second are systematic. The near-alignment of the radio and gamma-ray peaks strongly suggests that the radio and gamma-ray emission regions are co-located and both are the result of caustic formation.Comment: 20 pages, 3 figures, 2 tables. Accepted for publication in Ap