We develop a general method for power spectrum analysis of three dimensional redshift surveys. We present rigorous analytical estimates for the statistical uncertainty in the power and we are able to derive a rigorous optimal weighting scheme under the reasonable (and largely empirically verified) assumption that the long wavelength Fourier components are Gaussian distributed. We apply the formalism to the updated 1-in-6 QDOT IRAS redshift survey, and compare our results to data from other probes: APM angular correlations; the CfA and the Berkeley 1.2Jy IRAS redshift surveys. Our results bear out and further quantify the impression from e.g. counts-in-cells analysis that there is extra power on large scales as compared to the standard CDM model with Ωh ≃ 0.5. We apply likelihood analysis using the CDM spectrum with Ωh as a free parameter as a phenomenological family of models; we find the best fitting parameters in redshift space and transform the results to real space. Finally, we calculate the distribution of the estimated long wavelength power. This agrees remarkably well with the exponential distribution expected for Gaussian fluctuations, even out to powers of ten times the mean. Our results thus reveal no trace of periodicity or other non-Gaussian behavior.

The bulk flow, i.e. the dipole moment of the peculiar velocity field, is a sensitive probe of matter density fluctuations on very large scales. However, the peculiar velocity surveys for which the bulk flow has been calculated have non‐uniform spatial distributions of tracers, so that the bulk flow estimated does not correspond to that of a simple volume such as a sphere. Thus bulk flow estimates are generally not strictly comparable between surveys, even those whose effective depths are similar. In addition, the sparseness of typical surveys can lead to aliasing of small‐scale power into what is meant to be a probe of the largest scales. Here we introduce a new method of calculating bulk flow moments where velocities are weighted to give an optimal estimate of the bulk flow of an idealized survey, with the variance of the difference between the estimate and the actual flow being minimized. These ‘minimum variance’ estimates can be designed to estimate the bulk flow on a particular scale with minimal sensitivity to small‐scale power, and are comparable between surveys. We compile all major peculiar velocity surveys and apply this new method to them. We find that most surveys we studied are highly consistent with each other. Taken together the data suggest that the bulk flow within a Gaussian window of radius 50 h−1 Mpc is 407 ± 81 km s−1 toward l= 287°± 9°, b= 8°± 6°. The large‐scale bulk motion is consistent with predictions from the local density field. This indicates that there are significant density fluctuations on very large scales. A flow of this amplitude on such a large scale is not expected in the WMAP5 (Wilkinson Microwave Anisotropy Probe) normalized Λ cold dark matter cosmology, for which the predicted one‐dimensional rms velocity is ∼110 km s−1. The large amplitude of the observed bulk flow favours the upper values of the WMAP5 Ωmh2–σ8 error‐ellipse, but even the point at the top of the WMAP595 per cent confidence ellipse predicts a bulk flow which is too low compared to that observed at >98 per cent confidence level.

We compute the bispectrum for the galaxy distribution in the IRAS QDOT, 2 Jy, and 1.2 Jy redshift catalogs for wavenumbers 0.05 ≤ k ≤ 0.2 h Mpc −1 and compare the results with predictions from gravitational instability in perturbation theory. Taking into account redshift space distortions, nonlinear evolution, the survey selection function, and discreteness and finite volume effects, all three catalogs show evidence for the dependence of the bispectrum on configuration shape predicted by gravitational instability. Assuming Gaussian initial conditions and local biasing parametrized by linear and non-linear bias parameters b 1 and b 2 , a likelihood analysis yields 1/b 1 = 1.32 +0.36 −0.58 , 1.15 +0.39 −0.39 and b 2 /b 2 1 = −0.57 +0.45 −0.30 , −0.50 +0.31 −0.51 , for the for the 2 Jy and 1.2 Jy samples, respectively. This implies that IRAS galaxies trace dark matter increasingly weakly as the density contrast increases, consistent with their being under-represented in clusters. In a model with χ 2 non-Gaussian initial conditions, the bispectrum displays an amplitude and scale dependence different than that found in the Gaussian case; if IRAS galaxies do not have bias b 1 > 1 at large scales, χ 2 non-Gaussian initial conditions are ruled out at the 95% confidence level. The IRAS data do not distinguish between Lagrangian or Eulerian local bias.

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machinereadable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues. INTRODUCTIONIn light of the vast scientific resources made available through genomics, the science of deciphering molecular mechanisms is expanding rapidly. Scientists who once hunted for disease genes or sought to distinguish key concepts in evolution are now turning their attention to the details of molecular assembly and mechanism to further understand medicine and the key concepts underlying biology. The Biomolecular Interaction Network Database (BIND) was designed to store complete information about molecular assembly through a database structure in order to archive interactions and reactions arising from biopolymers (protein, RNA and DNA), as well as small molecules, lipids and carbohydrates. Detailed information about molecular mechanism, such as the chemical product(s) of an enzymatic reaction, can be encoded in BIND. The underlying ontology of the BIND database is chemistry, and as such, BIND is capable of storing information about molecular interactions to atomic resolution. The taxonomic scope of BIND is

The low-order moments, such as the bulk flow and shear, of the large-scale peculiar velocity field are sensitive probes of the matter density fluctuations on very large scales. In practice, however, peculiar velocity surveys are usually sparse and noisy, which can lead to the aliasing of small-scale power into what is meant to be a probe of the largest scales. Previously, we developed an optimal 'minimum variance' (MV) weighting scheme, designed to overcome this problem by minimizing the difference between the measured bulk flow (BF) and that which would be measured by an ideal survey. Here we extend this MV analysis to include the shear and octupole moments, which are designed to have almost no correlations between them so that they are virtually orthogonal. We apply this MV analysis to a compilation of all major peculiar velocity surveys, consisting of 4536 measurements. Our estimate of the BF on scales of ∼100 h −1 Mpc has a magnitude of |v| = 416 ± 78 km s −1 towards Galactic l = 282 • ± 11 • and b = 6 • ± 6 • . This result is in disagreement with cold dark matter with Wilkinson Microwave Anisotropy Probe 5 (WMAP5) cosmological parameters at a high confidence level, but is in good agreement with our previous MV result without an orthogonality constraint, showing that the shear and octupole moments did not contaminate the previous BF measurement. The shear and octupole moments are consistent with WMAP5 power spectrum, although the measurement noise is larger for these moments than for the BF. The relatively low shear moments suggest that the sources responsible for the BF are at large distances.