Lawrence Berkeley National Laboratory

About: Lawrence Berkeley National Laboratory is a facility organization based out in Berkeley, California, United States. It is known for research contribution in the topics: Catalysis & Laser. The organization has 28217 authors who have published 66584 publications receiving 4111321 citations. The organization is also known as: LBNL & LBL.

Fiji: an open-source platform for biological-image analysis

Abstract: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

PHENIX: a comprehensive Python-based system for macromolecular structure solution

Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. How­ever, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallo­graphic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.

Phaser crystallographic software

Abstract: Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.

Measurements of Omega and Lambda from 42 High-Redshift Supernovae

Abstract: We report measurements of the mass density, Omega_M, and cosmological-constant energy density, Omega_Lambda, of the universe based on the analysis of 42 Type Ia supernovae discovered by the Supernova Cosmology Project. The magnitude-redshift data for these SNe, at redshifts between 0.18 and 0.83, are fit jointly with a set of SNe from the Calan/Tololo Supernova Survey, at redshifts below 0.1, to yield values for the cosmological parameters. All SN peak magnitudes are standardized using a SN Ia lightcurve width-luminosity relation. The measurement yields a joint probability distribution of the cosmological parameters that is approximated by the relation 0.8 Omega_M - 0.6 Omega_Lambda ~= -0.2 +/- 0.1 in the region of interest (Omega_M <~ 1.5). For a flat (Omega_M + Omega_Lambda = 1) cosmology we find Omega_M = 0.28{+0.09,-0.08} (1 sigma statistical) {+0.05,-0.04} (identified systematics). The data are strongly inconsistent with a Lambda = 0 flat cosmology, the simplest inflationary universe model. An open, Lambda = 0 cosmology also does not fit the data well: the data indicate that the cosmological constant is non-zero and positive, with a confidence of P(Lambda > 0) = 99%, including the identified systematic uncertainties. The best-fit age of the universe relative to the Hubble time is t_0 = 14.9{+1.4,-1.1} (0.63/h) Gyr for a flat cosmology. The size of our sample allows us to perform a variety of statistical tests to check for possible systematic errors and biases. We find no significant differences in either the host reddening distribution or Malmquist bias between the low-redshift Calan/Tololo sample and our high-redshift sample. The conclusions are robust whether or not a width-luminosity relation is used to standardize the SN peak magnitudes.