ALBERT

Description: The advent of second-generation sequencing (2GS) has provided a range of significant new challenges for the visualization of sequence assemblies. These include the large volume of data being generated, short-read lengths and different data types and data formats associated with the diversity of new sequencing technologies. This article illustrates how Tablet—a high-performance graphical viewer for visualization of 2GS assemblies and read mappings—plays an important role in the analysis of these data. We present Tablet, and through a selection of use cases, demonstrate its value in quality assurance and scientific discovery, through features such as whole-reference coverage overviews, variant highlighting, paired-end read mark-up, GFF3-based feature tracks and protein translations. We discuss the computing and visualization techniques utilized to provide a rich and responsive graphical environment that enables users to view a range of file formats with ease. Tablet installers can be freely downloaded from http://bioinf.hutton.ac.uk/tablet in 32 or 64-bit versions for Windows, OS X, Linux or Solaris. For further details on the Tablet, contact tablet@hutton.ac.uk.

Description: The Byrud emerald deposit comprises pegmatite veins hosted within Cambrian black shales and Late Carboniferous quartz syenite sills intruded by a Permo-Triassic riebeckite granite. The emerald deposit genesis is consistent with a typical granite-related emerald vein system derived from dominantly magmatic fluids with minor contributions from metamorphic source(s). Muscovite from an emerald-bearing pegmatite at Byrud yielded an excellent Ar–Ar plateau age of 233.4 ± 2.0 Ma. Emerald display colour zonation alternating between emerald and beryl. Two dominant fluid inclusions types are identified as follows: two-phase (vapour+liquid) and three-phase (brine+vapour+halite) fluid inclusions and these are interpreted to represent conjugate fluids of a boiling system. The emerald was precipitated from these saline fluids with approximate overall salinities on the order of 31 mass per cent NaCl equivalent. Raman analyses indicate molar gas fractions for CO 2 , N 2 , CH 4 and H 2 S are approximately 0.8974, 0.0261, 0.0354 and 0.0410, respectively. Formational temperatures and pressures of approximately 160–385°C and below 1000 bars were derived from fluid inclusion data and lithostatic pressure estimates from fluid inclusion studies within the Oslo rift. The colour zonation observed in the Byrud emerald crystals is related to alternating emerald and beryl precipitation in the liquid and vapour portions, respectively, of a two-phase (boiling) system. This study provides a model for the alternating emerald versus colourless beryl growth zones observed in emerald crystals from the Byrud deposit in Norway. These growth zones are host to a number of primary fluid inclusions and are related to alternating emerald and beryl precipitation in the liquid and vapour portions, respectively, of a two-phase (boiling) system.

Description: The ratio of body-wave to surface-wave magnitude, m (sub b) :M (sub s) , has historically been one of the most effective methods for distinguishing earthquakes from underground explosions. In the context of the Comprehensive Nuclear-Test-Ban Treaty (CTBT), m (sub b) :M (sub s) is currently one of the experimental standard event-screening criteria being provisionally tested at the International Data Centre (IDC). An event in the IDC analyst-reviewed bulletin is screened out if the hypothesis that it is an underground explosion can be rejected with high confidence. Recently, two announced nuclear tests by the Democratic People's Republic of Korea have raised interest because the M (sub s) values for these explosions are high compared to historical explosions with similar m (sub b) . On an m (sub b) :M (sub s) plot, both explosions lie close to the contemporary IDC experimental screening line, M (sub s) =1.25m (sub b) -2.2. Although neither explosion was screened out by the IDC, the two explosions indicate that a revision of the line is advisable to ensure with high confidence that any future underground nuclear explosion is not screened out. Here, m (sub b) and M (sub s) magnitudes for 409 past underground nuclear explosions are collated and presented. The magnitudes include new measurements, an archive of historical measurements made over the years at AWE Blacknest, and a reworking of bulletin data. The revised m (sub b) :M (sub s) screening line based on these magnitudes is M (sub s) =m (sub b) -0.64. The effect of the revised line on event screening at the IDC is assessed. It is found that the new criterion screens out 42% of a set of events from 2008, whereas the old criterion screened out 87%, which is a large reduction. The revised provisional m (sub b) :M (sub s) screening line was agreed upon by the Waveform Expert Group at Working Group B of the CTBT Preparatory Commission in February 2010 and has been tested in operations at the IDC since 3 June 2010.