Shared Bioinformatics Databases within the Unipro UGENE Platform

Unipro UGENE is an open-source bioinformatics toolkit that integrates popular tools along with original instruments for molecular biologists within a unified user interface. Nowadays, most bioinformatics desktop applications, including UGENE, make use of a local data model while processing different types of data. Such an approach causes an inconvenience for scientists working cooperatively and relying on the same data. This refers to the need of making multiple copies of certain files for every workplace and maintaining synchronization between them in case of modifications. Therefore, we focused on delivering a collaborative work into the UGENE user experience. Currently, several UGENE installations can be connected to a designated shared database and users can interact with it simultaneously. Such databases can be created by UGENE users and be used at their discretion. Objects of each data type, supported by UGENE such as sequences, annotations, multiple alignments, etc., can now be easily imported from or exported to a remote storage. One of the main advantages of this system, compared to existing ones, is the almost simultaneous access of client applications to shared data regardless of their volume. Moreover, the system is capable of storing millions of objects. The storage itself is a regular database server so even an inexpert user is able to deploy it. Thus, UGENE may provide access to shared data for users located, for example, in the same laboratory or institution. UGENE is available at: http://ugene.net/download.html

The effect of methylfurans on the physicochemical and performance characteristics of finished motor gasoline

The physicochemical and performance characteristics of blends of commercial gasoline with the promising oxygenate antiknock additives 2-methylfuran and 2,5-dimethylfuran have been studied. The key parameters determining the compliance of gasoline with the GOST R 51866-2002 (EN 228-2004) requirements have been measured. A high antiknock activity of the test compounds has been demonstrated, and blending octane numbers have been calculated. It has also been found that the addition of 2-methylfuran and 2,5-dimethylfuran to gasoline substantially deteriorates its oxidation stability and increases gum content

OTR measurements and modeling of the electron beam optics at the E-cooling facility

Optics of the electron beam accelerated in the Pelletron, intended for the electron cooling of 8.9 GeV antiprotons in the Fermilab recycler storage ring, has been studied. The beam profile parameters were measured under the accelerating section using Optical Transition Radiation (OTR) monitor. The monitor employs a highly-reflective 2 inch-diameter aluminum OTR-screen with a thickness of 5 {micro}m and a digital CCD camera. The measurements were done in a pulse-signal mode in the beam current range of 0.03-0.8 A and at pulse durations ranging from 1 {micro}s to 4 {micro}s. Differential profiles measured in pulsed mode are compared with results obtained by modeling of the DC beam dynamics from the Pelletron cathode to the OTR monitor. The modeling was done with SAM, ULTRASAM and BEAM programs. An adjustment of the magnetic fields in the lenses of the accelerating section was done in the simulations. The simulated electron beam optics downstream of the accelerating section was in good agreement with the measurements made with pulsed beam

Optics of electron beam in the Recycler

Electron cooling of 8.9 GeV/c antiprotons in the Recycler ring (Fermilab) requires high current and good quality of the DC electron beam. Electron trajectories of {approx}0.2 A or higher DC electron beam have to be parallel in the cooling section, within {approx}0.2 mrad, making the beam envelope cylindrical. These requirements yielded a specific scheme of the electron transport from a gun to the cooling section, with electrostatic acceleration and deceleration in the Pelletron. Recuperation of the DC beam limits beam losses at as tiny level as {approx}0.001%, setting strict requirements on the return electron line to the Pelletron and a collector. To smooth the beam envelope in the cooling section, it has to be linear and known at the transport start. Also, strength of the relevant optic elements has to be measured with good accuracy. Beam-based optic measurements are being carried out and analyzed to get this information. They include beam simulations in the Pelletron, differential optic (beam response) measurements and simulation, beam profile measurements with optical transition radiation, envelope measurements and analysis with orifice scrapers. Current results for the first half-year of commissioning are presented. Although electron cooling is already routinely used for pbar stacking, its efficiency is expected to be improved

A global database of soil nematode abundance and functional group composition

As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.Peer reviewe

Soil nematode abundance and functional group composition at a global scale

Soil organisms are a crucial part of the terrestrial biosphere. Despite their importance for ecosystem functioning, few quantitative, spatially explicit models of the active belowground community currently exist. In particular, nematodes are the most abundant animals on Earth, filling all trophic levels in the soil food web. Here we use 6,759 georeferenced samples to generate a mechanistic understanding of the patterns of the global abundance of nematodes in the soil and the composition of their functional groups. The resulting maps show that 4.4 ± 0.64 × 1020 nematodes (with a total biomass of approximately 0.3 gigatonnes) inhabit surface soils across the world, with higher abundances in sub-Arctic regions (38% of total) than in temperate (24%) or tropical (21%) regions. Regional variations in these global trends also provide insights into local patterns of soil fertility and functioning. These high-resolution models provide the first steps towards representing soil ecological processes in global biogeochemical models and will enable the prediction of elemental cycling under current and future climate scenario

A global database of soil nematode abundance and functional group composition

This study uses direct measurements of soil nematode abundance from 6,825 georeferenced locations around the world, covering all continents and all terrestrial biomes. We describe the data sources, methodology and data processing steps to transform the data into a version that can be used for, for example, geospatial modeling. To do so, the samples were aggregated to the 1-km2 pixel level, each pixel is linked to 73 global covariate layers. These include on soil physiochemical properties, and vegetation, climate, and topographic, anthropogenic, and spectral reflectance information