The BioGRID Interaction Database: 2011 update

The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (http://www.thebiogrid.org). BioGRID currently holds 347 966 interactions (170 162 genetic, 177 804 protein) curated from both high-throughput data sets and individual focused studies, as derived from over 23 000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe) and thale cress (Arabidopsis thaliana), and efforts to expand curation across multiple metazoan species are underway. The BioGRID houses 48 831 human protein interactions that have been curated from 10 247 publications. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. The BioGRID 3.0 web interface contains new search and display features that enable rapid queries across multiple data types and sources. An automated Interaction Management System (IMS) is used to prioritize, coordinate and track curation across international sites and projects. BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene and other interaction meta-databases. The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including PSI MI XML. Source code for BioGRID 3.0 is freely available without any restrictions

A simple radionuclide-driven single-ion source

We describe a source capable of producing single barium ions through nuclear recoils in radioactive decay. The source is fabricated by electroplating 148Gd onto a silicon {\alpha}-particle detector and vapor depositing a layer of BaF2 over it. 144Sm recoils from the alpha decay of 148Gd are used to dislodge Ba+ ions from the BaF2 layer and emit them in the surrounding environment. The simultaneous detection of an {\alpha} particle in the substrate detector allows for tagging of the nuclear decay and of the Ba+ emission. The source is simple, durable, and can be manipulated and used in different environments. We discuss the fabrication process, which can be easily adapted to emit most other chemical species, and the performance of the source

A magnetically-driven piston pump for ultra-clean applications

A magnetically driven piston pump for xenon gas recirculation is presented. The pump is designed to satisfy extreme purity and containment requirements, as is appropriate for the recirculation of isotopically enriched xenon through the purification system and large liquid xenon TPC of EXO-200. The pump, using sprung polymer gaskets, is capable of pumping more than 16 standard liters per minute (SLPM) of xenon gas with 750 torr differential pressure.Comment: 6 pages, 5 figure

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. The new release 7.0 of the database has grown by an order of magnitude over the previous version and now includes 100 species and their collective 1.3 million proteins organized into 42.7 million pairwise ortholog groups. The InParanoid algorithm itself has been revised and is now both more specific and sensitive. Based on results from our recent benchmarking of low-complexity filters in homology assignment, a two-pass BLAST approach was developed that makes use of high-precision compositional score matrix adjustment, but avoids the alignment truncation that sometimes follows. We have also updated the InParanoid web site (http://InParanoid.sbc.su.se). Several features have been added, the response times have been improved and the site now sports a new, clearer look. As the number of ortholog databases has grown, it has become difficult to compare among these resources due to a lack of standardized source data and incompatible representations of ortholog relationships. To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters

Search for Neutrinoless Double-Beta Decay in 136^{136}Xe with EXO-200

We report on a search for neutrinoless double-beta decay of $^{136}$Xe with EXO-200. No signal is observed for an exposure of 32.5 kg-yr, with a background of ~1.5 x 10^{-3} /(kg yr keV) in the $\pm 1\sigma$ region of interest. This sets a lower limit on the half-life of the neutrinoless double-beta decay $T_{1/2}^{0\nu\beta\beta}$($^{136}$Xe) > 1.6 x 10$^{25}$ yr (90% CL), corresponding to effective Majorana masses of less than 140-380 meV, depending on the matrix element calculation

Gene Ontology annotations at SGD: new data sources and annotation methods

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current