Galaxy is an open-source project and an international development community has grown up that contributes improvements to the core software and, more importantly, to a growing pool of new tools and datatype definitions that can be added to individual Galaxy servers. These extensions are typically shared via the Galaxy Tool Shed [ 9], which is a public repository of tools and workflows, from where they can then be installed on individual Galaxy servers. Multiple tools were published in the past 2 years [ 10– 13].

The Basic Local Alignment Search Tool (BLAST) [ 1] has arguably become the best known and most widely used bioinformatics tool in molecular biology. Indeed, BLAST is now so ubiquitous that this term, like PCR (polymerase chain reaction), has become both a noun and a verb in the patois of molecular biology, with the acronym rarely spelt out, and is unfortunately frequently used without citation.

We may be witnessing the death of a galaxy

Proteogenomics combines genomic information with mass-spectrometry-derived experimental data for proteomic analysis. To search for evidence of novel proteins, the databases for proteomics search applications are generated from six-frame translations of genomics or transcript sequences or cDNA transcripts. With such large databases, proteomics search applications generate a large number of peptide spectral matches (PSMs). The University of Minnesota developed workflows in Galaxy-P ( https://usegalaxyp.org/) to automate proteogenomic analysis [ 30]. These workflows use the NCBI BLAST+ wrappers to compare the PSM peptides to known proteins to filter the PSM list for those that are more likely to be novel. An additional protein-protein BLAST (BLASTP) wrapper was deployed in Galaxy-P to use the remote search option of BLASTP to perform taxon-specific searches on NCBI servers. Implementation

Roberts and his colleagues say the data show some evidence of seismic vibrations during the eruption. The highest-energy X-rays recorded by Fermi’s GBM reached 3 million electron volts (MeV), or about a million times the energy of blue light, itself a record for giant flares. The researchers say this emission arose from a cloud of ejected electrons and positrons moving at about 99% the speed of light. The short duration of the emission and its changing brightness and energy reflect the magnetar’s rotation, ramping up and down like the headlights of a car making a turn. Roberts describes it as starting off as an opaque blob – he pictures it as resembling a photon torpedo from the “Star Trek” franchise – that expands and diffuses as it travels. The April 15 flare proves that these events constitute their own class of GRBs. Eric Burns, an assistant professor of physics and astronomy at Louisiana State University in Baton Rouge, led a study investigating additional suspects using data from numerous missions. The findings will appear in The Astrophysical Journal Letters. Bursts near the galaxy M81 in 2005 and the Andromeda galaxy (M31) in 2007 had already been suggested to be giant flares, and the team additionally identified a flare in M83, also seen in 2007 but newly reported. Add to these the giant flare from 1979 and those observed in our Milky Way in 1998 and 2004. Cuccuru G, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, et al. Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics. 2014;30(13):1928–9. This article describes our NCBI BLAST+ [ 16] wrappers for Galaxy and associated tools and datatype definitions. Currently, these tools have not been made available at the public server hosted by the Galaxy Project owing to concerns over the resulting computational load (J Taylor, personal communication, 2013). However, they are available from the Galaxy Tool Shed for automated installation into a local Galaxy instance, or from our source code repository (hosted by GitHub, Inc., see Availability and requirements section), and are released under the open-source Massachusetts Institute of Technology (MIT) licence. ApplicationsThe Amaterasu particle has an energy exceeding 240 exa-electron volts (EeV), millions of times more than particles produced in the Large Hadron Collider, the most powerful accelerator ever built, and equivalent to the energy of a golf ball travelling at 95mph. It comes only second to the Oh-My-God particle, another ultra-high-energy cosmic ray that came in at 320 EeV, detected in 1991. Rarely, magnetars produce enormous eruptions called giant flares that produce gamma rays, the highest-energy form of light. myExperiment Galaxy workflow for the identification of candidate genes clusters: http://www.myexperiment.org/workflows/4584.html

The Hubble Space Telescope is a project of international cooperation between NASA and ESA (European Space Agency). Goddard manages the telescope. The Space Telescope Science Institute (STScI) in Baltimore conducts science operations. STScI is operated for NASA by the Association of Universities for Research in Astronomy, in Washington, D.C.As the CLC Assembly Cell software is proprietary, our exemplar workflow, available from the Galaxy Tool Shed [ 22] and myExperiment [ 23], starts from a previously generated or imported transcriptome assembly. This workflow analyses a sample of 1000 sequences only and uses Galaxy data manipulation tools to produce a sorted tally table of species hits suitable for visualization within Galaxy as a pie chart.