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The Fermi, Swift, Wind, Mars Odyssey and INTEGRAL missions all participate in a GRB-locating system called the InterPlanetary Network (IPN). Now funded by the Fermi project, the IPN has operated since the late 1970s using different spacecraft located throughout the solar system. Because the signal reached each detector at different times, any pair of them can help narrow down a burst’s location in the sky. The greater the distances between spacecraft, the better the technique’s precision. Blankenberg D, Johnson JE, Taylor J, Nekrutenko A, The Galaxy Team. Wrangling Galaxy’s reference data. Bioinformatics. 2014;30(13):1917–9. A number of other ESA spacecraft, XMM-Newton, Solar Orbiter, BepiColombo, Gaia, and SOHO, also detected the GRB or its effects on our galaxy. The event was so bright that even today the residual radiation, known as the afterglow, is still visible and will remain so for a long time yet. “We will see the afterglow of this event for years to come,” says Volodymyr Savchenko, University of Geneva, Switzerland, who is currently analysing the Integral data.
Being much further away, around two billion light-years instead of several tens of thousands, meant that the GRB had to be exceptionally bright. Things that people think of as energetic, like supernova, are nowhere near energetic enough for this,” said Matthews. “You need huge amounts of energy, really high magnetic fields, to confine the particle while it gets accelerated.” It’s a small sample, but we now have a better idea of their true energies, and how far we can detect them,” Burns said. “A few percent of short GRBs may really be magnetar giant flares. In fact, they may be the most common high-energy outbursts we’ve detected so far beyond our galaxy – about five times more frequent than supernovae.” GRBs, the most powerful explosions in the cosmos, can be detected across billions of light-years. Those lasting less than about two seconds, called short GRBs, occur when a pair of orbiting neutron stars – both the crushed remnants of exploded stars – spiral into each other and merge. Astronomers confirmed this scenario for at least some short GRBs in 2017, when a burst followed the arrival of gravitational waves – ripples in space-time – produced when neutron stars merged 130 million light-years away. Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004;32 suppl 2:W327–31.
This may be a black hole slurping up a cloud of gas and dust
Most of the 29 magnetars now cataloged in our Milky Way galaxy exhibit occasional X-ray activity, but only two have produced giant flares. The most recent event, detected on Dec. 27, 2004, produced measurable changes in Earth’s upper atmosphere despite erupting from a magnetar located about 28,000 light-years away. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752 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. We now briefly outline several example workflows made possible by the tools and wrappers we describe in this manuscript. General tools for “Next Generation Sequencing” (NGS) are especially well served in Galaxy. However, the more specialised the tools become (typically, the further downstream your analysis), the less likely it is that a specific desired tool has already been wrapped for use in Galaxy. Although we have also implemented wrappers to facilitate basic genome assembly and gene calling, here we focus on what happens after assembly and gene calling has been performed, to answer the question “What can be learned from the predicted gene complement of a newly sequenced organism?”. The ionosphere, which helps protect life on Earth by absorbing harmful ultraviolet rays from the sun, is highly sensitive to changing magnetic and electrical conditions in space, usually connected to solar activity. It also expands and contracts in response to solar radiation.
Together, these tools can be used in a basic workflow that takes raw sequencing data as input, yielding a whole organism gene set that can be further analysed: A pulse of X-rays and gamma rays lasting just 140 milliseconds swept across the solar system on April 15, 2020. The event was a giant flare from a magnetar, a type of city-sized stellar remnant that boasts the strongest magnetic fields known. Watch to learn more.Over the years, astronomers have proposed a number of different properties for the dust grains and so Andrea and colleagues were able to test them against the X-ray data. They found that one model reproduced the rings extremely well. In this model, the dust grains were composed mostly of graphite, a crystalline form of carbon. They also used their data to reconstruct the X-ray emission from the GRB itself because that particular signal was not observed directly by any instrument. 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. Giant flares within our galaxy are so brilliant that they overwhelm our instruments, leaving them to hang onto their secrets,” Roberts said. “For the first time, GRB 200415A and distant flares like it allow our instruments to capture every feature and explore these powerful eruptions in unparalleled depth.” Statistically, a GRB as bright as GRB 221009A is only expected to happen once in many thousands of years, it may even be the brightest gamma-ray burst since human civilisation began. Astronomers therefore dubbed it BOAT – the brightest of all time. Galaxy Tool Shed Repository “Filter sequences by ID”: https://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/
On Dec. 11, 2021, NASA’s Neil Gehrels Swift Observatory and Fermi Gamma-ray Space Telescope detected a blast of high-energy light from the outskirts of a galaxy around 1 billion light-years away. The event has rattled scientists’ understanding of gamma-ray bursts (GRBs), the most powerful events in the universe.
An explosion on an unprecedented scale
As sequencing costs have fallen, for many organisms it is now practical to sequence the entire genome when interested primarily in a single gene family. In this situation, BLAST might be used within Galaxy as follows: Over the past few decades the BLAST suite has grown, with improvements such as gapped searches [ 36] and additional functionality such as Position-Specific Iterated BLAST (PSI-BLAST) [ 36, 37] and protein-domain searches with Reverse Position-Specific BLAST (RPS-BLAST) [ 38]. These Position-Specific Score Matrix (PSSM)-based tools underpin the NCBI Conserved Domain Database (CDD) and the associated web-based Conserved Domain Search service (CD-Search) [ 38, 39]. More recently, the NCBI BLAST team undertook an ambitious rewrite of the BLAST tool suite, converting the existing ‘legacy’ code base, which was written in the C programming language, to the C++ language. The new version was dubbed BLAST+ [ 16]. The difference between your typical gamma-ray burst and this one is about the same as the difference between the light bulb in your living room and the lit-up floodlights in a sports stadium,” says Andrew Levan, Radbound University, the Netherlands, who used the NASA/ESA/CSA James Webb Space Telescope and the NASA/ESA Hubble Space Telescope to observe the burst. 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. Applications
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