Giant flares from magnetars in the Milky Way and its satellites evolve in a distinct way, with a rapid rise to peak brightness followed by a more gradual tail of fluctuating emission. These variations result from the magnetar’s rotation, which repeatedly brings the flare location in and out of view from Earth, much like a lighthouse. 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?”.

Shortly before 4:42 a.m. EDT on April 15, 2020, a brief, powerful burst of X-rays and gamma rays swept past Mars, triggering the Russian High Energy Neutron Detector aboard NASA’s Mars Odyssey spacecraft, which has been orbiting the Red Planet since 2001. About 6.6 minutes later, the burst triggered the Russian Konus instrument aboard NASA’s Wind satellite, which orbits a point between Earth and the Sun located about 930,000 miles (1.5 million kilometers) away. After another 4.5 seconds, the radiation passed Earth, triggering instruments on NASA’s Fermi Gamma-ray Space Telescope, as well as on the European Space Agency’s INTEGRAL satellite and Atmosphere-Space Interactions Monitor (ASIM) aboard the International Space Station. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752 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].MAdLand is a database of fully sequenced plant and algal genomes, with an emphasis on non-seed plants and streptophyte algae that can be use for sequence similarity search. Future work will include additional wrappers for the remaining or new BLAST+ command line tools, exposing additional command line options via the Galaxy interface, and additional output file formats. Developments within Galaxy will also allow new functionality. For example, we hope to build on the Galaxy Visual Analysis Framework [ 40] to offer graphical representation of BLAST results within Galaxy, such as that offered by the NCBI web service. Similarly, managing local BLAST databases could be facilitated using the Data Manager Framework [ 35]. A team led by Benjamin Gompertz, an astrophysicist at the University of Birmingham in the United Kingdom, looked at the entire high-energy light curve, or the evolution of the event’s brightness over time. The scientists noted features that might provide a key for identifying similar incidents – long bursts from mergers – in the future, even ones that are dimmer or more distant. The more astronomers can find, the more they can refine their understanding of this new class of phenomena. 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.” This approach screens two proteins against all nucleotide sequences from the NCBI nucleotide sequence database (NCBI NT) within hours on our cluster, which leads to the identification of all organisms with an interesting gene structure for further investigation. As usual in Galaxy workflows, every parameter, including the proximity distance, can be changed and additional steps can be easily added. For example, additional filtering to refine the initial BLAST hits, or inclusion of a third query sequence, can be added. Identifying novel proteins

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. Simona Giacintucci, of the Naval Research Laboratory in Washington DC, the lead author of the study, described the blast as an astronomical version of the eruption of Mount St Helens in 1980, which ripped off the top of the volcano. “A key difference is that you could fit 15 Milky Way galaxies in a row into the crater this eruption punched into the cluster’s hot gas,” she said. 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. Many of the underlying tools wrapped for Galaxy run in a single thread, using only one CPU at any one time. Some of the wrappers described in this manuscript attain a significant speedup relative to the standalone tool, by dividing the input data into batches and running a separate instance of the underlying tool, in parallel, on each batch of data. This process is completely transparent to the user, and allows the BLAST+ wrappers, for example, to specify that input FASTA query files should be broken up into batches of 1000 sequences, and the resulting BLAST output files merged afterwards. Distributing the input data in this way also provides opportunity for data sanitisation, such as the removal of extremely long FASTA description lines (which can cause some of the wrapped tools to fail), and avoids any hard coded limits on the number of sequences supported by some tools (e.g., SignalP v3.0 has a built in default limit of 4000 input sequences).

An explosion on an unprecedented scale 

Galaxy Tool Shed Repository “find_genes_located_nearby_workflow”: https://toolshed.g2.bx.psu.edu/view/bgruening/find_genes_located_nearby_workflow/ Fischbach M, Voigt CA. Prokaryotic gene clusters: A rich toolbox for synthetic biology. Biotechnol J. 2010;5(12):1277–96. Run a fast assembler such as the CLC Assembly Cell (CLC bio, Aarhus, Denmark) which we have wrapped for use within Galaxy to generate an initial set of contigs [ 21].

Identification and analysis of gene clusters is an important task in synthetic biology [ 26, 27]. Unfortunately, identifying candidate gene clusters is complex and can take hours for a single genome. However, with prior knowledge about the expected genes in a cluster, the genome can be screened in a way that limits the search space dramatically. Observing this fluctuating tail is conclusive evidence of a giant flare. Seen from millions of light-years away, though, this emission is too dim to detect with today’s instruments. Because these signatures are missing, giant flares in our galactic neighborhood may be masquerading as much more distant and powerful merger-type GRBs. 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.” Blankenberg D, Johnson JE, Taylor J, Nekrutenko A, The Galaxy Team. Wrangling Galaxy’s reference data. Bioinformatics. 2014;30(13):1917–9.

The IPN placed the April 15 burst, called GRB 200415A, squarely in the central region of NGC 253, a bright spiral galaxy located about 11.4 million light-years away in the constellation Sculptor. This is the most precise sky position yet determined for a magnetar located beyond the Large Magellanic Cloud, a satellite of our galaxy and host to a giant flare in 1979, the first ever detected. Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, et al. Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. J Proteome Res. 2014;13(12):5898–908. Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T. BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics. 2010;26(20):2617–9. The ability to generate rapidly large amounts of genomic and transcriptomic sequence data for non-model organisms has enabled comparative genomic studies of a large number of plant pathogen effectors ( Haas et al., 2009; Baltrus et al., 2011). Prior to the commonplace production of genome scale data, manual workflows for functional characterisation of effector sequences, often involving copying and pasting sequences into online tools like NCBI BLAST ( Altschul et al., 1990; Camacho et al., 2009) were tractable. These labour-intensive approaches are impractical with large datasets, for which automated large-scale analyses become necessary. Adopting an automated workflow also brings benefits as, even when the level of data would be manageable, manual analyses can be difficult to reproduce without meticulous record keeping. This can affect the consistency of work within a research group, and also the utility of published literature, where the level of detail in the computational methods section can be inadequate for replication. Automated analyses are usually repeatable, and both the analytical processes and results can be logged in great detail, in a searchable framework. Andrea Tiengo, Scuola Universitaria Superiore IUSS Pavia, Italy, and a team of astronomers have analysed the data to derive the most accurate distance to each of these dust clouds. “The first cloud it hit appears to be on the very edge of our galaxy, far from where galactic dust clouds are usually observed,” Andrea says. The team then inferred the properties of the dust grains in the clouds because the X-rays are scattered according to the size, shape and composition of the dust.