Automated data reduction workflows for astronomy

Data from complex modern astronomical instruments often consist of a large number of different science and calibration files, and their reduction requires a variety of software tools. The execution chain of the tools represents a complex workflow that needs to be tuned and supervised, often by individual researchers that are not necessarily experts for any specific instrument. The efficiency of data reduction can be improved by using automatic workflows to organise data and execute the sequence of data reduction steps. To realize such efficiency gains, we designed a system that allows intuitive representation, execution and modification of the data reduction workflow, and has facilities for inspection and interaction with the data. The European Southern Observatory (ESO) has developed Reflex, an environment to automate data reduction workflows. Reflex is implemented as a package of customized components for the Kepler workflow engine. Kepler provides the graphical user interface to create an executable flowchart-like representation of the data reduction process. Key features of Reflex are a rule-based data organiser, infrastructure to re-use results, thorough book-keeping, data progeny tracking, interactive user interfaces, and a novel concept to exploit information created during data organisation for the workflow execution. Reflex includes novel concepts to increase the efficiency of astronomical data processing. While Reflex is a specific implementation of astronomical scientific workflows within the Kepler workflow engine, the overall design choices and methods can also be applied to other environments for running automated science workflows.Comment: 12 pages, 7 figure

MUSE library of stellar spectra

Context. Empirical stellar spectral libraries have applications in both extragalactic and stellar studies, and they confer an advantage over theoretical libraries because they naturally include all relevant chemical species and physical processes. In recent years we have seen a stream of new sets of high-quality spectra, but increasing the spectral resolution and widening the wavelength coverage means resorting to multi-order echelle spectrographs. Assembling the spectra from many pieces results in lower fidelity of their shapes. Aims: We aim to offer the community a library of high-signal-to-noise spectra with reliable continuum shapes. Furthermore, the use of an integral field unit (IFU) alleviates the issue of slit losses. Methods: Our library was built with the MUSE (Multi-Unit Spectroscopic Explorer) IFU instrument. We obtained spectra over nearly the entire visual band (lambda ~ 4800-9300 AA). Results: We assembled a library of 35 high-quality MUSE spectra for a subset of the stars from the X-shooter Spectral Library. We verified the continuum shape of these spectra with synthetic broadband colors derived from the spectra. We also report some spectral indices from the Lick system, derived from the new observations. Conclusions: We offer a high-fidelity set of stellar spectra covering the Hertzsprung-Russell diagram. These can be used for both extragalactic and stellar studies and demonstrate that the IFUs are excellent tools for building reliable spectral libraries

Astro-WISE: Chaining to the Universe

The recent explosion of recorded digital data and its processed derivatives threatens to overwhelm researchers when analysing their experimental data or when looking up data items in archives and file systems. While current hardware developments allow to acquire, process and store 100s of terabytes of data at the cost of a modern sports car, the software systems to handle these data are lagging behind. This general problem is recognized and addressed by various scientific communities, e.g., DATAGRID/EGEE federates compute and storage power over the high-energy physical community, while the astronomical community is building an Internet geared Virtual Observatory, connecting archival data. These large projects either focus on a specific distribution aspect or aim to connect many sub-communities and have a relatively long trajectory for setting standards and a common layer. Here, we report "first light" of a very different solution to the problem initiated by a smaller astronomical IT community. It provides the abstract "scientific information layer" which integrates distributed scientific analysis with distributed processing and federated archiving and publishing. By designing new abstractions and mixing in old ones, a Science Information System with fully scalable cornerstones has been achieved, transforming data systems into knowledge systems. This break-through is facilitated by the full end-to-end linking of all dependent data items, which allows full backward chaining from the observer/researcher to the experiment. Key is the notion that information is intrinsic in nature and thus is the data acquired by a scientific experiment. The new abstraction is that software systems guide the user to that intrinsic information by forcing full backward and forward chaining in the data modelling.Comment: To be published in ADASS XVI ASP Conference Series, 2006, R. Shaw, F. Hill and D. Bell, ed

Notitie Denktank Overlijdensschade. Nieuwe richting benadering en berekening overlijdensschade

In 2009 is een werkgroep onder de naam Denktank Overlijdensschade gestart met het bestuderen van een ander, aan de huidige tijd aangepast model voor de berekening van overlijdensschade. Doelstelling was te komen tot een, ook voor nabestaanden, transparantie systematiek welke recht doet aan de vorderingsgerechtigdheid van de nabestaanden. In 2014 heeft de Denktank Overlijdensschade haar werkzaamheden voltooid met het opleveren van een nieuwe rekenmethodiek. In deze Notitie wordt beschreven hoe de Denktank tot deze nieuwe benadering van het berekenen van overlijdensschade is gekomen, welke onderzoeken daaraan ten grondslag liggen en wat de uiteindelijke rekenregel is, die nu voorgesteld wordt. Kern van de nieuwe methodiek is het uitgangspunt dat het gezin als economische eenheid wordt beschouwd, voor én na het overlijden

Detection of a Thick Disk in the edge-on Low Surface Brightness Galaxy ESO 342-G017: I. VLT Photometry in V and R Bands

We report the detection of a thick disk in the edge-on, low surface brightness (LSB), late-type spiral ESO 342-G017, based on ultra-deep images in the V and R bands obtained with the VLT Test Camera during Science Verification on UT1. All steps in the reduction procedure are fully described, which, together with an extensive analysis of systematic and statistic uncertainties, has resulted in surface brightness photometry that is reliable for the detection of faint extended structure to a level of V = 27.5 and R = 28.5 mag/square arcsec. The faint light apparent in these deep images is well-modeled by a thick exponential disk with an intrinsic scale height about 2.5 times that of the thin disk, and a comparable or somewhat larger scale length. Deprojection including the effects of inclination and convolution with the PSF allow us to estimate that the thick disk contributes 20-40% of the total (old) stellar disk luminosity of ESO 342-G017. To our knowledge, this is the first detection of a thick disk in an LSB galaxy, which are generally thought to be rather unevolved compared to higher surface brightness galaxies.Comment: Accepted for publication in Astronomy & Astrophysics; 18 pages, 12 figure

The JVAS/CLASS search for 6-arcsec to 15-arcsec image separation lensing

The Jodrell Bank-VLA Astrometric Survey (JVAS) and the Cosmic Lens All Sky Survey (CLASS) have been systematically searched for multiple gravitational imaging of sources with image separations between 6 arcsec and 15 arcsec, associated with galaxy group and cluster lensing masses. The radio and optical follow-up observations of all candidates are presented. From a total of similar to 15000 sources only one weak candidate remains and this is not contained in the statistically complete sample of flat-spectrum JVAS/CLASS sources of 11670 sources. A simple Press-Schechter analysis is performed. For singular isothermal sphere lenses the lack of multiple image systems is inconsistent with the currently favoured cosmologies with (Omega (M), Omega (A)) = (0.3, 0.7) at the 4.2 sigma level. Cored isothermal lenses reduce the expected number of lens systems and we suggest that the most probable interpretation of our results is that the surface mass density of groups and clusters of galaxies is not high enough to cause multiple imaging and the presence of the mass concentrations associated with individual galaxies is required to produce image separations such as those in B0957+561

The Enhanced Resolution Imager and Spectrograph for the VLT

ERIS, the Enhanced Resolution Imager and Spectrograph, is an instrument that both extends and enhances the fundamental diffraction limited imaging and spectroscopy capability for the VLT. It replaces two instruments that were being maintained beyond their operational lifetimes, combines their functionality on a single focus, provides a new wavefront sensing module for natural and laser guide stars that makes use of the Adaptive Optics Facility, and considerably improves on their performance. The observational modes ERIS provides are integral field spectroscopy at 1-2.5 {\mu}m, imaging at 1-5 {\mu}m with several options for high contrast imaging, and longslit spectroscopy at 3-4 {\mu}m, The instrument is installed at the Cassegrain focus of UT4 at the VLT and, following its commissioning during 2022, has been made available to the community.Comment: 19 pages with 29 figures; submitted to A&

Host Specific Diversity in Lactobacillus johnsonii as Evidenced by a Major Chromosomal Inversion and Phage Resistance Mechanisms

Genetic diversity and genomic rearrangements are a driving force in bacterial evolution and niche adaptation. We sequenced and annotated the genome of Lactobacillus johnsonii DPC6026, a strain isolated from the porcine intestinal tract. Although the genome of DPC6026 is similar in size (1.97mbp) and GC content (34.8%) to the sequenced human isolate L. johnsonii NCC 533, a large symmetrical inversion of approximately 750 kb differentiated the two strains. Comparative analysis among 12 other strains of L. johnsonii including 8 porcine, 3 human and 1 poultry isolate indicated that the genome architecture found in DPC6026 is more common within the species than that of NCC 533. Furthermore a number of unique features were annotated in DPC6026, some of which are likely to have been acquired by horizontal gene transfer (HGT) and contribute to protection against phage infection. A putative type III restriction-modification system was identified, as were novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements. Interestingly, these particular elements are not widely distributed among L. johnsonii strains. Taken together these data suggest intra-species genomic rearrangements and significant genetic diversity within the L. johnsonii species and indicate towards a host-specific divergence of L. johnsonii strains with respect to genome inversion and phage exposure

Protein Glycosylation in Helicobacter pylori: Beyond the Flagellins?

Glycosylation of flagellins by pseudaminic acid is required for virulence in Helicobacter pylori. We demonstrate that, in H. pylori, glycosylation extends to proteins other than flagellins and to sugars other than pseudaminic acid. Several candidate glycoproteins distinct from the flagellins were detected via ProQ-emerald staining and DIG- or biotin- hydrazide labeling of the soluble and outer membrane fractions of wild-type H. pylori, suggesting that protein glycosylation is not limited to the flagellins. DIG-hydrazide labeling of proteins from pseudaminic acid biosynthesis pathway mutants showed that the glycosylation of some glycoproteins is not dependent on the pseudaminic acid glycosylation pathway, indicating the existence of a novel glycosylation pathway. Fractions enriched in glycoprotein candidates by ion exchange chromatography were used to extract the sugars by acid hydrolysis. High performance anion exchange chromatography with pulsed amperometric detection revealed characteristic monosaccharide peaks in these extracts. The monosaccharides were then identified by LC-ESI-MS/MS. The spectra are consistent with sugars such as 5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic acid (Pse5Ac7Ac) previously described on flagellins, 5-acetamidino-7-acetamido-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic acid (Pse5Am7Ac), bacillosamine derivatives and a potential legionaminic acid derivative (Leg5AmNMe7Ac) which were not previously identified in H. pylori. These data open the way to the study of the mechanism and role of protein glycosylation on protein function and virulence in H. pylori