pulsar_spectra: A pulsar flux density catalogue and spectrum fitting repository

We present the pulsar_spectra software repository, an open-source pulsar flux density catalogue and automated spectral fitting software that finds the best spectral model and produces publication-quality plots. The Python-based software includes features that enable users in the astronomical community to add newly published spectral measurements to the catalogue as they become available. The spectral fitting software is an implementation of the method described in Jankowski et al. (2018) which uses robust statistical methods to decide on the best-fitting model for individual pulsar spectra. pulsar_spectra is motivated by the need for a centralised repository for pulsar flux density measurements to make published measurements more accessible to the astronomical community and provide a suite of tools for measuring spectra

libAnnotationSBML: a library for exploiting SBML annotations

Summary: The Systems Biology Markup Language (SBML) is an established community XML format for the markup of biochemical models. With the introduction of SBML level 2 version 3, specific model entities, such as species or reactions, can now be annotated using ontological terms. These annotations, which are encoded using the resource description framework (RDF), provide the facility to specify definite terms to individual components, allowing software to unambiguously identify such components and thus link the models to existing data resources

MWA Tied-Array Processing IV: A Multi-Pixel Beamformer for Pulsar Surveys and Ionospheric Corrected Localisation

The Murchison Widefield Array (MWA) is a low-frequency aperture array capable of high-time and frequency resolution astronomy applications such as pulsar studies. The large field-of-view of the MWA (hundreds of square degrees) can also be exploited to attain fast survey speeds for all-sky pulsar search applications, but to maximise sensitivity requires forming thousands of tied-array beams from each voltage-capture observation. The necessity of using calibration solutions that are separated from the target observation both temporally and spatially makes pulsar observations vulnerable to uncorrected, frequency-dependent positional offsets due to the ionosphere. These offsets may be large enough to move the source away from the centre of the tied-array beam, incurring sensitivity drops of $\sim$30-50\% in Phase II extended array configuration. We analyse these offsets in pulsar observations and develop a method for mitigating them, improving both the source position accuracy and the sensitivity. This analysis prompted the development of a multi-pixel beamforming functionality that can generate dozens of tied-array beams simultaneously, which runs a factor of ten times faster compared to the original single-pixel version. This enhancement makes it feasible to observe multiple pulsars within the vast field of view of the MWA and supports the ongoing large-scale pulsar survey efforts with the MWA. We explore the extent to which ionospheric offset correction will be necessary for the MWA Phase III and the low-frequency Square Kilometre Array (SKA-Low).Comment: 10 pages, 5 figure

A targeted search for repeating fast radio bursts with the MWA

We present a targeted search for low-frequency (144--215\,MHz) FRB emission from five repeating FRBs using 23.3\,hr of archival data taken with the Murchison Widefield Array (MWA) Voltage Capture System (VCS) between 2014 September and 2020 May. This is the first time that the MWA VCS has been used to search for FRB signals from known repeaters, which enables much more sensitive FRB searches than previously performed with the standard MWA correlator mode. We performed a standard single pulse search with a temporal and spectral resolution of $400\,\mu$s and 10\,kHz, respectively, over a $100\,\text{pc}\,\text{cm}^{-3}$ dispersion measure (DM) range centred at the known DM of each studied repeating FRB. No FRBs exceeding a $6\sigma$ threshold were detected. The fluence upper limits in the range of 32--1175\,Jy\,ms and 36--488\,Jy\,ms derived from 10 observations of FRB 20190711A and four observations of FRB 20201124A respectively, allow us to constrain the spectral indices of their bursts to $\gtrsim-1$ if these two repeaters were active during the MWA observations. If free-free absorption is responsible for our non-detection, we can constrain the size of the absorbing medium in terms of the electron temperature $T$ to $<1.00\times(T/10^4\text{K})^{-1.35}\,\text{pc}$, $<0.92\times(T/10^4\text{K})^{-1.35}\,\text{pc}$ and $<[0.22\text{--}2.50]\times(T/10^4\text{K})^{-1.35}\,\text{pc}$ for FRB 20190117A, 20190711A, and 20201124A, respectively. However, given that the activities of these repeaters are not well characterised, our non-detections could also suggest they were inactive during the MWA observations.Comment: Accepted for publication in MNRA

Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description

Independent discovery of a nulling pulsar with unusual subpulse drifting properties with the Murchison Widefield Array

We report the independent discovery of PSR J0026-1955 with the Murchison Widefield Array (MWA) in the ongoing Southern-sky MWA Rapid Two-metre pulsar survey. J0026-1955 has a period of ∼1.306 s, a dispersion measure of ∼20.869 pc cm-3, and a nulling fraction of ∼77%. This pulsar highlights the advantages of the survey's long dwell times (∼80 minutes), which, when fully searched, will be sensitive to the expected population of similarly bright, intermittent pulsars with long nulls. A single-pulse analysis in the MWA's 140-170 MHz band also reveals a complex subpulse drifting behavior, including both rapid changes of the drift rate characteristic of mode switching pulsars, as well as a slow, consistent evolution of the drift rate within modes. In some longer drift sequences, interruptions in the otherwise smooth drift rate evolution occur preferentially at a particular phase, typically lasting a few pulses. These properties make this pulsar an ideal test bed for prevailing models of drifting behavior such as the carousel model

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

<p>Abstract</p> <p>Background</p> <p>Metabolic reconstructions (MRs) are common denominators in systems biology and represent biochemical, genetic, and genomic (BiGG) knowledge-bases for target organisms by capturing currently available information in a consistent, structured manner. <it>Salmonella enterica </it>subspecies I serovar Typhimurium is a human pathogen, causes various diseases and its increasing antibiotic resistance poses a public health problem.</p> <p>Results</p> <p>Here, we describe a community-driven effort, in which more than 20 experts in <it>S</it>. Typhimurium biology and systems biology collaborated to reconcile and expand the <it>S</it>. Typhimurium BiGG knowledge-base. The consensus MR was obtained starting from two independently developed MRs for <it>S</it>. Typhimurium. Key results of this reconstruction jamboree include i) development and implementation of a community-based workflow for MR annotation and reconciliation; ii) incorporation of thermodynamic information; and iii) use of the consensus MR to identify potential multi-target drug therapy approaches.</p> <p>Conclusion</p> <p>Taken together, with the growing number of parallel MRs a structured, community-driven approach will be necessary to maximize quality while increasing adoption of MRs in experimental design and interpretation.</p

A strategy to incorporate prior knowledge into correlation network cutoff selection

Correlation networks are frequently used to statistically extract biological interactions between omics markers. Network edge selection is typically based on the statistical significance of the correlation coefficients. This procedure, however, is not guaranteed to capture biological mechanisms. We here propose an alternative approach for network reconstruction: a cutoff selection algorithm that maximizes the overlap of the inferred network with available prior knowledge. We first evaluate the approach on IgG glycomics data, for which the biochemical pathway is known and well-characterized. Importantly, even in the case of incomplete or incorrect prior knowledge, the optimal network is close to the true optimum. We then demonstrate the generalizability of the approach with applications to untargeted metabolomics and transcriptomics data. For the transcriptomics case, we demonstrate that the optimized network is superior to statistical networks in systematically retrieving interactions that were not included in the biological reference used for optimization