Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator

BACKGROUND: Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces) in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. RESULTS: We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reproduced or shared among users. Availability: (interactive), (download). CONCLUSION: From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous analytical tools

Competitive exclusion and Hebbian couplings in random generalised Lotka-Volterra systems

We study communities emerging from generalised random Lotka--Volterra dynamics with a large number of species with interactions determined by the degree of niche overlap. Each species is endowed with a number of traits, and competition between pairs of species increases with their similarity in trait space. This leads to a model with random Hopfield-like interactions. We use tools from the theory of disordered systems, notably dynamic mean field theory, to characterise the statistics of the resulting communities at stable fixed points and determine analytically when stability breaks down. Two distinct types of transition are identified in this way, both marked by diverging abundances, but differing in the behaviour of the integrated response function. At fixed points only a fraction of the initial pool of species survives. We numerically study the eigenvalue spectra of the interaction matrix between extant species. We find evidence that the two types of dynamical transition are, respectively, associated with the bulk spectrum or an outlier eigenvalue crossing into the right half of the complex plane.Comment: 14 pages, 9 figures + Supplemen

Irreversibility at macromolecular scales in the flake graphite of the lithium-ion battery anode.

Charging a commercial lithium-ion battery intercalates lithium into the graphite-based anode, creating various lithium carbide structures. Despite their economic importance, these structures and the dynamics of their charging-discharging transitions are not well-understood. We have videoed single microcrystals of high-quality, natural graphite undergoing multiple lithiation-delithiation cycles. Because the equilibrium lithium-carbide compounds corresponding to full, half, and one-third charge are gold, red, and blue respectively, video observations give direct insight into both the macromolecular structures and the kinematics of charging and discharging. We find that the transport during the first lithiation is slow and orderly, and follows the core-shell or shrinking annuli model with phase boundaries moving at constant velocities (i.e. non-diffusively). Subsequent lithiations are markedly different, showing transport that is both faster and disorderly, which indicates that the initially pristine graphite is irreversibly and considerably altered during the first cycle. In all cases deintercalation is not the time-reverse of intercalation. These findings both illustrate how lithium enters nearly defect-free host material, and highlight the differences between the idealized case and an actual, cycling graphite anode

Bioinformatic workflows : G-PIPE as an implementation

We present G-PIPE, a graphic pipeline generator for PISE that allows the definition of pipelines, parameterization of its component methods, and storage of metadata in XML formats. Our implementation goes beyond macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reproduced or shared among users. We also discuss the role of ontologies as as guidance systems in order to provide users with the possibility to define abstract work-flows, and execute them. A relevant baseline ontology is presented. Availability: http://if-web.imb.uq.edu.a

Route networks within the air transport system:A comparative study of two European low-cost airlines using network metrics

This paper presents a comparative analysis of the route networks of two European low-cost airlines in 2015. A case study is presented which highlights the key differences and similarities of their route network characteristics that they operate, aimed toward improving understanding of the current Air Transport System (ATS) for modeling and simulation purposes

A state level analyses of suicide and the COVID-19 pandemic in Mexico

BACKGROUND: While suicide rates in high- and middle-income countries appeared stable in the early stages of the pandemic, we know little about within-country variations. We sought to investigate the impact of COVID-19 on suicide in Mexico’s 32 states and to identify factors that may have contributed to observed variations between states. METHODS: Interrupted time-series analysis to model the trend in monthly suicides before COVID-19 (from Jan 1, 2010, to March 31, 2020), comparing the expected number of suicides derived from the model with the observed number for the remainder of the year (April 1 to December 31, 2020) for each of Mexico’s 32 states. Next, we modeled state-level trends using linear regression to study likely contributing factors at ecological level. RESULTS: Suicide increased slightly across Mexico during the first nine months of the pandemic (RR 1.03; 95%CI 1.01–1.05). Suicides remained stable in 19 states, increase in seven states (RR range: 1.12–2.04) and a decrease in six states (RR range: 0.46–0.88). Suicide RR at the state level was positively associated with population density in 2020 and state level suicide death rate in 2019. CONCLUSIONS: The COVID-19 pandemic had a differential effect on suicide death within the 32 states of Mexico. Higher population density and higher suicide rates in 2019 were associated with increased suicide. As the country struggles to cope with the ongoing pandemic, efforts to improve access to primary care and mental health care services (including suicide crisis intervention services) in these settings should be given priority. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12888-022-04095-8

Wintering Area DDE Source to Migratory White-Faced Ibis Revealed by Satellite Telemetry and Prey Sampling

Locations of contaminant exposure for nesting migratory species are difficult to fully understand because of possible additional sources encountered during migration or on the wintering grounds. A portion of the migratory white-faced ibis (Plegadis chihi) nesting at Carson Lake, Nevada continues to be exposed to dichloro-diphenyl-dichloroethylene (DDE) with no change, which is unusual, observed in egg concentrations between 1985 and 2000. About 45 to 63% of the earliest nesting segment shows reduced reproductive success correlated with elevated egg concentrations of \u3e 4 µg/g wet weight (ww). Local prey (primarily earthworms) near nests contained little DDE so we tracked the migration and wintering movements of 20 adult males during 2000-2004 to determine the possible source. At various wintering sites, we found a correlation (r2 = 0.518, P = 0.0125, N = 11) between DDE in earthworm composites and DDE in blood plasma of white-faced ibis wintering there, although the plasma was collected on their breeding grounds soon after arrival. The main source of DDE was wintering areas in the Mexicali Valley of Baja California Norte, Mexico, and probably the adjacent Imperial Valley, California, USA. This unusual continuing DDE problem for white-face ibis is associated with: the long-term persistence in soil of DDE; the earthworms’ ability to bioconcentrate DDE from soil; the proclivity of white-faced ibis to feed on earthworms in agricultural fields; the species extreme sensitivity to DDE in their eggs; and perhaps its life history strategy of being a “capital breeder”. We suggest surveying and sampling white-faced ibis eggs at nesting colonies, especially at Carson Lake, to monitor the continuing influence of DDE

Crystallization Of The CHAP Domain Of The Endolysin From Staphylococcus Aureus Bacteriophage K

CHAPK is the N-terminal cysteine, histidine-dependent amidohydrolase/peptidase domain (CHAP domain) of the Staphylococcus aureus bacteriophage K endolysin LysK. It is formed from the first 165 residues of LysK and functions by cleaving specific peptidoglycan peptide bonds, causing bacterial lysis. CHAPK can lyse S. aureus when applied exogenously, making it a good candidate for the treatment of multidrug-resistant Staphylococcus aureus infections. Here, the crystallization of CHAPK and the collection of native and derivative data to high resolution, which allowed structure solution, are reported. The structure may help to elucidate the mechanism of action and in the design of chimeric proteins or mutants with improved antibacterial activity