New Zealand eScience Infrastructure

Roundabouts are hastily spreading around the world, mainly because of their good safety performance, and several countries have recently updated their standards and guidelines. However, inconsistencies in design standards and practices are observed. In this paper, a critical review of the Australasian, EU, and US standards and guidelines is performed. As a result, key issues of the existing standards are identified, along with research areas to fill the knowledge gaps and recommendations for improvement in a case study, Italy. These recommendations are mainly based on the concepts of design flexibility and performance based design. Indeed, rigid standards, which do not really take into account safety and operational consequences of the design decisions and the need to balance opposing demands, might produce undesirable outcomes.

This report records and discusses the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3). The report includes a description of the keynote presentation of the workshop, which served as an overview of sustainable scientific software. It also summarizes a set of lightning talks in which speakers highlighted to-the-point lessons and challenges pertaining to sustaining scientific software. The final and main contribution of the report is a summary of the discussions, future steps, and future organization for a set of self-organized working groups on topics including developing pathways to funding scientific software; constructing useful common metrics for crediting software stakeholders; identifying principles for sustainable software engineering design; reaching out to research software organizations around the world; and building communities for software sustainability. For each group, we include a point of contact and a landing page that can be used by those who want to join that group’s future activities. The main challenge left by the workshop is to see if the groups will execute these activities that they have scheduled, and how the WSSSPE community can encourage this to happen.

The Aotearoa Genomic Data Repository (AGDR) is an initiative to provide a secure within-nation option for the storage, management and sharing of non-human genomic data generated from biological and environmental samples originating in Aotearoa New Zealand. This resource has been developed to follow the principles of Māori Data Sovereignty, and to enable the right of kaitiakitanga (guardianship), so that iwi, hapū and whānau (tribes, kinship groups and families) can effectively exercise their responsibilities as guardians over biological entities that they regard as taonga (precious or treasured). While the repository is designed to facilitate the sharing of data-making it findable by researchers and interoperable with data held in other genomic repositories-the decision-making process regarding who can access the data is entirely in the hands of those holding kaitiakitanga over each data set. No data are made available to the requesting researcher until the request has been approved, and the conditions for access (which can vary by data set) have been agreed to. Here we describe the development of the AGDR, from both a cultural perspective, and a technical one, and outline the processes that underpin its operation.

The California Department of Transportation is studying a pavement rehabilitation strategy that involves the pulverization of failed hot-mix asphalt (HMA) pavements and uses the pulverized material as a granular base material in the reconstruction of the pavement. Advantages of this technique include a reduction in the use of virgin aggregates, a reduction in the amount of construction traffic, and removal of the potential for reflective cracking from the existing pavement layers. The construction and performance of four pilot projects in District 2 in northeastern California were used to evaluate this rehabilitation strategy. The characteristics and performance of the pulverized material were evaluated by comprehensive laboratory and field testing. The laboratory testing covered basic index tests and comprehensive triaxial testing. Multistage repeated-load permanent strain triaxial tests on different material gradations, stress levels, moisture contents, with and without stabilizing agents (lime and cement), and the degree of compaction were used to investigate the resilient and permanent strain characteristics. Testing was conducted on saturated samples to evaluate the effect of saturation on the pulverized material. The effects of the number of load repetitions were also investigated. The performance of the pulverized material was also compared with two typical virgin aggregate base materials from California. A life cycle cost analysis of this rehabilitation technique when compared to a typical HMA overlay showed that the recycling option was cheaper in both the short term and over the life of the pavement.

Computational biology has provided widely used and powerful software tools for testing and making inferences about biological data. In the face of increasing volumes of data, heuristic methods that trade software speed for mathematical completeness must be employed. We are interested in whether trade-offs between speed and accuracy are reasonable. Also, what factors are indicative of accurate software? In this work we mine published benchmarks of computational biology software, we collect data on the relative accuracy and speed of different software and then test to see what factors influence accuracy e.g. speed, author reputation, journal impact or recency. We found that author reputation, journal impact, the number of citations, software speed and age are not reliable predictors of software accuracy. This implies that useful bioinformatics software is not only the domain of famous researchers, and that any researchers are capable of producing good software. In addition, we found that there exists an excessive number of slow and inaccurate software tools across multiple sub-disciplines of bioinformatics. Meanwhile, there are very few tools of middling accuracy and speed. We hypothesise that a strong publication bias is unduly influencing the publication and development of bioinformatic software tools. In other words, at present software that is not highly ranked on speed and not highly ranked on accuracy is difficult to publish due to editorial and reviewer practices. This leaves an unfortunate gap in the literature upon which future software refinements could be constructed.

2018 RSE international survey

BACKGROUND: The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each developing lymphocyte by a process called V(D)J recombination, which assembles specific, independent gene segments into mature composite genes. The full set of composite genes in an individual at a single point in time is referred to as the immune repertoire. V(D)J recombination is the distinguishing feature of adaptive immunity and enables effective immune responses against an essentially infinite array of antigens. Characterization of immune repertoires is critical in both basic research and clinical contexts. Recent technological advances in repertoire profiling via high-throughput sequencing have resulted in an explosion of research activity in the field. This has been accompanied by a proliferation of software tools for analysis of repertoire sequencing data. Despite the widespread use of immune repertoire profiling and analysis software, there is currently no standardized format for output files from V(D)J analysis. Researchers utilize software such as IgBLAST and IMGT/High V-QUEST to perform V(D)J analysis and infer the structure of germline rearrangements. However, each of these software tools produces results in a different file format, and can annotate the same result using different labels. These differences make it challenging for users to perform additional downstream analyses. RESULTS: To help address this problem, we propose a standardized file format for representing V(D)J analysis results. The proposed format, VDJML, provides a common standardized format for different V(D)J analysis applications to facilitate downstream processing of the results in an application-agnostic manner. The VDJML file format specification is accompanied by a support library, written in C++ and Python, for reading and writing the VDJML file format. CONCLUSIONS: The VDJML suite will allow users to streamline their V(D)J analysis and facilitate the sharing of scientific knowledge within the community. The VDJML suite and documentation are available from https://vdjserver.org/vdjml/ . We welcome participation from the community in developing the file format standard, as well as code contributions.

Quality training in computational skills for life scientists is essential to allow them to deliver robust, reproducible and cutting-edge research. A pan-European bioinformatics programme, ELIXIR, has adopted a well-established and progressive programme of computational lab and data skills training from Software and Data Carpentry, aimed at increasing the number of skilled life scientists and building a sustainable training community in this field. This article describes the Pilot action, which introduced the Carpentry training model to the ELIXIR community.

The 2024 Workflows Community Summit report presents the outcomes of a three-day international gathering that brought together 111 experts from 18 countries to discuss future trends and challenges in scientific workflows. The summit focused on six key areas: time-sensitive workflows, convergence of AI and HPC workflows, multi-facility workflows, heterogeneous HPC environments, user experience and interfaces, and FAIR computational workflows. Discussions highlighted emerging challenges such as integrating AI with traditional HPC, managing workflows across diverse facilities, addressing heterogeneity in computing environments, and ensuring workflows are findable, accessible, interoperable, and reusable (FAIR). The report outlines recent advances, ongoing challenges, and provides recommendations for each topic area, emphasizing the need for standardization, improved interoperability, and the development of more sophisticated tools and frameworks to support the evolving landscape of scientific workflows in the era of exascale computing and AI integration.

Cardiac surgeons face a significant degree of uncertainty when deciding upon coronary artery bypass graft configurations for patients with coronary artery disease. This leads to significant variation in preferred configuration between different surgeons for a particular patient. Additionally, for the majority of cases, there is no consensus regarding the optimal grafting strategy. This situation results in the tendency for individual surgeons to opt for a "one size fits all" approach and use the same grafting configuration for the majority of their patients neglecting the patient-specific nature of the diseased coronary circulation. Quantitative metrics to assess the adequacy of coronary bypass graft flows have recently been advocated for routine intraoperative use by cardiac surgeons. In this work, a novel patient-specific 1D-0D computational model called "COMCAB" is developed to provide the predictive haemodynamic parameters of functional graft performance that can aid surgeons to avoid configurations with grafts that have poor flow and thus poor patency. This model has significant potential for future expanded applications.

A high-quality reference genome can be a valuable resource for threatened species by providing a foundation to assess their evolutionary potential to adapt to future pressures such as environmental change. We assembled the genome of a female hihi (Notiomysits cincta), a threatened passerine bird endemic to Aotearoa New Zealand. The assembled genome is 1.06 Gb, and is of high quality and highly contiguous, with a contig N50 of 7.0 Mb, estimated QV of 44 and a BUSCO completeness of 96.8%. A male assembly of comparable quality was generated in parallel. A population linkage map was used to scaffold the autosomal contigs into chromosomes. Female and male sequence coverage and comparative genomics analyses were used to identify Z-, and W-linked contigs. In total, 94.6% of the assembly length was assigned to putative nuclear chromosome scaffolds. Native DNA methylation was highly correlated between sexes, with the W chromosome contigs more highly methylated than autosomal chromosomes and Z contigs. 43 differentially methylated regions were identified, and these may represent interesting candidates for the establishment or maintenance of sex differences. By generating a high-quality reference assembly of the heterogametic sex, we have created a resource that enables characterization of genome-wide diversity and facilitates the investigation of female-specific evolutionary processes. The reference genomes will form the basis for fine-scale assessment of the impacts of low genetic diversity and inbreeding on the adaptive potential of the species and will therefore enable tailored and informed conservation management of this threatened taonga (treasured) species.

Interpolation methods for vector fields whose components are staggered on horizontal Arakawa C or D grids are presented. The interpolation methods extend bilinear and area-weighted interpolation, which are widely used in Earth sciences, to work with vector fields (essentially discretized versions of differential 1-forms and 2-forms). The interpolation methods, which conserve the total flux and enforce Stokes’ theorem to near-machine accuracy, are a natural complement to discrete exterior calculus and finite element exterior calculus discretization methods.

Advances in sequencing technologies and declining costs are increasing the accessibility of large-scale biodiversity genomic datasets. To maximize the impact of these data, a careful, considered approach to data management is essential. However, challenges associated with the management of such datasets remain, exacerbated by uncertainty among the research community as to what constitutes best practices. As an interdisciplinary team with diverse data management experience, we recognize the growing need for guidance on comprehensive data management practices that minimize the risks of data loss, maximize efficiency for stand-alone projects, enhance opportunities for data reuse, facilitate Indigenous data sovereignty and uphold the FAIR and CARE Guiding Principles. Here, we describe four fictional personas reflecting differing user experiences with data management to identify data management challenges across the biodiversity genomics research ecosystem. We then use these personas to demonstrate realistic considerations, compromises and actions for biodiversity genomic data management. We also launch the Biodiversity Genomics Data Management Hub (https://genomicsaotearoa.github.io/data-management-resources/), containing tips, tricks and resources to support biodiversity genomics researchers, especially those new to data management, in their journey towards best practice. The Hub also provides an opportunity for those biodiversity researchers whose expertise lies beyond genomics and are keen to advance their data management journey. We aim to support the biodiversity genomics community in embedding data management throughout the research lifecycle to maximize research impact and outcomes.

Objectives Flow competition between coronary artery bypass grafts (CABG) and native coronary arteries is a significant problem affecting arterial graft patency. The objectives of this study were to compare the predictive hemodynamic flow resulting from various total arterial grafting configurations and to evaluate whether the use of computational fluid dynamics (CFD) models capable of predicting flow can assist surgeons to make better decisions for individual patients by avoiding poorly functioning grafts. Methods Sixteen cardiac surgeons declared their preferred CABG configuration using bilateral internal mammary and radial arteries for each of 5 patients who had differing degrees of severe triple vessel coronary disease. Surgeons selected both a preferred 'aortic' strategy, with at least one graft arising from the ascending aorta, and a preferred “anaortic” strategy which could be performed as a “no-aortic touch” operation. CT coronary angiograms of the 5 patients were coupled to CFD models using a novel flow solver “COMCAB.” Twelve different CABG configurations were compared for each patient of which 4 were “aortic” and 8 were “anaortic.” Surgeons then selected their preferred grafting configurations after being shown predictive hemodynamic metrics including functional assessment of stenoses (instantaneous wave-free ratio; fractional flow reserve), transit time flowmetry graft parameters (mean graft flow; pulsatility index) and myocardial perfusion. Results A total of 87.5% (7/8) of “anaortic” configurations compared to 25% (1/4) of “aortic” configurations led to unsatisfactory grafts in at least 1 of the 5 patients ( P = 0.038). The use of the computational models led to a significant decrease in the selection of unsatisfactory grafting configurations when surgeons employed “anaortic” (21.25% (17/80) vs. 1.25% (1/80), P < 0.001) but not “aortic” techniques (5% (4/80) vs. 0% (0/80), P = 0.64). Similarly, there was an increase in the selection of ideal configurations for “anaortic” (6.25% (5/80) vs. 28.75% (23/80), P < 0.001) but not “aortic” techniques (65% (52/80) vs. 61.25% (49/80), P = 0.74). Furthermore, surgeons who planned to use more than one unique “anaortic” configuration across all 5 patients increased (12.5% (2/16) vs. 87.5% (14/16), P <0.001). Conclusions “COMCAB” is a promising tool to improve personalized surgical planning particularly for CABG configurations involving composite or sequential grafts which are used more frequently in anaortic operations.

Abstract We propose an algorithm to detect and track coastal precipitation systems and we apply it to 18 years of the high-resolution (8 km and 30 min) Climate Prediction Center CMORPH precipitation estimates in the tropics. Coastal precipitation in the Maritime Continent and Central America contributes to up to 80% of the total rainfall. It also contributes strongly to the diurnal cycle over land with the largest contribution from systems lasting between 6 and 12 h and contributions from longer-lived systems peaking later in the day. While the diurnal cycle of coastal precipitation is more intense over land in the summer hemisphere, its timing is independent of seasons over both land and ocean because the relative contributions from systems of different lifespans are insensitive to the seasonal cycle. We investigate the hypothesis that coastal precipitation is enhanced prior to the arrival of the Madden–Julian oscillation (MJO) envelope over the Maritime Continent. Our results support this hypothesis and show that, when considering only coastal precipitation, the diurnal cycle appears reinforced even earlier over islands than previously reported. We discuss the respective roles of coastal and large-scale precipitation in the propagation of the MJO over the Maritime Continent. We also document a shift in diurnal cycle with the phases of the MJO, which results from changes in the relative contributions of short-lived versus long-lived coastal systems.

To improve the effective utilisation of its supercomputing platforms, the New Zealand eScience Infrastructure (NeSI) offers, in addition to user support and the installation of a comprehensive software stack, a consultancy service to some of its users. Here we present lessons learned from this work and how additional improvements can be made to further enhance productivity of researchers on computing platforms.

Open Science Grid (OSG) is a consortium that enables many scientific breakthroughs by providing researchers with access to shared High Throughput Computing (HTC) compute clusters in support of large-scale collaborative research. To meet the demand on campus, Georgia Institute of Technology (GT)’s Partnership for an Advanced Computing Environment (PACE) team launched a centralized OSG support project, powered by Buzzard, an NSF-funded OSG cluster. We describe Buzzard’s unique multi-tenant architecture, which supports multiple projects on a single CPU/GPU pool, for the benefit of other institutions considering a similar approach to support OSG on their campuses.

The 15 January 2022, Hunga Tonga Hunga Ha'apai volcanic eruption generated a tsunami that spread across the Pacific Ocean and prompted a tsunami advisory in Aotearoa New Zealand (NZ). Concurrently, a severe weather warning was issued for ex-Tropical Cyclone Cody, passing east of NZ and producing heightened swells along the North Island coast. Numerous boats were significantly damaged or sunk in Tūtūkākā Marina, Northland, NZ. Mariners raised concerns over the perceived lack of tsunami warnings. We interviewed mariners in Tūtūkākā to understand their experiences on the night of 15 January 2022 and their needs and expectations of tsunami warnings. The complexity of the multi-hazard event made it difficult to assess and convey the severity of the expected tsunami. We found that mariners require information about expected wave height and arrival time, weather, and sea conditions to inform their anticipatory mitigation actions. This event shows the importance of multi-hazard risk assessments to produce effective warnings and action advice.

The Rakeiora program was designed for high impact precision health research in Aotearoa New Zealand. It required a genomics platform to facilitate linkage of whole genome DNA sequencing data, healthcare records, and mātauranga whakapapa (genealogical knowledge) in a powerful, secure, and transparently governed computational environment. A team of Māori and non-Māori with diverse professional and cultural expertise co-developed Rakeiora; embedding te ao Māori (Māori world) was crucial, including principles derived from: tikanga Māori (Māori traditional rules, values, culture), Te Tiriti o Waitangi (agreement between the British Crown and many Māori chiefs), and data sovereignty. This internationally unique prospective hard-wiring of Indigenous values into a computational platform created a robust infrastructure which benefits all participants. Application of best practice standards and tools facilitate transparency, provide kaitiaki (guardians) control and governance over data and analyses, and enable genomic, bioinformatic and statistical analyses by researchers within a computational 'walled garden'. Although a prototype, the platform is designed to be scalable, accommodating diverse data types and communities, each with their own specific interests and needs. This paper outlines part of the Rakeiora program - the creation, development and technological aspects of the genomic analysis platform and its potential to enable precision health research in Aotearoa.

R-ecology-lesson v2017.04.0 Initial release of the Data Carpentry R ecology lesson.