FILER: a framework for harmonizing and querying large-scale functional genomics knowledge

ABSTRACT Querying massive functional genomic and annotation data collections, linking and summarizing the query results across data sources/data types are important steps in high-throughput genomic and genetic analytical workflows. However, these steps are made difficult by the heterogeneity and breadth of data sources, experimental assays, biological conditions/tissues/cell types and file formats. FILER (FunctIonaL gEnomics Repository) is a framework for querying large-scale genomics knowledge with a large, curated integrated catalog of harmonized functional genomic and annotation data coupled with a scalable genomic search and querying interface. FILER uniquely provides: (i) streamlined access to >50 000 harmonized, annotated genomic datasets across >20 integrated data sources, >1100 tissues/cell types and >20 experimental assays; (ii) a scalable genomic querying interface; and (iii) ability to analyze and annotate user’s experimental data. This rich resource spans >17 billion GRCh37/hg19 and GRCh38/hg38 genomic records. Our benchmark querying 7 × 109 hg19 FILER records shows FILER is highly scalable, with a sub-linear 32-fold increase in querying time when increasing the number of queries 1000-fold from 1000 to 1 000 000 intervals. Together, these features facilitate reproducible research and streamline integrating/querying large-scale genomic data within analyses/workflows. FILER can be deployed on cloud or local servers (https://bitbucket.org/wanglab-upenn/FILER) for integration with custom pipelines and is freely available (https://lisanwanglab.org/FILER).

Automating Finite Element Methods for Geodynamics via Firedrake

Firedrake is an automated system for solving partial differential equations using the finite element method. By applying sophisticated performance optimisations through automatic code-generation techniques, it provides a means to create accurate, efficient, flexible, easily extensible, scalable, transparent and reproducible research software, that is ideally suited to simulating a wide-range of problems in geophysical fluid dynamics. Here, we demonstrate the applicability of Firedrake for geodynamical simulation, with a focus on mantle dynamics. The accuracy and efficiency of the approach is confirmed via comparisons against a suite of analytical and benchmark cases of systematically increasing complexity, whilst parallel scalability is demonstrated up to 12288 compute cores, where the problem size and the number of processing cores are simultaneously increased. In addition, Firedrake's flexibility is highlighted via straightforward application to different physical (e.g. complex nonlinear rheologies, compressibility) and geometrical (2-D and 3-D Cartesian and spherical domains) scenarios. Finally, a representative simulation of global mantle convection is examined, which incorporates 230 Myr of plate motion history as a kinematic surface boundary condition, confirming its suitability for addressing research problems at the frontiers of global mantle dynamics research.

Right Ventricular Response to Acute Hypoxia Exposure: A Systematic Review

Background: Acute hypoxia exposure is associated with an elevation of pulmonary artery pressure (PAP), resulting in an increased hemodynamic load on the right ventricle (RV). In addition, hypoxia may exert direct effects on the RV. However, the RV responses to such challenges are not fully characterized. The aim of this systematic review was to describe the effects of acute hypoxia on the RV in healthy lowland adults.Methods: We systematically reviewed PubMed and Web of Science and article references from 2005 until May 2021 for prospective studies evaluating echocardiographic RV function and morphology in healthy lowland adults at sea level and upon exposure to simulated altitude or high-altitude.Results: We included 37 studies in this systematic review, 12 of which used simulated altitude and 25 were conducted in high-altitude field conditions. Eligible studies reported at least one of the RV variables, which were all based on transthoracic echocardiography assessing RV systolic and diastolic function and RV morphology. The design of these studies significantly differed in terms of mode of ascent to high-altitude, altitude level, duration of high-altitude stay, and timing of measurements. In the majority of the studies, echocardiographic examinations were performed within the first 10 days of high-altitude induction. Studies also differed widely by selectively reporting only a part of multiple RV parameters. Despite consistent increase in PAP documented in all studies, reports on the changes of RV function and morphology greatly differed between studies.Conclusion: This systematic review revealed that the study reports on the effects of acute hypoxia on the RV are controversial and inconclusive. This may be the result of significantly different study designs, non-compliance with international guidelines on RV function assessment and limited statistical power due to small sample sizes. Moreover, the potential impact of other factors such as gender, age, ethnicity, physical activity, mode of ascent and environmental factors such as temperature and humidity on RV responses to hypoxia remained unexplored. Thus, this comprehensive overview will promote reproducible research with improved study designs and methods for the future large-scale prospective studies, which eventually may provide important insights into the RV response to acute hypoxia exposure.

Analytical Challenges and Metrological Approaches to Ensuring Dietary Supplement Quality: International Perspectives

The increased utilization of metrology resources and expanded application of its’ approaches in the development of internationally agreed upon measurements can lay the basis for regulatory harmonization, support reproducible research, and advance scientific understanding, especially of dietary supplements and herbal medicines. Yet, metrology is often underappreciated and underutilized in dealing with the many challenges presented by these chemically complex preparations. This article discusses the utility of applying rigorous analytical techniques and adopting metrological principles more widely in studying dietary supplement products and ingredients, particularly medicinal plants and other botanicals. An assessment of current and emerging dietary supplement characterization methods is provided, including targeted and non-targeted techniques, as well as data analysis and evaluation approaches, with a focus on chemometrics, toxicity, dosage form performance, and data management. Quality assessment, statistical methods, and optimized methods for data management are also discussed. Case studies provide examples of applying metrological principles in thorough analytical characterization of supplement composition to clarify their health effects. A new frontier for metrology in dietary supplement science is described, including opportunities to improve methods for analysis and data management, development of relevant standards and good practices, and communication of these developments to researchers and analysts, as well as to regulatory and policy decision makers in the public and private sectors. The promotion of closer interactions between analytical, clinical, and pharmaceutical scientists who are involved in research and product development with metrologists who develop standards and methodological guidelines is critical to advance research on dietary supplement characterization and health effects.

Unsupervised Character Recognition with Graphene Memristive Synapses

Memristive devices being applied in neuromorphic computing are envisioned to significantly improve the power consumption and speed of future computing platforms. The materials used to fabricate such devices will play a significant role in their viability. Graphene is a promising material, with superb electrical properties and the ability to be produced sustainably. In this paper, we demonstrate that a fabricated graphene-pentacene memristive device can be used as synapses within Spiking Neural Networks (SNNs) to realise Spike Timing Dependent Plasticity (STDP) for unsupervised learning in an efficient manner. Specifically, we verify operation of two SNN architectures tasked for single digit (0-9) classification: (i) a simple single-layer network, where inputs are presented in 5x5 pixel resolution, and (ii) a larger network capable of classifying the Modified National Institute of Standards and Technology (MNIST) dataset, where inputs are presented in 28x28 pixel resolution. Final results demonstrate that for 100 output neurons, after one training epoch, a test set accuracy of up to 86% can be achieved, which is higher than prior art using the same number of output neurons. We attribute this performance improvement to homeostatic plasticity dynamics that we used to alter the threshold of neurons during training. Our work presents the first investigation of the use of green-fabricated graphene memristive devices to perform a complex pattern classification task. This can pave the way for future research in using graphene devices with memristive capabilities in neuromorphic computing architectures. In favour of reproducible research, we make our code and data publicly available https://anonymous.4open.science/r/c69ab2e2-b672-4ebd-b266-987ee1fd65e7.

Rigour and reproducibility in Canadian research: call for a coordinated approach

Shortcomings in the rigour and reproducibility of research have become well-known issues and persist despite repeated calls for improvement. A coordinated effort among researchers, institutions, funders, publishers, learned societies, and regulators may be the most effective way of tackling these issues. The UK Reproducibility Network (UKRN) has fostered collaboration across various stakeholders in research and are creating the infrastructure necessary to advance rigorous and reproducible research practices across the United Kingdom. Other Reproducibility Networks, modelled on UKRN, are now emerging in other countries. Canada could benefit from a comparable network to unify the voices around research quality and maximize the value of Canadian research.

CyVerse for Reproducible Research: RNA-Seq Analysis

Posing complex research questions poses complex reproducibility challenges. Datasets may need to be managed over long periods of time. Reliable and secure repositories are needed for data storage. Sharing big data requires advance planning and becomes complex when collaborators are spread across institutions and countries. Many complex analyses require the larger compute resources only provided by cloud and high-performance computing infrastructure. Finally at publication, funder and publisher requirements must be met for data availability and accessibility and computational reproducibility. For all of these reasons, cloud-based cyberinfrastructures are an important component for satisfying the needs of data-intensive research. Learning how to incorporate these technologies into your research skill set will allow you to work with data analysis challenges that are often beyond the resources of individual research institutions. One of the advantages of CyVerse is that there are many solutions for high-powered analyses that do not require knowledge of command line (i.e., Linux) computing. In this chapter we will highlight CyVerse capabilities by analyzing RNA-Seq data. The lessons learned will translate to doing RNA-Seq in other computing environments and will focus on how CyVerse infrastructure supports reproducibility goals (e.g., metadata management, containers), team science (e.g., data sharing features), and flexible computing environments (e.g., interactive computing, scaling).