Abstract
The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics ...Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.
There are growing demands for predicting the prospects of achieving the global elimination of neglected tropical diseases as a result of the institution of large-scale nation-wide intervention ...programs by the WHO-set target year of 2020. Such predictions will be uncertain due to the impacts that spatial heterogeneity and scaling effects will have on parasite transmission processes, which will introduce significant aggregation errors into any attempt aiming to predict the outcomes of interventions at the broader spatial levels relevant to policy making. We describe a modeling platform that addresses this problem of upscaling from local settings to facilitate predictions at regional levels by the discovery and use of locality-specific transmission models, and we illustrate the utility of using this approach to evaluate the prospects for eliminating the vector-borne disease, lymphatic filariasis (LF), in sub-Saharan Africa by the WHO target year of 2020 using currently applied or newly proposed intervention strategies. METHODS AND RESULTS: We show how a computational platform that couples site-specific data discovery with model fitting and calibration can allow both learning of local LF transmission models and simulations of the impact of interventions that take a fuller account of the fine-scale heterogeneous transmission of this parasitic disease within endemic countries. We highlight how such a spatially hierarchical modeling tool that incorporates actual data regarding the roll-out of national drug treatment programs and spatial variability in infection patterns into the modeling process can produce more realistic predictions of timelines to LF elimination at coarse spatial scales, ranging from district to country to continental levels. Our results show that when locally applicable extinction thresholds are used, only three countries are likely to meet the goal of LF elimination by 2020 using currently applied mass drug treatments, and that switching to more intensive drug regimens, increasing the frequency of treatments, or switching to new triple drug regimens will be required if LF elimination is to be accelerated in Africa. The proportion of countries that would meet the goal of eliminating LF by 2020 may, however, reach up to 24/36 if the WHO 1% microfilaremia prevalence threshold is used and sequential mass drug deliveries are applied in countries.
We have developed and applied a data-driven spatially hierarchical computational platform that uses the discovery of locally applicable transmission models in order to predict the prospects for eliminating the macroparasitic disease, LF, at the coarser country level in sub-Saharan Africa. We show that fine-scale spatial heterogeneity in local parasite transmission and extinction dynamics, as well as the exact nature of intervention roll-outs in countries, will impact the timelines to achieving national LF elimination on this continent.
The Poisson equation has many applications across the broad areas of science and engineering. Most quantum algorithms for the Poisson solver presented so far either suffer from lack of accuracy ...and/or are limited to very small sizes of the problem and thus have no practical usage. In this regard, our previous work (Robson in 2022 IEEE International Conference on Quantum Computing and Engineering (QCE), 2022) showed a proof-of-concept demonstration in advancing quantum Poisson solver algorithm and validated preliminary results for a simple case of
3
×
3
problem. In this work, we delve into comprehensive research details, presenting the results on up to
15
×
15
problems that include step-by-step improvements in Poisson equation solutions, scaling performance, and experimental exploration. In particular, we demonstrate the implementation of eigenvalue amplification by a factor of up to
2
8
, achieving a significant improvement in the accuracy of our quantum Poisson solver and comparing that to the exact solution. Additionally, we present success probability results, highlighting the reliability of our quantum Poisson solver. Moreover, we explore the scaling performance of our algorithm against the circuit depth and width, demonstrating how our approach scales with larger problem sizes and thus further solidifies the practicality of easy adaptation of this algorithm in real-world applications. We also discuss a multilevel strategy for how this algorithm might be further improved to explore much larger problems with greater performance. Finally, through our experiments on the IBM quantum hardware, we conclude that though overall results on the existing NISQ hardware are dominated by the error in the
CNOT
gates, this work opens a path to realizing a multidimensional Poisson solver on near-term quantum hardware.
The Poisson equation has many applications across the broad areas of science and engineering. Most quantum algorithms for the Poisson solver presented so far either suffer from lack of accuracy ...and/or are limited to very small sizes of the problem, and thus have no practical usage. Here we present an advanced quantum algorithm for solving the Poisson equation with high accuracy and dynamically tunable problem size. After converting the Poisson equation to a linear system through the finite difference method, we adopt the HHL algorithm as the basic framework. Particularly, in this work we present an advanced circuit that ensures the accuracy of the solution by implementing non-truncated eigenvalues through eigenvalue amplification, as well as by increasing the accuracy of the controlled rotation angular coefficients, which are the critical factors in the HHL algorithm. Consequently, we are able to drastically reduce the relative error in the solution while achieving higher success probability as the amplification level is increased. We show that our algorithm not only increases the accuracy of the solutions but also composes more practical and scalable circuits by dynamically controlling problem size in NISQ devices. We present both simulated and experimental results and discuss the sources of errors. Finally, we conclude that though overall results on the existing NISQ hardware are dominated by the error in the CNOT gates, this work opens a path to realizing a multidimensional Poisson solver on near-term quantum hardware.
The Poisson equation has many applications across the broad areas of science and engineering. Most quantum algorithms for the Poisson solver presented so far, either suffer from lack of accuracy ...and/or are limited to very small sizes of the problem, and thus have no practical usage. Here we present an advanced quantum algorithm for solving the Poisson equation with high accuracy and dynamically tunable problem size. After converting the Poisson equation to the linear systems through the finite difference method, we adopt the Harrow-Hassidim-Lloyd (HHL) algorithm as the basic framework. Particularly, in this work we present an advanced circuit that ensures the accuracy of the solution by implementing non-truncated eigenvalues through eigenvalue amplification as well as by increasing the accuracy of the controlled rotation angular coefficients, which are the critical factors in the HHL algorithm. We show that our algorithm not only increases the accuracy of the solutions, but also composes more practical and scalable circuits by dynamically controlling problem size in the NISQ devices. We present both simulated and experimental solutions, and conclude that overall results on the quantum hardware are dominated by the error in the CNOT gates.
First experiences with the Polish Optical Internet Binczewski, Artur; Meyer, Norbert; Nabrzyski, Jarosław ...
Computer networks (Amsterdam, Netherlands : 1999),
12/2001, Letnik:
37, Številka:
6
Journal Article
Recenzirano
The paper describes the new development programme of the Polish information infrastructure. The programme, called in Polish PIONIER: (English—PIONEER) Polish Optical Internet, Advanced Applications, ...Services and Technologies for the Information Society, has been proposed to the Polish State Committee for Scientific Research and has been accepted. The aim of the programme is to create an advanced infrastructure together with tools, services and applications available to the entire scientific community and eventually to government and local administrations as well as society in general. Services and applications are expected to appear as selected pilot realizations in order to verify deployed technologies. Some of the pilot realizations and testbeds are also presented in the paper.
We present an overview of the recently funded "Merging Science and Cyberinfrastructure Pathways: The Whole Tale" project (NSF award #1541450). Our approach has two nested goals: 1) deliver an ...environment that enables researchers to create a complete narrative of the research process including exposure of the data-to-publication lifecycle, and 2) systematically and persistently link research publications to their associated digital scholarly objects such as the data, code, and workflows. To enable this, Whole Tale will create an environment where researchers can collaborate on data, workspaces, and workflows and then publish them for future adoption or modification. Published data and applications will be consumed either directly by users using the Whole Tale environment or can be integrated into existing or future domain Science Gateways.
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