Similar Software Tools Research Articles

GeoTaichi: A Taichi-powered high-performance numerical simulator for multiscale geophysical problems

This study introduces GeoTaichi, an open-source high-performance numerical simulator designed for addressing multiscale geophysical problems. By leveraging the power of the Taichi parallel language, GeoTaichi maximizes the utilization of modern computer resources on multicore CPU and GPU architectures. It offers robust and reliable modules for the discrete element method (DEM), material point method (MPM), and coupled material point-discrete element method (MPDEM). These modules enable efficient solving of large-scale problems while being implemented in pure Python. The design philosophy of GeoTaichi focuses on creating a framework that is readable, extensible, and user-friendly. This paper highlights the coupling procedure of MPDEM, the code structures, and the most important features of GeoTaichi. Rigorous benchmark tests have been conducted to verify the validity and robustness of GeoTaichi. Additionally, the performance of GeoTaichi is compared with similar software tools in the field, underscoring a notable improvement in both computational efficiency and memory savings when compared to existing alternatives. Program summaryProgram title: GeoTaichiCPC Library link to program files:https://doi.org/10.17632/858bmcf7j6.1Developer's repository link:https://github.com/Yihao-Shi/GeoTaichiLicensing provisions: GNU General Public License v3.0Programming language: PythonNature of problem: The simulations of large-deformation geophysical flows and their interaction with structures play a crucial role in the field of geophysics. To address the complexities of these nonlinear problems, the discrete element method (DEM), material point method (MPM), and their coupling (MPDEM) have proven to be highly suitable numerical schemes. However, these schemes impose substantial computational demands, necessitating the development of an efficient framework that can harness modern computer resources on multicore CPU and GPU architectures.Solution method: The open-source code GeoTaichi implements the DEM, MPM, and coupled MPDEM, encompassing a range of constitutive models and contact laws for different geologic materials. The clump particle model is also introduced in DEM to solve granular mechanics involving complex-shaped particles. One significant advantage of GeoTaichi is its utilization of the Taichi parallel language, which is designed to be user-friendly and easily extensible for customized applications.

Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning.

Metagenome binning is a key step, downstream of metagenome assembly, to group scaffolds by their genome of origin. Although accurate binning has been achieved on datasets containing multiple samples from the same community, the completeness of binning is often low in datasets with a small number of samples due to a lack of robust species co-abundance information. In this study, we exploited the chromatin conformation information obtained from Hi-C sequencing and developed a new reference-independent algorithm, Metagenome Binning with Abundance and Tetra-nucleotide frequencies-Long Range (metaBAT-LR), to improve the binning completeness of these datasets. This self-supervised algorithm builds a model from a set of high-quality genome bins to predict scaffold pairs that are likely to be derived from the same genome. Then, it applies these predictions to merge incomplete genome bins, as well as recruit unbinned scaffolds. We validated metaBAT-LR's ability to bin-merge and recruit scaffolds on both synthetic and real-world metagenome datasets of varying complexity. Benchmarking against similar software tools suggests that metaBAT-LR uncovers unique bins that were missed by all other methods. MetaBAT-LR is open-source and is available at https://bitbucket.org/project-metabat/metabat-lr.

Avaliação de validade de um sistema computacional na identificação de estudos duplicados

Abstract Objective To evaluate the performance of the Systematic Review Support web-based system for the identification of duplicate records compared with similar software tools. Methods A methodological study was conducted assessing the automated process of de-duplication performed by the Systematic Review Support web-based system (version 1.0) versus the EndNote X9® and Rayyan® systems, adopting hand-checking as the benchmark reference for comparisons. A set of studies on three topics related to cystic fibrosis retrieved from the Pubmed, Embase and Web of Science electronic databases was used for testing purposes. The sensitivity, specificity, accuracy and area under the ROC curve of the software systems were compared to the benchmark values for performance evaluation. Results The database searches retrieved 1332 studies, of which 273 (20.5%) were true duplicates. The Systematic Review Support tool identified a larger proportion of true duplicates than the other systems tested. The sensitivity, specificity and accuracy of the Systematic Review Support tool exceeded 98%. Conclusion and implications for practice The Systematic Review Support system provided a high level of sensitivity, specificity and accuracy in identifying duplicate studies, optimizing time and effort by reviewers in the health field.

MetPy: A Meteorological Python Library for Data Analysis and Visualization

Abstract MetPy is an open-source, Python-based package for meteorology, providing domain-specific functionality built extensively on top of the robust scientific Python software stack, which includes libraries like NumPy, SciPy, Matplotlib, and xarray. The goal of the project is to bring the weather analysis capabilities of GEMPAK (and similar software tools) into a modern computing paradigm. MetPy strives to employ best practices in its development, including software tests, continuous integration, and automated publishing of web-based documentation. As such, MetPy represents a sustainable, long-term project that fills a need for the meteorological community. MetPy’s development is substantially driven by its user community, both through feedback on a variety of open, public forums like Stack Overflow, and through code contributions facilitated by the GitHub collaborative software development platform. MetPy has recently seen the release of version 1.0, with robust functionality for analyzing and visualizing meteorological datasets. While previous versions of MetPy have already seen extensive use, the 1.0 release represents a significant milestone in terms of completeness and a commitment to long-term support for the programming interfaces. This article provides an overview of MetPy’s suite of capabilities, including its use of labeled arrays and physical unit information as its core data model, unit-aware calculations, cross sections, skew T and GEMPAK-like plotting, station model plots, and support for parsing a variety of meteorological data formats. The general road map for future planned development for MetPy is also discussed.

AUTOMATION OF PARTIAL TASKS IN THE DESIGN OF ROBOTIC ARMS

The design of robotic arms is a demanding process, especially in terms of the demands placed on developers' knowledge and experience and the time required for the design. Therefore, the development aimed to create procedures for possible automation of some of the individual tasks of the robotic arm design process, which are further applied in the development of a software tool for the automation of partial tasks in the design of robotic arms RobotDesigner. The benefits and functions of RobotDesigner are demonstrated in the example of optimization of a simple manipulator with 5 degrees of freedom for a given manipulation task. The optimization results show that the use of this software tool significantly speeds up and streamlines the sub-tasks of design and optimization of arms. By using iterative processes and artificial intelligence, using similar software tools and connecting them to CAD systems, it will not only be possible in the future to fully automate the robot arm design process but also to generate and compare different structures and design solutions to find the most optimal for the task, which the robot will perform.

Accident Damage Analysis Module (ADAM): Novel European Commission tool for consequence assessment—Scientific evaluation of performance

This paper summarises the scientific evaluation of the performance of a novel modelling tool, the Accident Damage Assessment Module (ADAM), developed by the Joint Research Centre (JRC) of the European Commission (EC) to assess the consequences of an industrial accident resulting from an unintended release of a dangerous substance. The ADAM tool is specifically intended to assist Competent Authorities in the European Union (EU) and European Economic Area (EEA), and their supporting research institutions, responsible for the implementation of the Seveso Directive in their countries, as well as governmental and research organisations of EU Accession and Candidate Countries, and European Neighbourhood Policy countries involved in chemical accident prevention and preparedness. In particular, the tool provides decision-making support to various functions associated with industrial risk management, enforcement and oversight, including risk analysis, land-use and emergency planning, inspection and monitoring, and the preparation and review of safety reports.Consequence assessment models are characterised by high level of complexity and of uncertainty. It is therefore of paramount importance to assess their limits. The scientific evaluation was conducted across the entire consequence assessment cycle, including the source terms and the physical effects calculations associated with the concentration toxics after airborne dispersion, the thermal radiation of chemical fires, and the explosion of vapour flammable clouds. The evaluation described in this paper was conducted on a series of relevant scenarios, by benchmarking the outcome of ADAM with the results obtained by similar software tools and with the experimental data obtained on a series of reference field campaigns, as taken from the literature.

X-Pro Milestone: Comparative Evaluation against Similar Software Tools, Current Status, and Planned Future Directions

Computerized and partially computerized exams rely on item banks from which items are selected to produce tests; however, studies show that the availability of item banks is rather limited because the development of an item bank can involve investing a great amount of time and effort. X-Pro Milestone is a portable, personalized, featured, and syllabus-specific item-bank software tool that is capable of helping users maintain high-quality item-banks and producing printer-friendly multi-form exam instances along with proper answer keys for each exam-form. Motivated by the acceptance the earlier versions of this software tool, it is thoroughly re-engineered and re-implemented based on a comprehensive set of requirements that are responsive to user needs. In this paper, the latest release of this software is presented and the latest improvements are explained. We also cover the special Descriptive Markup Language (DML) used in constructing item banks. Further, the software is comparatively evaluated against a set of similar software tools available in the market based on a set of more than twenty features. We demonstrate that X-Pro Milestone is superior to other software tools based on a wide spectrum of features and functionalities that are not available in other software tools. We also cover the current status of this software tool and draw its future planned directions.

Measuring deuteron beam parameters with solid-state track detectors in experiments with the QUINTA target assembly

The results of measurements of the beam parameters on the target upon irradiation of the QUINTA subcritical uranium assembly with deuterons with energies of 1, 4, and 8 GeV are presented. Data on the position of the incident particle beam relative to the assembly axis and on the actual geometric parameters of the beam make it possible to analyze information on the spatial distributions of reaction rates within the target assembly correctly, comparing such distributions obtained at different irradiation sessions and modeling the experiments with the use of MCNPX, GEANT4, FLUKA, and other similar software tools.

An FPGA-based platform for accelerated offline spike sorting

There is a push in electrophysiology experiments to record simultaneously from many channels (upwards of 64) over long time periods (many hours). Given the relatively high sampling rates (10–40kHz) and resolutions (12–24bits per sample), these experiments accumulate exorbitantly large amounts of data (e.g. 100GB per experiment), which can be very time-consuming to process. Here, we present an FPGA-based spike-sorting platform that can increase the speed of offline spike sorting by at least 25 times, effectively reducing the time required to sort data from long experiments from several hours to just a few minutes. We attempted to preserve the flexibility of software by implementing several different algorithms in the design, and by providing user control over parameters such as spike detection thresholds. The results of sorting a published benchmark dataset using this hardware tool are shown to be comparable to those using similar software tools.

Simulation of electron spin resonance spectroscopy in diverse environments: An integrated approach

We discuss in this work a new software tool, named E-SpiReS (Electron Spin Resonance Simulations), aimed at the interpretation of dynamical properties of molecules in fluids from electron spin resonance (ESR) measurements. The code implements an integrated computational approach (ICA) for the calculation of relevant molecular properties that are needed in order to obtain spectral lines. The protocol encompasses information from atomistic level (quantum mechanical) to coarse grained level (hydrodynamical), and evaluates ESR spectra for rigid or flexible single or multi-labeled paramagnetic molecules in isotropic and ordered phases, based on a numerical solution of a stochastic Liouville equation. E-SpiReS automatically interfaces all the computational methodologies scheduled in the ICA in a way completely transparent for the user, who controls the whole calculation flow via a graphical interface. Parallelized algorithms are employed in order to allow running on calculation clusters, and a web applet Java has been developed with which it is possible to work from any operating system, avoiding the problems of recompilation. E-SpiReS has been used in the study of a number of different systems and two relevant cases are reported to underline the promising applicability of the ICA to complex systems and the importance of similar software tools in handling a laborious protocol. Program summary Program title: E-SpiReS Catalogue identifier: AEEM_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v2.0 No. of lines in distributed program, including test data, etc.: 311 761 No. of bytes in distributed program, including test data, etc.: 10 039 531 Distribution format: tar.gz Programming language: C (core programs) and Java (graphical interface) Computer: PC and Macintosh Operating system: Unix and Windows Has the code been vectorized or parallelized?: Yes RAM: 2 048 000 000 Classification: 7.2 External routines: Babel-1.1, CLAPACK, BLAS, CBLAS, SPARSEBLAS, CQUADPACK, LEVMAR Nature of problem: Ab initio simulation of cw-ESR spectra of radicals in solution Solution method: E-SpiReS uses an hydrodynamic approach to calculate the diffusion tensor of the molecule, DFT methodologies to evaluate magnetic tensors and linear algebra techniques to solve numerically the stochastic Liouville equation to obtain an ESR spectrum. Running time: Variable depending on the task. It takes seconds for small molecules in the fast motional regime to hours for big molecules in viscous and/or ordered media.

Conservation analysis of large biochemical networks

Large biochemical networks pose a unique challenge from the point of view of evaluating conservation laws. The computational problem in most cases exceeds the capability of available software tools, often resulting in inaccurate computation of the number and form of conserved cycles. Such errors have profound effects on subsequent calculations, particularly in the evaluation of the Jacobian which is a critical quantity in many other calculations. The goal of this paper is to outline a new algorithm that is computationally efficient and robust at extracting the correct conservation laws for very large biochemical networks. We show that our algorithm can perform the conservation analysis of large biochemical networks, and can evaluate the correct conserved cycles when compared with other similar software tools. Biochemical simulators such as Jarnac and COPASI are successful at extracting only a subset of the conservation laws that our algorithm can. This is illustrated with examples for some large networks which show the advantages of our method.

On the Accuracy of the Signal‐to‐Noise Estimates Obtained with the Exposure‐Time Calculator of the Wide Field Planetary Camera 2 on Board the Hubble Space Telescope

ABSTRACTWe have studied the accuracy and reliability of the exposure‐time calculator (ETC) of the Wide Field Planetary Camera 2 (WFPC2) on board the Hubble Space Telescope (HST) with the objective of determining how well it represents actual observations and therefore how much confidence can be invested in it and in similar software tools. We have found, for example, that the ETC gives, in certain circumstances, very optimistic values for the signal‐to‐noise ratio (S/N) of point sources. These values overestimate by up to a factor of 2 the HST performance when simulations are needed to plan deep‐imaging observations, thus bearing serious implications on observing‐time allocation. For this particular case, we calculate the corrective factors to compute the appropriate S/N and detection limits, and we show how these corrections vary with field crowding and sky background. We also compare the ETC of the WFPC2 with a more general ETC tool, which takes into account the real effects of pixel size and charge diffusion. Our analysis indicates that similar problems may afflict other ETCs in general, showing the limits to which they are bound and the caution with which their results must be taken.

Automatic Source Code Generation for Microcontrollers

Every designer and programmer very often uses keyboard handling and display driving in his microcontroller system. The programming of these types of system interface can be performed automatically by using proper software tools. The tools for code design and generation of a control object in the Windows operating system appear in several programming languages (Visual C++, Borland C, Delphi etc.). Similar software tools are not commonly available especially for small microcontroller systems and singlechip microcontrollers though they would be very useful. Some experiences with the design of an automatic code generator are presented.

Refinement of the HEPAR expert system: tools and techniques

Methods and tools for the static and dynamic verification and validation of software systems are commonplace in the field of software engineering. In the field of expert systems, where it is more difficult to ensure that a system meets the specifications and expectations than in traditional software engineering, such tools are generally not available. In this paper, the need for more support of the development process by methods and tools is illustrated by the approach taken in building the HEPAR system, a rule-based expert system that can be used as a supportive tool in the diagnosis of disorders of the liver and biliary tract. At a certain stage in the development of this system an incremental development methodology has been adopted, in which implementation of parts of the expert system was followed by dynamic validation. For this purpose, a collection of software tools were implemented as extensions to a rule-based expert-system shell. These tools provide valuable information about the effects of modification of the HEPAR knowledge base, and indicate places in the knowledge base for refinement. It is believed that similar software tools may prove helpful in the development of other expert systems as well.