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The MFEM (Modular Finite Element Methods) library is a high-performance C++ library for finite element discretizations. MFEM supports numerous types of finite element methods and is the discretization engine powering many computational physics and engineering applications across a number of domains. This paper describes some of the recent research and development in MFEM, focusing on performance portability across leadership-class supercomputing facilities, including exascale supercomputers, as well as new capabilities and functionality, enabling a wider range of applications. Much of this work was undertaken as part of the Department of Energy's Exascale Computing Project (ECP) in collaboration with the Center for Efficient Exascale Discretizations (CEED). [ABSTRACT FROM AUTHOR]

The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in scientific research. The diversity of independently developed applications, evolving versions and heterogeneous components highlights the need for rigorous methodologies to navigate these complexities. In response to these challenges, the SBGrid team builds, installs and configures over 530 specialized software applications for use in the on‐premises and cloud‐based computing environments of SBGrid Consortium members. To address the intricacies of supporting this diverse application collection, the team has developed the Capsule Software Execution Environment, generally referred to as Capsules. Capsules rely on a collection of programmatically generated bash scripts that work together to isolate the runtime environment of one application from all other applications, thereby providing a transparent cross‐platform solution without requiring specialized tools or elevated account privileges for researchers. Capsules facilitate modular, secure software distribution while maintaining a centralized, conflict‐free environment. The SBGrid platform, which combines Capsules with the SBGrid collection of structural biology applications, aligns with FAIR goals by enhancing the findability, accessibility, interoperability and reusability of scientific software, ensuring seamless functionality across diverse computing environments. Its adaptability enables application beyond structural biology into other scientific fields. [ABSTRACT FROM AUTHOR]

Due to their widespread adoption, frequent use, and diverse sensor capabilities, smartphones have become a powerful tool for academic studies focused on sampling human behaviour. While packing many technological advances, the need for researchers to develop their own software packages in order to run smartphone-based studies has resulted in a clear barrier to entry for researchers without the financial means, time, or technical knowledge required to overcome this technical barrier. We present AWARE-Light, a new smartphone application for data collection from study participants, which is accompanied by a website that provides any researcher the possibility to easily configure their own study. To highlight the possibilities of our tool, we present a research scenario on digital phenotyping for mental health. Furthermore, we describe the methodological configuration possibilities offered by our tool, and complement the technical configuration possibilities with recommendations from the existing literature. [ABSTRACT FROM AUTHOR]

Getting scientific software installed correctly and ensuring it performs well has been a ubiquitous problem for several decades now, which is compounded currently by the changing landscape of computational science with the (re‐)emergence of different microprocessor families, and the expansion to additional scientific domains like artificial intelligence and next‐generation sequencing. The European Environment for Scientific Software Installations (EESSI) project aims to provide a ready‐to‐use stack of scientific software installations that can be leveraged easily on a variety of platforms, ranging from personal workstations to cloud environments and supercomputer infrastructure, without making compromises with respect to performance. In this article, we provide a detailed overview of the project, highlight potential use cases, and demonstrate that the performance of the provided scientific software installations can be competitive with system‐specific installations. [ABSTRACT FROM AUTHOR]

We present an interactive COMSOL web application that allows both expert and non-expert users to numerically evaluate the electric potential, ionic concentration distribution, velocity profile, and ionic current along a molecular structure surface characterizing actin filaments. This online computational and visualization tool runs on a high performance server (http://marucholab.physics.utsa.edu:2036), that enables users to perform multiple analyses and comparisons without compromising computational resources. As a unique feature, the multiphysics formulation accounts for the filament surface roughness, the finite filament size, and the ionic condensation, providing a deeper understanding of the electrochemical phenomena taking place at the interface between the irregular charged shape of the filament and its biological environment. Overall, the interactive component allows investigators to characterize polyelectrolyte properties of healthy and abnormal actin filaments in physiological and pathological conditions.

Motivation: Software Is an essential component In driving scientific and technical advances in the atmospheric and oceanic sciences, leading to broader societal benefits. Society now relies upon software tools to [...]

This European Materials Modelling Council (EMMC) study provides an outline of the survey intent and ambitions, followed by an analysis of the results and a follow up discussion, focused on the future perspectives of the EMMC. The survey covers materials modelling and characterisation communities in both academia and industry. It provides a profile of the surveyed players in these communities and a scaled measure on their usage of computational methodologies. The survey outcomes include: (i) summary views of the recent as well as perceived future trends of materials modelling and its associated fields, with respect to two focus areas surveyed, Model Development and Software, (ii) the main adoption factors and associated bottlenecks for computational methods and software, (iii) the most targeted materials properties and digital twins approaches, and (iv) the wider communities expectations of how EMMC can help facilitate, fulfil and drive further the European Materials Modelling Roadmap to the benefit of the European Commission’s (ECs’) research and innovation.

In the field of bioinformatics, a large number of classical software becomes a necessary research tool. To measure the influence of scientific software as one kind of important intellectual products, a few strategies have been proposed to identify the software names from full texts of papers to collect the usage data of packages in bioinformatics research. However, the performance of these strategies is limited because of the highly imbalance of data in the full texts. This study proposes EnsembleSVMs-CRF, a two-step refinement strategy based on ensemble learning that gradually increases the sentences that contain software mentions to improve the performance of named entity recognition. The experiment on the bioinformatics corpus shows that the performance of EnsembleSVMs-CRF, in terms of the local F1 (78.81%) and the global F1-A (73.49%), is superior to the rule-based bootstrapping method and direct CRF. Application of this strategy to the articles published between 2013 and 2017 in 27 bioinformatics journals extracted 8,239 unique packages. The most popular 50 packages thus identified demonstrate that most of them are professional software which generally requires inter-discipline knowledge, rather than programming skill. Meanwhile, we found that researchers in bioinformatics tend to use free scientific software, and the application of general software is increasing compared with professional software. [ABSTRACT FROM AUTHOR]

This European Materials Modelling Council (EMMC) study provides an outline of the survey intent and ambitions, followed by an analysis of the results and a follow up discussion, focused on the future perspectives of the EMMC. The survey covers materials modelling and characterisation communities in both academia and industry. It provides a profile of the surveyed players in these communities and a scaled measure on their usage of computational methodologies. The survey outcomes include: (i) summary views of the recent as well as perceived future trends of materials modelling and its associated fields, with respect to two focus areas surveyed, Model Development and Software, (ii) the main adoption factors and associated bottlenecks for computational methods and software, (iii) the most targeted materials properties and digital twins approaches, and (iv) the wider communities expectations of how EMMC can help facilitate, fulfil and drive further the European Materials Modelling Roadmap to the benefit of the European Commission’s (ECs’) research and innovation.

'SneakerNet,' or the manual transfer of data using a disk or USB stick from one computer system to another, should be long dead, but this noncompliant transfer process still survives. In this edition of 'Focus on Quality,' we discuss why SneakerNet should be consigned to the graveyard of technology., Walk through any laboratory and you'll see a variety of spectrometers with their own data systems to control the instrument, to acquire and process data, and then report the results. [...]

Provenance is recognized as a central challenge to establish the reliability and provide security in computational systems. In scientific workflows, provenance is considered essential to support experiments' reproducibility, interpretation of results, and problem diagnosis. We consider that these requirements can also be used in new application domains, such as software processes and IoT. However, for a better understanding and use of provenance data, efficient and user-friendly mechanisms are needed. Ontology, complex networks, and software visualization can help in this process by generating new data insights and strategic information for decision-making. This paper presents the Visionary framework, designed to assist in the understanding and use of provenance data through ontologies, complex network analysis, and software visualization techniques. The framework captures the provenance data and generates new information using ontologies and structural analysis of the provenance graph. The visualization presents and highlights inferences and results obtained with the data analysis. Visionary is an application domain-free framework adapted to any system that uses the PROV provenance model. Evaluations were carried out, and some evidence was found that the framework assists in the understanding and analysis of provenance data when decision-making is needed. [ABSTRACT FROM AUTHOR]

Anyone who has watched an episode of CSI is aware of the value of forensic science--and particularly the impact of DNA, considered the gold standard of the forensic disciplines--on developing [...]

Software development for data reduction and analysis at large research facilities is increasingly professionalized, and internationally coordinated. To foster software quality and sustainability, and to facilitate collaboration, representatives from software groups of European neutron and muon facilities have agreed on a set of guidelines for development practices, infrastructure, and functional and non-functional product properties. These guidelines have been derived from actual practices in software projects from the EU funded consortium 'Science and Innovation with Neutrons in Europe in 2020' (SINE2020), and have been enriched through extensive literature review. Besides guiding the work of the professional software engineers in our computing groups, we hope to influence scientists who are willing to contribute their own data treatment software to our community. Moreover, this work may also provide inspiration to scientific software development beyond the neutron and muon field. [ABSTRACT FROM AUTHOR]

Scientific software is a fundamental player in modern science, participating in all stages of scientific knowledge production. Software occasionally supports the development of trivial tasks, while at other instances it determines procedures, methods, protocols, results, or conclusions related with the scientific work. The growing relevance of scientific software as a research product with value of its own has triggered the development of quantitative science studies of scientific software. The main objective of this study is to illustrate a link-based webometric approach to characterize the online mentions to scientific software across different analytical frameworks. To do this, the bibliometric software VOSviewer is used as a case study. Considering VOSviewer's official website as a baseline, online mentions to this website were counted in three different analytical frameworks: academic literature via Google Scholar (988 mentioning publications), webpages via Majestic (1,330 mentioning websites), and tweets via Twitter (267 mentioning tweets). Google scholar mentions shows how VOSviewer is used as a research resource, whilst mentions in webpages and tweets show the interest on VOSviewer's website from an informational and a conversational point of view. Results evidence that URL mentions can be used to gather all sorts of online impacts related to non-traditional research objects, like software, thus expanding the analytical scientometric toolset by incorporating a novel digital dimension. [ABSTRACT FROM AUTHOR]

Abstract Background OCaml is a functional programming language with strong static types, Hindley–Milner type inference and garbage collection. In this article, we share our experience in prototyping chemoinformatics and structural bioinformatics software in OCaml. Results First, we introduce the language, list entry points for chemoinformaticians who would be interested in OCaml and give code examples. Then, we list some scientific open source software written in OCaml. We also present recent open source libraries useful in chemoinformatics. The parallelization of OCaml programs and their performance is also shown. Finally, tools and methods useful when prototyping scientific software in OCaml are given. Conclusions In our experience, OCaml is a programming language of choice for method development in chemoinformatics and structural bioinformatics.

Scientific software from all areas of scientific research is pivotal to obtaining novel insights. Yet the coding standards adherence of scientific software is rarely assessed, even though it might lead to incorrect scientific results in the worst case. Therefore, we have developed an open source tool and benchmark called SoftWipe, that provides a relative software coding standards adherence ranking of 48 computational tools from diverse research areas. SoftWipe can be used in the review process of software papers and to inform the scientific software selection process. [ABSTRACT FROM AUTHOR]

Background: Software is now ubiquitous within research. In addition to the general challenges common to all software development projects, research software must also represent, manipulate, and provide data for complex theoretical constructs. Ensuring this process of theory-software translation is robust is essential to maintaining the integrity of the science resulting from it, and yet there has been little formal recognition or exploration of the challenges associated with it. Methods: We thematically analyse the outputs of the discussion sessions at the Theory-Software Translation Workshop 2019, where academic researchers and research software engineers from a variety of domains, and with particular expertise in high performance computing, explored the process of translating between scientific theory and software. Results: We identify a wide range of challenges to implementing scientific theory in research software and using the resulting data and models for the advancement of knowledge. We categorise these within the emergent themes of design, infrastructure, and culture, and map them to associated research questions. Conclusions: Systematically investigating how software is constructed and its outputs used within science has the potential to improve the robustness of research software and accelerate progress in its development. We propose that this issue be examined within a new research area of theory-software translation, which would aim to significantly advance both knowledge and scientific practice.

Precise point positioning (PPP) has the ability to give precise positioning with high accuracy. That may be an alternative to precise Deferential GNSS (DGNSS), in addition to being a low-cost alternative among all processing strategies of Global Navigation Satellite System (GNSS), especially when online services are used. To see the assessment study of PPP in the determination of crustal velocity, 66 days of GNSS data distributed in the period 2013–2015 were used. Composing a network of eight stations called the Northern Egyptian Permanent GNSS Network (N-EPGN) with nine IGS stations was processed. Scientific software GAMIT/GLOBK and Bernese used to calculate the final precise coordinate and the associated velocity of each station in the International Terrestrial Reference Frame (ITRF 2008). Each campaign consists of 3 days. These data were processed by PPP approach. The final precise coordinate and the associated velocity of each EPGN station estimated. The final results compare to those different methods of analysis and programs refer to high level of agreement between the coordinates and velocity which confirm that PPP approach can be applied for the investigation of crustal deformation. [ABSTRACT FROM AUTHOR]

Scientific software projects evolve rapidly in their initial development phase, yet at the end of a funding period, the completion of a research project, thesis, or publication, further engagement in the project may slow down or cease completely. To retain the invested effort for the sciences, this software needs to be preserved or handed over to a succeeding developer or team, such as the next generation of (PhD) students. Comparable guides provide top-down recommendations for project leads. This paper intends to be a bottom-up approach for sustainable hand-over processes from a developer's perspective. An important characteristic in this regard is the project's size, by which this guideline is structured. Furthermore, checklists are provided, which can serve as a practical guide for implementing the proposed measures. [ABSTRACT FROM AUTHOR]

In recent years, open and data‐driven science has fostered very important scientific breakthroughs. This study describes the challenges and opportunities for the scientific community devoted to bed form dynamics research in adopting such scientific paradigms through, for example, engineered data sharing, formal recognition of scientists who collect the data, and collaborative development of free accessible software. It highlights that once these actions are completed, the potential application of deep learning techniques could substantially improve bed form models and the scientific understanding of bed form dynamics. Likewise, it discusses the potential of Bedforms‐ATM, a free available software, to standardize some bed form data analysis techniques. We propose that the technical challenges be tackled by following scholarly accepted/proposed standards (e.g. FAIR Guiding Principles, Geoscience Papers of the Future), using the body of knowledge being built on the matter by some institutions (e.g. Federation of Earth Science Information Partners), and through technical discussions at scientific meetings such as MARID. © 2020 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

In this work we formally derive and prove the correctness of the algorithms and data structures in a parallel, distributed-memory, generic finite element framework that supports h-adaptivity on computational domains represented as forest-of-trees. The framework is grounded on a rich representation of the adaptive mesh suitable for generic finite elements that is built on top of a low-level, light-weight forest-of-trees data structure handled by a specialized, highly parallel adaptive meshing engine, for which we have identified the requirements it must fulfill to be coupled into our framework. Atop this two-layered mesh representation, we build the rest of the data structures required for the numerical integration and assembly of the discrete system of linear equations. We consider algorithms that are suitable for both subassembled and fully assembled distributed data layouts of linear system matrices. The proposed framework has been implemented within the FEMPAR scientific software library, using p4est as a practical forest-of-octrees demonstrator. A strong scaling study of this implementation when applied to Poisson and Maxwell problems reveals remarkable scalability up to 32.2K CPU cores and 482.2M degrees of freedom. Besides, a comparative performance study of FEMPAR and the state-of-the-art deal.II finite element software shows at least comparative performance, and at most a factor of 2{3 improvement in the h-adaptive approximation of a Poisson problem with first- and second-order Lagrangian finite elements, respectively. [ABSTRACT FROM AUTHOR]

AUTOMATION EQUIPMENT AUTOSAMPLERS Agilent Technologies Life Sciences & Chemical Analysis 800-227-9770 Analytik Jena US 800-452-6788 Biotage CDS Analytical Elemental Scientific Environmental EXpress FLIR Systems FOSS North America Gerstel Meinhard Elemental [...]

Background: Evaluation of the quality of research software is a challenging and relevant issue, still not sufficiently addressed by the scientific community. Methods: Our contribution begins by defining, precisely but widely enough, the notions of research software and of its authors followed by a study of the evaluation issues, as the basis for the proposition of a sound assessment protocol: the CDUR procedure. Results: CDUR comprises four steps introduced as follows: Citation, to deal with correct RS identification, Dissemination, to measure good dissemination practices, Use, devoted to the evaluation of usability aspects, and Research, to assess the impact of the scientific work. Conclusions: Some conclusions and recommendations are finally included. The evaluation of research is the keystone to boost the evolution of the Open Science policies and practices. It is as well our belief that research software evaluation is a fundamental step to induce better research software practices and, thus, a step towards more efficient science.