Science Gateway Research Articles

Unleashing quantum algorithms with Qinterpreter: bridging the gap between theory and practice across leading quantum computing platforms

Quantum computing is a rapidly emerging and promising field with the potential to transform various research domains including drug design, network technologies, and sustainable energy solutions. Due to the inherent complexity and divergence from classical computing, several major quantum computing libraries have been developed to implement quantum algorithms, namely IBM Qiskit, Amazon Braket, Cirq, PyQuil, and PennyLane. These libraries enable quantum simulations on classical computers and execution on corresponding quantum hardware, such as Qiskit programs on IBM quantum computers. Despite the variations among these platforms, the core concepts remain the same. One notable challenge is the absence of a Python-based quantum interpreter to connect these five frameworks, a gap that remains to be fully addressed. In response, our work introduces a tool called Qinterpreter, accessible through a user-friendly web interface, the Quantum Science Gateway QubitHub, which operates alongside Jupyter Notebooks. Built using the Python Object-Oriented Programming System, Qinterpreter unifies the five well-known quantum libraries into a single framework. Designed as an educational tool for students and researchers entering the quantum domain, Qinterpreter enables the straightforward development and execution of quantum circuits across such platforms. This work highlights the quantum programming versatility and accessibility of Qinterpreter and underscores our ultimate goal of pervading Quantum Computing through younger, less specialized, and diverse cultural and national communities.

Developing interoperable, accessible software via the atomic, molecular, and optical sciences gateway: A case study of the B-spline atomic R-matrix code graphical user interface.

The Atomic, Molecular, and Optical Science (AMOS) Gateway is a comprehensive cyberinfrastructure for research and educational activities in computational AMO science. The B-Spline atomic R-Matrix (BSR) suite of programs is one of several computer programs currently available on the gateway. It is an excellent example of the gateway's potential to increase the scientific productivity of AMOS users. While the suite is available to be used in batch mode, its complexity does not make it well-suited to the approach taken in the gateway's default setup. The complexity originates from the need to execute many different computations and to construct generally complex workflows, requiring numerous input files that must be used in a specific sequence. The BSR graphical user interface described in this paper was developed to considerably simplify employing the BSR codes on the gateway, making BSR available to a large group of researchers and students interested in AMO science.

PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations.

Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. We illustrate PigmentHunter's capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna-Matthews-Olson protein, and ring deformation in photosystems I and II.

Abstracts From the First Annual Research Day Hosted by the Michigan State University College of Osteopathic Medicine, Novi, Michigan, May 15, 2023.

The Spartan Medical Research Journal (SMRJ) is pleased to publish abstracts from the First Annual Research Day hosted by the Michigan State University College of Osteopathic Medicine (MSUCOM), held in Novi, Michigan, on May 15, 2023. Sponsored by MSUCOM, the Statewide Campus System (SCS), and Research, Innovation, and Scholarly Engagement (RISE), this event showcased a total of 139 selected research abstracts following a meticulous blinded review by the MSUCOM Research Day Planning Committee and SMRJ editorial staff. These abstracts were subsequently presented at the MSUCOM First Annual Research Day in 2023, with awards for exceptional oral and poster presentations conferred on May 15, 2023. Of the 139 presentations that were ultimately chosen, 45 authors consented and elected to have their abstracts published in SMRJ. The abstracts from 2023 encompass a wide array of contemporary medical and clinical subjects, incorporating a variety of research designs that cover basic science, clinical research, case reports, medical education, and quality improvement. While abstracts offer concise overview of research projects or presentations, they do not permit a comprehensive evaluation of the scientific rigor employed in the respective works. Although these abstracts offer preliminary results that may necessitate further refinement and validation, they serve a vital function in disseminating novel research concepts and advancements in the discipline of medicine. This knowledge-sharing promotes meaningful dialogue among researchers, clinicians, and educators, thereby making a valuable contribution to the collective body of knowledge in the fields of medical sciences and osteopathic medicine. Andrea Amalfitano, DO, PhD Osteopathic Heritage Foundation Professor of Pediatrics, Microbiology and Molecular Genetics Professor, BioMolecular Science Gateway Editor-in-Chief, Spartan Medical Research Journal (SMRJ) MSU College of Osteopathic Medicine- Statewide Campus System C. Patricia Obando S., PhD Associate Dean and DIO, Graduate Medical Education Associate Professor- MSU College of Osteopathic Medicine- Statewide Campus System Rana Ismail, PhD, MSc, CPHQ Director of Research Editor, Spartan Medical Research Journal (SMRJ) MSU College of Osteopathic Medicine- Statewide Campus System Francis Akenami, BMLS, PhD, MSc, FIMLS Managing Editor Spartan Medical Research Journal (SMRJ) MSU College of Osteopathic Medicine- Statewide Campus System.

DataPLANT Cloud Oriented Service Infrastructure

A core objective of the DataPLANT consortium is to provide a science gateway as a comprised of flexible cloud based (micro) services. The setup keeps both on-premise installation and future integration into a joint NFDI common infrastructure. We are presenting the DataPLANT DataHUB which provides various RDM workflows to support research data scientists in different phases of the data life cycle – from the development to the publication of the results obtained.

Identification and taxonomic position of a new Pseudoomphalina species from Pakistan based on light, scanning electron microscopy, and molecular analysis.

Khanspur, a small town located near Ayubia National Park, is a famous mountainous resort lying in Galyat area of Khyber Pakhtunkhwa. It is included in one of the richest biodiversity hotspots in the country. Despite of extensive previous studies, many new species are awaiting to be documented, including macrofungi. In this study, a new macrofungus Pseudoomphalina khanspurensis is analyzed by both light and scanning electron microscopy as well as DNA sequences based on nrITS and nrLSU regions. The sister species P. cokeri differs by its red to purple, dark to reddish brown, broadly convex to applanate pileus, purple blue to brownish stipe, and numerous cylindrical to lageniform cheilocystidia. HIGHLIGHTS: This is the first report of genus Pseudoomphalina from Pakistan and first study based on Scanning electron microscopy. These species have been described with detailed micro-morphological and molecular makers (nrITS and nrLSU). General distribution, ecology, diagnostic features and comparisons with alies have been provided. Graphical representation of DNA extraction and geographical locations of sampling sites are also illustrated. Softwares such as CIPRES Science Gateway Portal, MUSCLE, BioEdit, FigTree, Adobe illustrator and Adobe Photoshop are used in the current study. No member of this genus is already described from Pakistan.

New 3D Visualization Technologies as a Part of Scientific Gateway and Portal

Our paper describes the use and also the great importance of new modern tools of 3D visualization technologies as one of the main components of the Science Gateway (SG), and portals. As new technologies of 3D visualization are improved and developed, so are new scientific portals and gateways, which are also created by using new 3D technologies such as Virtual Reality (VR), Augmented Reality (AR), Mixed Reality (MR), etc. Our paper aims to point out and explain with several examples where we supported the use of new modern technologies of 3D visualization as part of the science gateway in the portal. Our research focuses on the creation of visualization tools in the fields of natural disasters, astronomy and astrophysics, education, water management, and many other sectors.

Simulation for All: The Atomic, Molecular, and Optical Science Gateway

Simulation for All: The Atomic, Molecular, and Optical Science Gateway

First Report of Fusarium commune Associated with a Root Rot of Grapevine in China.

During last decade, species belonging to Fusarium, Rosellinia, Armillaria and Dactylonectria were confirmed as phytopathogens causing grapevine root diseases (Highet and Nair 1995; Teixeira et al. 1995; Calamit et al. 2021; Ye et al. 2021). From 2020 to 2021, grapevine decline was observed in several vineyards in Beijing region, China. Leaves turned yellow with brown necrotic patches and roots were poorly developed, which was suggesting that a root disease was affecting the vines. The disease incidence was up to 10-15% of the vineyard for sample collection. Symptomatic root samples (cv. 'Red Globe') were collected and tissue fragments were excised at the margin of the symptomatic tissue in order to isolate the potential pathogen. The surface was sterilized using 1.5% sodium hypochlorite for 3 min, followed by 70% ethanol for 30 sec, and rinsed three times with sterile distilled water (Ye et al. 2020). Tissues were dried and placed onto potato dextrose agar (PDA) plates, followed by incubation at 25°C under dark conditions for 3 d. Hyphal tips of fungi growing from the samples were transferred onto new PDA plates and incubated until they produced conidia. Next, single spores were transferred onto new PDA plates and incubated at 25°C for 7 d. Eight isolates numbered with JZB3110172 to JZB3110179 were obtained and their culture characters were identical, and the re-isolation percentage was 100%. Colonies were white to orange, with abundant fluffy aerial mycelium. Macroconidia were fusiform with a slightly curved apical cell and a foot-shaped basal cell, and measured 16.2-43.2 μm × 2.7-4.9 μm (n=50); microconidia were cylindrical, straight to slightly curved, 5.1-13 × 2.1-3.9 μm (n=50). Morphological characters of the isolates resembled to Fusarium commune (Skovgaard et al. 2003). For phylogenetic analysis, genomic DNA of the eight isolates was extracted with a DNA extraction kit (DNeasy plant Mini Kit). PCR amplifications of two phylogenetic markers (EF-1α and RPB2) were performed using the primers EF-1/EF-2 (Geiser et al. 2004) and RPB2-5F2/RPB2-7cR (Liu et al. 1995), respectively. The sequences were deposited in GenBank ON457645 to ON457660. Comparison of base pairs on Maximum likelihood (ML) phylogenetic analysis was conducted using the RAxML-HPC2 tool on XSEDE on the CIPRES Science Gateway platform (http://www.phylo.org/). The sequences of EF-1α and RPB2 of the eight isolates showed 99 to 100% similarity to the reference isolates of F. commune. In the phylogenetic tree, the isolates from this study clustered with the representative strains of F. commune (NRRL 52764, NRRL 28387 and NRRL 52744). Based on morphological characters and the phylogenetic results, all of isolates were identified as F. commune. Koch's postulates were conducted on healthy, 3-month-old grapevine 'Marselan'. Plant roots were trimmed with sterile scissors and then soaked in a spore suspension (1.0 × 106 spores mL-1) or sterile water (as the control) for 30 min. The inoculated grapevines were transplanted into pots and kept in the greenhouse at 25°C. After 14 days, all the inoculated plants developed necrosis and turned yellow. No symptoms were observed on the control. Koch's postulates were fulfilled by re-isolating the fungus from necrotic root tissues. The isolates obtained from the artificially infected tissue were identified again as F. commune based on morphological and molecular analyses. Overall, this is the first report of F. commune associated with a grapevine root rot globally, which lays a foundation for further study and developing disease control methods.

The Characteristics of Influencers and Opinion Leaders of Science Gateways and Cyberinfrastructure for Innovation Diffusion

To maximize national investments in science gateways (SG) and cyberinfrastructure (CI), understanding and harnessing the factors that enable user adoption is critically valuable. In this paper, we discuss how the social science concepts of influencers and opinion leaders apply in SG/CI domains and help drive user adoption. We identify three key aspects of influencers based on a systematic analysis of 132 interviews with SG/CI users and experts from 2016-2019: who they are, what qualities they possess, and how they communicate. We find that SG/CI influencers will be most effective if they possess mentoring roles, are active and visible members of an academic or professional community, and if they facilitate growth within SG/CI at the individual and community levels. We also outline 12 techniques organized under 4 methodological approaches which SG/CI staff can employ to recruit influencers to help promote adoption.

Science Gateways: Accelerating Research and Education—Part II

Science Gateways: Accelerating Research and Education—Part II

An Intersectional Application of Expectancy-Value Theory in an Undergraduate Chemistry Course

The underrepresentation of women and Black, Latinx, and Native Americans within the United States scientific workforce is a persistent and multifaceted problem warranting an intersectional approach. Applying intersectionality to the expectancy-value theory of motivation, we examined initial motivation and subsequent achievement among a sample of undergraduate students ( N = 687) enrolled in the science, technology, engineering, and mathematics (STEM) gateway course of introductory chemistry at a diverse 4-year university. We found no racial/ethnic group differences in initial motivation, but small ( d = .30) group differences in achievement. Results revealed a pattern of gender differences across both underrepresented (i.e., Black, Latinx, and Native American) and well-represented (i.e., White, Asian American) racial/ethnic groups such that, relative to men, women began the class with lower levels of confidence about their performance, but greater utility value and attainment value in learning chemistry. Consistent with expectancy-value theory, motivation at the beginning of the semester positively predicted final exam scores across gender and racial/ethnic intersectional groups. For Black, Latinx, and Native American students, attainment value was an especially strong predictor of subsequent achievement. Our findings point to the need to cultivate social contexts within undergraduate STEM education that promotes all aspects of science motivation among students from underrepresented groups. Online slides for instructors who want to use this article for teaching are available on PWQ's website at http://journals.sagepub.com/doi/suppl/10.1177/03616843231153390 .

Scalable Scientific Interactive Research Computing With Project Scinco

Interactive computing with Jupyter notebooks has transformed the state-of-the-art of scientific research computing. Users can perform a multitude of computational tasks in real time, including data cleansing, analysis, visualization, and post-processing, with Jupyter notebooks. Additionally, the ability to write and execute code and include supporting text and images in the same document has made it popular for use in scholarly articles and teaching. These capabilities complement the batch computing services provided by HPC centers exposed through traditional science gateways. However, integrating Jupyter into science gateways and other advanced computing ecosystems introduces new challenges related to scalability, collaboration, and reproducibility. In this paper, we discuss Project Scinco (Scalable Interactive Computing), an open-source platform for scalable, reproducible, interactive scientific computing, designed to be run in academic computing centers and incorporated into science gateways. We describe the prime features, architecture, deployment choices, and challenges of project Scinco.

Science Gateways and the Humanities: An Exploratory Study of Their Rare Partnership

<italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Researchers and educators in humanities such as computational linguists, digital humanists, and those doing historical reconstructions are increasingly heavy users of computational and/or data resources. Many know about activities, working groups, and initiatives around the FAIR (Findable, Accessible, Interoperable, Reusable) principles and are a driving force for improving the sharing of data and software. However, it seems humanities researchers are less aware of the science gateways community and the end-to-end solutions that science gateways could provide, therefore lacking a driving force for adoption of this technology. Some may be creating their own gateways outside the community; others may wish to use computational and data infrastructures but may perceive a lack of support or opportunities. Hypotheses about the reasons that humanities are not well represented as gateways builders and users include lack of funding and support by computer centers. This small-scale exploratory study will clarify some of the challenges and needs faced by computational researchers in the humanities that may explain their relatively low participation in the science gateways community. For this paper, we present the results of 19 interviews with 7 women, 11 men, and 1 non-binary individual from seven states and DC in the US with a range of professional backgrounds and roles.</i>

Hubzero: Community Growth for Four Science Gateways Supporting Open Science

The research landscape has become increasingly interdisciplinary and complex with novel hardware, software, data, and lab instruments. Reproducibility of research results, the usability of tools, and sharing of methods are all crucial for timely collaboration for research and teaching. Hubzero is a widely used science gateway framework designed to support online communities with efficient sharing and publication processes. The paper discusses the growth of communities for the four science gateways nanoHUB, MyGeoHub, QUBEShub, and HubICL using the Hubzero Platform to foster open science and tackling education with a diverse set of approaches and target communities.

Science Gateways: Accelerating Research and Education—Part I

Science Gateways: Accelerating Research and Education—Part I

The Pulsar Science Collaboratory: Exploring Pulsars Through a Science Gateway

The Pulsar Science Collaboratory (PSC) is a research project engaging high-school students, teachers, and undergraduates in searching for pulsars in data collected with radio telescopes. The goals are to stimulate student interest in STEM careers, to prepare teachers in implementing authentic research with students by training them within a professional scientific community, to promote the student use of information technologies, and to assist the research community through pulsar discoveries. The learning is facilitated through online training, in-person workshops and camps, discussion forums, participation in capstone events, conferences, etc. The PSC is powered by HUBzero, a platform for building science gateways, which combines analytical tools, community management, course components, and collaborations in one ecosystem. Participants gain access to radio astronomy data after the successful completion of training workshops and passing a certification test. The PSC students make authentic research contributions to the scientific community, the field of pulsars, and radio astronomy.

Putting the R into PlatfoRms

&#x0D; This paper looks at the question of how and why to bring about greater reusability of Research Platforms (variously called Virtual Laboratories, Virtual Research Environments, or Science Gateways). It begins with some context for the Australian Research Data Commons, where the authors are based. It then examines the infrastructure concerns that are driving the need for platforms to be created and remain sustainable, and the connection from this to reusability. The paper then proceeds to discuss the ways in which FAIR is being extended to a range of research objects and infrastructure elements, before reviewing the work of the FAIR4VREs WG. The core of the paper is an examination, with examples or case studies, of four different paradigms for platform reusability: accessing, adopting, adapting, and abstracting. The paper concludes by examining actions undertaken by the ARDC to increase the likelihood of reusability.&#x0D; &#x0D;

First Report of Bacterial Wilt Caused by Enterobacter mori of Strawberry in Beijing, China.

Strawberry (Fragaria × ananassa) is an economically important crop in China, and a crucial part of urban agriculture in Beijing. In November 2020, wilt symptoms were observed in strawberry seedlings in several greenhouses in the Pinggu District of Beijing city (40.14° N; 117.12° E). The average disease incidence was 20%. Water-soaked lesions appeared along the veins of diseased strawberry leaves and bacterial ooze was also present on severely affected leaves. Bisected crowns had a reddish-brown discoloration in the xylem which later turned black. Three diseased strawberry seedlings were collected for pathogen identification. Isolations were conducted from stem, crown, leaf, and roots of diseased strawberry plants. Samples were surface sterilized by immersion in 70% ethanol for 30 s and rinsed three times with sterile distilled water, before being placed on potato dextrose agar (PDA) medium and incubated at 28℃. Several bacterial colonies grew on the medium after 24 h. Colonies were then purified on Lysogeny broth (LB) agar plates using the streak plate method. Twenty-nine isolates were obtained from 36 diseased tissue samples, which were from stem(10), crown(12), leaf(2) and roots(5) separately. All isolates appeared white, round, opaque and smooth on LB plates. To identify the isolates, genomic DNA was extracted from nine purified bacterial colonies (CM1 to CM9). The fragments of atpD, gyrB, infB and rpoB gene were amplified and sequenced with primers atpD 01-F/ atpD 02-R, gyrB 01-F/ gyrB 02-R, and infB 01-F/ infB 02-R (Brady et al. 2008) and RpoB-F/ RpoB-R (Mollet et al. 1997), respectively. All atpD, gyrB, infB and rpoB sequences belonging to the isolates were identical. The sequences of atpD, gyrB, infB and rpoB gene of isolates CM1 and CM3 were deposited in GenBank under accession numbers ON055247, ON055248, ON055249, ON055250, ON055251, ON055252, OL771192 and OL771193. BLAST searches were conducted with the sequences of atpD, gyrB, infB and rpoB. The atpD, gyrB, infB and rpoB sequences of the obtained isolate showed 99.53%, 99.06%, 99.19% and 99.80% identity with the corresponding sequences of Enterobacter mori strains, respectively. Phylogenetic analysis was performed using the maximum likelihood (ML) method with the CIPRES Science Gateway platform (http://www.phylo.org/) based on the combined atpD, gyrB, infB and rpoB sequences (Brady et al. 2013; Palmer et al. 2018). In the phylogenetic tree, the isolates were clustered together with E. mori strain LMG 25706. To confirm the pathogenicity, 200 μL of bacterial suspensions (108 CFU/mL) of the two isolates were injected into the crown of six healthy Fragaria × ananassa cv. Bennihope strawberry seedlings respectively with 1 mL sterilized syringe, and the control seedlings were injected with sterile water. The seedlings were kept in a moist chamber (28°C, 16-h light and 8-h dark period) for 2 days. Then all the seedlings were transferred to the greenhouse with conditions similar to those where the diseased plants were collected. Forty days after inoculation, old leaves started to wilt and leaf midvein necrosis, along with xylem discoloration, was observed in inoculated plants. No symptoms were observed in the control group. Pathogenicity tests were conducted three times with similar results. The bacteria were re-isolated from the symptomatic diseased strawberry plants and confirmed as E. mori by morphological and sequence analyses as above, fulfilling Koch's postulates. To the best of our knowledge, this is the first report of strawberry bacterial wilt caused by E. mori. Due to the significant crop loss from this disease, more research is needed in epidemiology and disease management.

Science gateway adoption using plug‐in middleware for evidence‐based healthcare data management

SummaryThere is a growing need for next‐generation science gateways to increase the accessibility of emerging large‐scale datasets for data consumers (e.g., clinicians, researchers) who aim to combat COVID‐19‐related challenges. Such science gateways that enable access to distributed computing resources for large‐scale data management need to be made more programmable, extensible, and scalable. In this article, we propose a novel socio‐technical approach for developing a next‐generation healthcare science gateway, namely, OnTimeEvidence that addresses data consumer challenges surrounding the COVID‐19 pandemic related data analytics. OnTimeEvidence implements an intelligent agent, namely, Vidura Advisor that integrates an evidence‐based filtering method to transform manual practices and improve scalability of data analytics. It also features a plug‐in management middleware that improves the programmability and extensibility of the science gateway capabilities using microservices. Lastly, we present a usability study that shows the important factors from data consumers' perspective to adopt OnTimeEvidence with chatbot‐assisted middleware support to increase their productivity and collaborations to access vast publication archives for rapid knowledge discovery tasks.