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Gridded monthly rainfall estimates can be used for a number of research applications, including hydrologic modeling and weather forecasting. Automated interpolation algorithms, such as the “autoKrige” function in R, can produce gridded rainfall estimates that validate well but produce unrealistic spatial patterns. In this work, an optimized geostatistical kriging approach is used to interpolate relative rainfall anomalies, which are then combined with long-term means to develop the gridded estimates. The optimization consists of the following: 1) determining the most appropriate offset (constant) to use when log-transforming data; 2) eliminating poor quality data prior to interpolation; 3) detecting erroneous maps using a machine learning algorithm; and 4) selecting the most appropriate parameterization scheme for fitting the model used in the interpolation. Results of this effort include a 30-yr (1990–2019), high-resolution (250-m) gridded monthly rainfall time series for the state of Hawai‘i. Leave-one-out cross validation (LOOCV) is performed using an extensive network of 622 observation stations. LOOCV results are in good agreement with observations (R2 = 0.78; MAE = 55 mm month−1; 1.4%); however, predictions can underestimate high rainfall observations (bias = 34 mm month−1; −1%) due to a well-known smoothing effect that occurs with kriging. This research highlights the fact that validation statistics should not be the sole source of error assessment and that default parameterizations for automated interpolation may need to be modified to produce realistic gridded rainfall surfaces. Data products can be accessed through the Hawai‘i Data Climate Portal (HCDP; http://www.hawaii.edu/climate-data-portal). Significance Statement A new method is developed to map rainfall in Hawai‘i using an optimized geostatistical kriging approach. A machine learning technique is used to detect erroneous rainfall maps and several conditions are implemented to select the optimal parameterization scheme for fitting the model used in the kriging interpolation. A key finding is that optimization of the interpolation approach is necessary because maps may validate well but have unrealistic spatial patterns. This approach demonstrates how, with a moderate amount of data, a low-level machine learning algorithm can be trained to evaluate and classify an unrealistic map output.

Tapis is a hosted, multi-tenant, RESTful API framework for distributed computational research, providing support for data management and code execution across institutional boundaries. Using Tapis APIs, a user can program portable, reproducible workflows that leverage sensors, instruments, experimental facilities and a network of national and regional cyberinfrastructure. Tapis builds on NSF investments into the Abaco, Agave, and CHORDs projects to provide a production-grade framework for use across a wide range of domains of science and engineering. Including support for streaming/sensor data, portable, reproducible workflows leveraging containerized applications, and a novel, decentralized security kernel, Tapis will be the underlying cyberinfrastructure for modern research., Funded by NSF #1931439 and #1931575.

SARS-CoV-2 worldwide spread and evolution has resulted in variants containing mutations resulting in immune evasive epitopes that decrease vaccine efficacy. We acquired SARS-CoV-2 positive clinical samples and compared the worldwide emerged spike mutations from Variants of Concern/Interest, and developed an algorithm for monitoring the evolution of SARS-CoV-2 in the context of vaccines and monoclonal antibodies. The algorithm partitions logarithmic-transformed prevalence data monthly and Pearson’s correlation determines exponential emergence of amino acid substitutions (AAS) and lineages. The SARS-CoV-2 genome evaluation indicated 49 mutations, with 44 resulting in AAS. Nine of the ten most worldwide prevalent (>70%) spike protein changes have Pearson’s coefficient r > 0.9. The tenth, D614G, has a prevalence >99% and r-value of 0.67. The resulting algorithm is based on the patterns these ten substitutions elucidated. The strong positive correlation of the emerged spike protein changes and algorithmic predictive value can be harnessed in designing vaccines with relevant immunogenic epitopes. Monitoring, next-generation vaccine design, and mAb clinical efficacy must keep up with SARS-CoV-2 evolution, as the virus is predicted to remain endemic.

SARS-CoV-2 worldwide emergence and evolution has resulted in variants containing mutations resulting in immune evasive epitopes that decrease vaccine efficacy. We acquired clinical samples, analyzed SARS-CoV-2 genomes, used the most worldwide emerged spike mutations from Variants of Concern/Interest, and developed an algorithm for monitoring the SARS-CoV-2 vaccine platform. The algorithm partitions logarithmic-transformed prevalence data monthly and Pearson’s correlation determines exponential emergence. The SARS-CoV-2 genome evaluation indicated 49 mutations. Nine of the ten most worldwide prevalent (>70%) spike protein changes have r-values >0.9. The tenth, D614G, has a prevalence >99% and r-value of 0.67. The resulting algorithm is based on the patterns these ten substitutions elucidated. The strong positive correlation of the emerged spike protein changes and algorithmic predictive value can be harnessed in designing vaccines with relevant immunogenic epitopes. SARS-CoV-2 is predicted to remain endemic and continues to evolve, so must SARS-CoV-2 monitoring and next-generation vaccine design.

Using genomics, bioinformatics and statistics, herein we demonstrate the effect of statewide and nationwide quarantine on the introduction of SARS-CoV-2 variants of concern (VOC) in Hawai’i. To define the origins of introduced VOC, we analyzed 260 VOC sequences from Hawai’i, and 301,646 VOC sequences worldwide, deposited in the GenBank and global initiative on sharing all influenza data (GISAID), and constructed phylogenetic trees. The trees define the most recent common ancestor as the origin. Further, the multiple sequence alignment used to generate the phylogenetic trees identified the consensus single nucleotide polymorphisms in the VOC genomes. These consensus sequences allow for VOC comparison and identification of mutations of interest in relation to viral immune evasion and host immune activation. Of note is the P71L substitution within the E protein, the protein sensed by TLR2 to produce cytokines, found in the B.1.351 VOC may diminish the efficacy of some vaccines. Based on the phylogenetic trees, the B.1.1.7, B.1.351, B.1.427, and B.1.429 VOC have been introduced in Hawai'i multiple times since December 2020 from several definable geographic regions. From the first worldwide report of VOC in GenBank and GISAID, to the first arrival of VOC in Hawai’i, averages 320 days with quarantine, and 132 days without quarantine. As such, the effect of quarantine is shown to significantly affect the time to arrival of VOC in Hawai’i, both during and following quarantine. Further, the collective 2020 quarantine of 43-states in the United States demonstrates a profound impact in delaying the arrival of VOC in states that did not practice quarantine, such as Utah. Our data demonstrates that at least 76% of all definable SARS-CoV-2 VOC have entered Hawai’i from California, with the B.1.351 variant in Hawai’i originating exclusively from the United Kingdom. These data provide a foundation for policy-makers and public-health officials to apply precision public health genomics to real-world policies such as mandatory screening and quarantine.

The future for science gateways warrants exploration as we consider the possibilities that extend well beyond ’science’ and high-performance computing into new interfaces, applications and user communities. In this paper, we look retrospectively at the successes of representative gateways thus far. This serves to highlight existing gaps gateways need to overcome in areas such as accessibility, usability and interoperability, and in the need for broader outreach by drawing insights from technology adoption research. We explore two particularly promising opportunities for gateways - computational social sciences and virtual reality – and make the case for the gateway community to be more intentional in engaging with users to encourage adoption and implementation, especially in the area of educational usage. We conclude with a call for focused attention on legal hurdles in order to realize the full future potential of science gateways. This paper serves as a roadmap for a vision of science gateways in the next ten years.

The Tapis framework, an NSF-funded project, is an open-source, scalable API platform that enables researchers to perform distributed computational experiments securely and achieve faster scientific results with increased reproducibility. Tapis Streams API focuses on supporting scientific use cases that require working with real-time sensor data. The Streams Service, built on the top of the CHORDS time-series data service, allows storing, processing, annotating, querying, and archiving time-series data. This paper focuses on the new Tapis Streams API functionality that enables researchers to design and execute real-time data-driven event workflow for their research. We describe the architecture and design choices towards achieving this new capability with Streams API. Specifically, we demonstrate the integration of Streams API with Kapacitor, a native data processing engine for time-series database InfluxDB, and Abaco, an NSF Funded project, web service, and distributed computing platform providing function-as-a-Service (FaaS). The Streams API, which includes a wrapper interface for the Kapacitor alerting system, can define and enable alerts. Finally, simulation results from the water-quality use case depict that Streams API’s new capabilities can support real-time streaming data event-driven workflows.

Modern computational research increasingly spans multiple, geographically distributed data centers and leverages instruments, experimental facilities and a network of national and regional cyberinfrastructure (CI). Tapis is an open-source API platform developed at the Texas Advanced Computing Center at the University of Texas at Austin to increase reproducibility and minimize time-to-solution for distributed computational experiments. Core features of Tapis include data management and code execution, a fine-grained permissions system enabling objects to be saved privately, shared with individuals or “published” to a community, and provenance endpoints exposing the detailed history Tapis collects on analyses, enabling workflows to be repeated and results reproduced. In this paper, we describe the evolution of the Tapis platform, from its origins in 2008, and discuss the growth and success of the project as well as challenges and limitations that have led to a new design effort, funded by the National Science Foundation in September of 2019. We present a detailed overview of the new system, including reference architecture and new features such as support for streaming/sensor data, and we discuss some of the early science use cases driving its design. We conclude with the roadmap for future work.

Granting agencies invest millions of dollars on the generation and analysis of data, making these products extremely valuable. However, without sufficient annotation of the methods used to collect and analyze the data, the ability to reproduce and reuse those products suffers. This lack of assurance of the quality and credibility of the data at the different stages in the research process essentially wastes much of the investment of time and funding and fails to drive research forward to the level of potential possible if everything was effectively annotated and disseminated to the wider research community. In order to address this issue for the Hawai’i Established Program to Stimulate Competitive Research (EPSCoR) project, a water science gateway was developed at the University of Hawai‘i (UH), called the ‘Ike Wai Gateway. In Hawaiian, ‘Ike means knowledge and Wai means water. The gateway supports research in hydrology and water management by providing tools to address questions of water sustainability in Hawai‘i. The gateway provides a framework for data acquisition, analysis, model integration, and display of data products. The gateway is intended to complement and integrate with the capabilities of the Consortium of Universities for the Advancement of Hydrologic Science’s (CUAHSI) Hydroshare by providing sound data and metadata management capabilities for multi-domain field observations, analytical lab actions, and modeling outputs. Functionality provided by the gateway is supported by a subset of the CUAHSI’s Observations Data Model (ODM) delivered as centralized web based user interfaces and APIs supporting multi-domain data management, computation, analysis, and visualization tools to support reproducible science, modeling, data discovery, and decision support for the Hawai’i EPSCoR ‘Ike Wai research team and wider Hawai‘i hydrology community. By leveraging the Tapis platform, UH has constructed a gateway that ties data and advanced computing resources together to support diverse research domains including microbiology, geochemistry, geophysics, economics, and humanities, coupled with computational and modeling workflows delivered in a user friendly web interface with workflows for effectively annotating the project data and products. Disseminating results for the ‘Ike Wai project through the ‘Ike Wai data gateway and Hydroshare makes the research products accessible and reusable.

Computational scalability has become an important requirement for processing the massive amounts of data generated in contemporary sequencing-based experiments. The availability of large computational resources through academic, regional or national cyber-infrastructure efforts, as well as through inexpensive cloud offerings, has shifted the bottleneck, which now lies in the extensive expertise necessary to create reproducible and scalable bioinformatics pipelines and deploy them to such diverse infrastructures. We present here MetaFlow|mics, a comprehensive pipeline for the analysis of microbiome marker data using best practices and state-of-the-art cyberinfrastructure standards to ensure reproducibility. MetaFlow|mics provides seamless scalability and extensibility, allowing users to build and test their pipelines on a laptop with small datasets and to subsequently run them on large datasets on an HPC or on the Cloud with a change to a single line of code. Our framework is built on top of the Nextflow workflow management system and provides an interoperable architecture that leverages self-contained Docker and Singularity instances with all the dependencies and requirements needed to quickly deploy and use the pipeline.

The University of Hawai'i Information Technology Services Cyber-infrastructure team in partnership with the United States Geological Survey developed the Hawai'i groundwater recharge tool, a decision support tool, as part of the 'Ike Wai Gateway to support water sustainability research for the state of Hawai'i. To enable the development of the tool within the existing University of Hawai'i Agave platform that the 'Ike Wai Gateway is built on, the Metadata application programmatic interface (API) and Agave infrastructure needed to be extended to store and retrieve spatial data and handle a larger number of requests. The development team successfully added the functionality to the local University of Hawai'i Agave platform instance to support the storage of deserialized vector data and metadata that can be spatially queried across hundreds of thousands of records to enable decision support applications within a science gateway.

Although many Archaea have AMP-Acs (acetyl-coenzyme A synthetase) and ADP-Acs, the extant methanogenic genus Methanosarcina is the only identified Archaeal genus that can utilize acetate via acetate kinase (Ack) and phosphotransacetylase (Pta). Despite the importance of ack as the potential urkinase in the ASKHA phosphotransferase superfamily, an origin hypothesis does not exist for the acetate kinase in Bacteria, Archaea, or Eukarya. Here we demonstrate that Archaeal AMP-Acs and ADP-Acs contain paralogous ATPase motifs previously identified in Ack, which demonstrate a novel relation between these proteins in Archaea. The identification of ATPase motif conservation and resulting structural features in AMP- and ADP-acetyl-CoA synthetase proteins in this study expand the ASKHA superfamily to include acetyl-CoA synthetase. Additional phylogenetic analysis showed that Pta and MaeB sequences had a common ancestor and that the Pta lineage within the halophilc archaea was an ancestral lineage. These results suggested that divergence of a duplicated maeB within an ancient halophilic, archaeal lineage formed a putative pta ancestor. These results provide a potential scenario for the establishment of the Ack/Pta pathway and provide novel insight into the evolution of acetate metabolism for all three domains of life.