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Commercially available wearable devices (wearables) show promise for continuous physiological monitoring. Previous works have demonstrated that wearables can be used to detect the onset of acute infectious diseases, particularly those characterized by fever. We aimed to evaluate whether these devices could be used for the more general task of syndromic surveillance. We obtained wearable device data (Oura Ring) from 63,153 participants. We constructed a dataset using participants wearable device data and participants responses to daily online questionnaires. We included days from the participants if they (1) completed the questionnaire, (2) reported not experiencing fever and reported a self-collected body temperature below 38 °C (negative class), or reported experiencing fever and reported a self-collected body temperature at or above 38 °C (positive class), and (3) wore the wearable device the nights before and after that day. We used wearable device data (i.e., skin temperature, heart rate, and sleep) from the nights before and after participants fever day to train a tree-based classifier to detect self-reported fevers. We evaluated the performance of our model using a five-fold cross-validation scheme. Sixteen thousand, seven hundred, and ninety-four participants provided at least one valid ground truth day; there were a total of 724 fever days (positive class examples) from 463 participants and 342,430 non-fever days (negative class examples) from 16,687 participants. Our model exhibited an area under the receiver operating characteristic curve (AUROC) of 0.85 and an average precision (AP) of 0.25. At a sensitivity of 0.50, our calibrated model had a false positive rate of 0.8%. Our results suggest that it might be possible to leverage data from these devices at a public health level for live fever surveillance. Implementing these models could increase our ability to detect disease prevalence and spread in real-time during infectious disease outbreaks.

BACKGROUND: Females have been historically excluded from biomedical research due in part to the documented presumption that results with male subjects will generalize effectively to females. This has been justified in part by the assumption that ovarian rhythms will increase the overall variance of pooled random samples. But not all variance in samples is random. Human biometrics are continuously changing in response to stimuli and biological rhythms; single measurements taken sporadically do not easily support exploration of variance across time scales. Recently we reported that in mice, core body temperature measured longitudinally shows higher variance in males than cycling females, both within and across individuals at multiple time scales. METHODS: Here, we explore longitudinal human distal body temperature, measured by a wearable sensor device (Oura Ring), for 6 months in females and males ranging in age from 20 to 79 years. In this study, we did not limit the comparisons to female versus male, but instead we developed a method for categorizing individuals as cyclic or acyclic depending on the presence of a roughly monthly pattern to their nightly temperature. We then compared structure and variance across time scales using multiple standard instruments. RESULTS: Sex differences exist as expected, but across multiple statistical comparisons and timescales, there was no one group that consistently exceeded the others in variance. When variability was assessed across time, females, whether or not their temperature contained monthly cycles, did not significantly differ from males both on daily and monthly time scales. CONCLUSIONS: These findings contradict the viewpoint that human females are too variable across menstrual cycles to include in biomedical research. Longitudinal temperature of females does not accumulate greater measurement error over time than do males and the majority of unexplained variance is within sex category, not between them.

There is significant variability in neutralizing antibody responses (which correlate with immune protection) after COVID-19 vaccination, but only limited information is available about predictors of these responses. We investigated whether device-generated summaries of physiological metrics collected by a wearable device correlated with post-vaccination levels of antibodies to the SARS-CoV-2 receptor-binding domain (RBD), the target of neutralizing antibodies generated by existing COVID-19 vaccines. One thousand, one hundred and seventy-nine participants wore an off-the-shelf wearable device (Oura Ring), reported dates of COVID-19 vaccinations, and completed testing for antibodies to the SARS-CoV-2 RBD during the U.S. COVID-19 vaccination rollout. We found that on the night immediately following the second mRNA injection (Moderna-NIAID and Pfizer-BioNTech) increases in dermal temperature deviation and resting heart rate, and decreases in heart rate variability (a measure of sympathetic nervous system activation) and deep sleep were each statistically significantly correlated with greater RBD antibody responses. These associations were stronger in models using metrics adjusted for the pre-vaccination baseline period. Greater temperature deviation emerged as the strongest independent predictor of greater RBD antibody responses in multivariable models. In contrast to data on certain other vaccines, we did not find clear associations between increased sleep surrounding vaccination and antibody responses.

Early detection of diseases such as COVID-19 could be a critical tool in reducing disease transmission by helping individuals recognize when they should self-isolate, seek testing, and obtain early medical intervention. Consumer wearable devices that continuously measure physiological metrics hold promise as tools for early illness detection. We gathered daily questionnaire data and physiological data using a consumer wearable (Oura Ring) from 63,153 participants, of whom 704 self-reported possible COVID-19 disease. We selected 73 of these 704 participants with reliable confirmation of COVID-19 by PCR testing and high-quality physiological data for algorithm training to identify onset of COVID-19 using machine learning classification. The algorithm identified COVID-19 an average of 2.75 days before participants sought diagnostic testing with a sensitivity of 82% and specificity of 63%. The receiving operating characteristic (ROC) area under the curve (AUC) was 0.819 (95% CI [0.809, 0.830]). Including continuous temperature yielded an AUC 4.9% higher than without this feature. For further validation, we obtained SARS CoV-2 antibody in a subset of participants and identified 10 additional participants who self-reported COVID-19 disease with antibody confirmation. The algorithm had an overall ROC AUC of 0.819 (95% CI [0.809, 0.830]), with a sensitivity of 90% and specificity of 80% in these additional participants. Finally, we observed substantial variation in accuracy based on age and biological sex. Findings highlight the importance of including temperature assessment, using continuous physiological features for alignment, and including diverse populations in algorithm development to optimize accuracy in COVID-19 detection from wearables.

Multi-scale computational modeling is a major branch of computational biology as evidenced by the US federal interagency Multi-Scale Modeling Consortium and major international projects. It invariably involves specific and detailed sequences of data analysis and simulation, often with multiple tools and datasets, and the community recognizes improved modularity, reuse, reproducibility, portability and scalability as critical unmet needs in this area. Scientific workflows are a well-recognized strategy for addressing these needs in scientific computing. While there are good examples if the use of scientific workflows in bioinformatics, medical informatics, biomedical imaging and data analysis, there are fewer examples in multi-scale computational modeling in general and cardiac electrophysiology in particular. Cardiac electrophysiology simulation is a mature area of multi-scale computational biology that serves as an excellent use case for developing and testing new scientific workflows. In this article, we develop, describe and test a computational workflow that serves as a proof of concept of a platform for the robust integration and implementation of a reusable and reproducible multi-scale cardiac cell and tissue model that is expandable, modular and portable. The workflow described leverages Python and Kepler-Python actor for plotting and pre/post-processing. During all stages of the workflow design, we rely on freely available open-source tools, to make our workflow freely usable by scientists.

In 2016, a team of earth scientists directly engaged a team of computer scientists to identify cyberinfrastructure (CI) approaches that would speed up an earth science workflow. This paper describes the evolution of that workflow as the two teams bridged CI and an image segmentation algorithm to do large scale earth science research. The Pacific Research Platform (PRP) and The Cognitive Hardware and Software Ecosystem Community Infrastructure (CHASE-CI) resources were used to significantly decreased the earth science workflow's wall-clock time from 19.5 days to 53 minutes. The improvement in wall-clock time comes from the use of network appliances, improved image segmentation, deployment of a containerized workflow, and the increase in CI experience and training for the earth scientists. This paper presents a description of the evolving innovations used to improve the workflow, bottlenecks identified within each workflow version, and improvements made within each version of the workflow, over a three-year time period.

Reproducibility of computational studies is a hallmark of scientificmethodology. It enables researchers to build with confidence on the methods andfindings of others, reuse and extend computational pipelines, and thereby drivescientific progress. Since many experimental studies rely on computationalanalyses, biologists need guidance on how to set up and document reproducibledata analyses or simulations. In this paper, we address several questions about reproducibility. Forexample, what are the technical and non-technical barriers to reproduciblecomputational studies? What opportunities and challenges do computationalnotebooks offer to overcome some of these barriers? What tools are availableand how can they be used effectively? We have developed a set of rules to serve as a guide to scientists with aspecific focus on computational notebook systems, such as Jupyter Notebooks,which have become a tool of choice for many applications. Notebooks combinedetailed workflows with narrative text and visualization of results. Combinedwith software repositories and open source licensing, notebooks are powerfultools for transparent, collaborative, reproducible, and reusable data analyses.

With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine. Additionally, the workflow tool reduces user input time by automating repetitive processes and facilitates access to GPU clusters, whose high-performance processing power makes simulations of large numerical scale possible. The presented workflow tool facilitates the management and deployment of large sets of MD simulations on heterogeneous computing resources. The workflow tool also performs systematic analysis on the simulation outputs and enhances simulation reproducibility, execution scalability, and MD method development including benchmarking and validation.

Scientific workflows integrate data and computing interfaces as configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiK workflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing and future extensibility.

Environmental sensor networks are now commonly being deployed within environmental observatories and as components of smaller-scale ecological and environmental experiments. Effectively using data from these sensor networks presents technical challenges that are difficult for scientists to overcome, severely limiting the adoption of automated sensing technologies in environmental science. The Realtime Environment for Analytical Processing (REAP) is an NSF-funded project to address the technical challenges related to accessing and using heterogeneous sensor data from within the Kepler scientific workflow system. Using distinct use cases in terrestrial ecology and oceanography as motivating examples, we describe workflows and extensions to Kepler to stream and analyze data from observatory networks and archives. We focus on the use of two newly integrated data sources in Kepler: DataTurbine and OPeNDAP. Integrated access to both near real-time data streams and data archives from within Kepler facilitates both simple data exploration and sophisticated analysis and modeling with these data sources.

Research has shown that climate change creates warmer temperatures and drier conditions, leading to longer wildfire seasons and increased wildfire risks in the United States. These factors have, in turn, led to increases in the frequency, extent, and severity of wildfires in recent years. Given the danger posed by wildland fires to people, property, wildlife, and the environment, there is an urgent need to provide tools for effective wildfire management. Early detection of wildfires is essential to minimizing potentially catastrophic destruction. To that end, in this paper, we present our work on integrating multiple data sources into SmokeyNet, a deep learning model using spatiotemporal information to detect smoke from wildland fires. We present Multimodal SmokeyNet and SmokeyNet Ensemble for multimodal wildland fire smoke detection using satellite-based fire detections, weather sensor measurements, and optical camera images. An analysis is provided to compare these multimodal approaches to the baseline SmokeyNet in terms of accuracy metrics, as well as time-to-detect, which is important for the early detection of wildfires. Our results show that incorporating weather data in SmokeyNet improves performance numerically in terms of both F1 and time-to-detect over the baseline with a single data source. With a time-to-detect of only a few minutes, SmokeyNet can be used for automated early notification of wildfires, providing a useful tool in the fight against destructive wildfires. [ABSTRACT FROM AUTHOR]

Summary: Wildfires are a global crisis, but current fire models fail to capture vegetation response to changing climate. With drought and elevated temperature increasing the importance of vegetation dynamics to fire behavior, and the advent of next generation models capable of capturing increasingly complex physical processes, we provide a renewed focus on representation of woody vegetation in fire models. Currently, the most advanced representations of fire behavior and biophysical fire effects are found in distinct classes of fine‐scale models and do not capture variation in live fuel (i.e. living plant) properties. We demonstrate that plant water and carbon dynamics, which influence combustion and heat transfer into the plant and often dictate plant survival, provide the mechanistic linkage between fire behavior and effects. Our conceptual framework linking remotely sensed estimates of plant water and carbon to fine‐scale models of fire behavior and effects could be a critical first step toward improving the fidelity of the coarse scale models that are now relied upon for global fire forecasting. This process‐based approach will be essential to capturing the influence of physiological responses to drought and warming on live fuel conditions, strengthening the science needed to guide fire managers in an uncertain future. [ABSTRACT FROM AUTHOR]

Plain Language Summary: The Editors and Staff of Earth and Space Science acknowledge the importance of hundreds of peer reviewers who contributed to the scientific rigor of the papers published in the journal. The Editors wish to publicly recognize the 839 reviewers who gave selflessly of their time and expertise in 2022. [ABSTRACT FROM AUTHOR]

In this research, we investigated two approaches to detect job anomalies and/or contention for large scale computing efforts: 1. Preemptive job scheduling using binomial classification long short-term memory networks 2. Forecasting intra-node computing loads from the active jobs and additional job(s) For approach 1, we achieved a 14% improvement in computational resources utilization and an overall classification accuracy of 85% on real tasks executed in a High Energy Physics computing workflow. For this paper, we present the preliminary results used in second approach.

The challenge of sustainably producing goods and services for healthy living on a healthy planet requires simultaneous consideration of economic, societal, and environmental dimensions in manufacturing. Enabling technology for data driven manufacturing paradigms like Smart Manufacturing (a.k.a. Industry 4.0) serve as the technological backbone from which sustainable approaches to manufacturing can be implemented. Unfortunately, these technologies are typically associated with broader and deeper factory automation that is often too expensive and complex for the small and medium sized manufacturers (SMMs) that comprise the majority of manufacturing business in the USA and for whom their most valuable asset are the people whose jobs automation while replace. This paper describes an edge intelligent platform to integrate internet‐of‐things technologies with computing hardware, software, computational workflows for machine learning, and data ingestion, enabling SMMs to transition into smart manufacturing paradigms by leveraging the intelligence of their people. The platform leverages consumer grade electronics and sensors (affordable and portable), customized software with open source software packages (accessible), and existing communication network infrastructures (scalable). The software systems are implemented via Kubernetes orchestration of Docker containerization to ensure scalability and programmability. The platform is adaptive via computational workflow engines that produce information from data by processing with low‐cost edge computing devices while efficiently accessing resources of cloud servers as needed. The proposed edge platform connects workers to technological resources that provide computational intelligence (i.e., silicon‐based sensing and computation for data collection and contextualization) to enable decision making at the edge of advanced manufacturing. [ABSTRACT FROM AUTHOR]

Modern scientific simulations produce very large datasets, making interactive exploration of such data computationally prohibitive. An increasingly common data reduction technique is to store visualizations and other data extracts in a database. The Cinema project is one such approach, storing visualizations in an image database for post hoc exploration and interactive image-based analysis. This work focuses on developing efficient algorithms that can quantify various types of multivariate dependencies existing within multivariable datasets. It applies specific mutual information measures for the quantification of salient regions from multivariate image data. Using such information measures, the opacity of the images is modulated so that the salient regions are automatically highlighted and the domain scientists can interactively explore the most relevant regions for scientific discovery. [ABSTRACT FROM AUTHOR]

On behalf of the Editorial Board and Staff of Earth and Space Science, I thank the reviewers whose selfless dedication to science has ensured, once again, that the papers published in our journal in 2021 highlight the best Earth and space science in a manner that does justice to the authors and their work. All of us at Earth Peer reviewing is a demanding and often thankless job. It is however an essential component of the scientific process, ensuring the highest standards of integrity and rigor. Without the work of reviewers, who check data and procedures for possible bias and to ensure reproducibility, and who share their expertise to verify that the interpretations and conclusions of a paper are consistent with assumptions and existing knowledge, it would not be possible to trust in the scientific process. Our journal is particularly indebted to our reviewers: Earth and Space Science is a multidisciplinary journal that highlights methods, instruments, data and algorithms, and therefore we rely heavily on the direct expertise of our reviewers to verify and vouch for the quality of the papers we publish. We are indebted to all our reviewers, and we are delighted to acknowledge them publicly in this Editorial. Plain Language Summary: The Editors and Staff of Earth and Space Science acknowledge the importance of hundreds of peer reviewers who contributed to the scientific rigor of the papers published in the journal. The Editors wish to publicly recognize the 881 reviewers who gave selflessly of their time and expertise in 2021. Key Points: The editors thank the 2021 peer reviewers [ABSTRACT FROM AUTHOR]

This article provides a brief overview of 18 projects funded in Track D—Data and Model Sharing to Enable AI Innovation—of the 2020 Cohort of the National Science Foundation's (NSF) Convergence Accelerator (CA) program. The NSF CA is focused on transitioning research to practice for societal impact. The projects described here were funded for one year in phase I of the program, beginning September 2020. Their focus is on delivering tools, technologies, and techniques to assist in sharing data as well as data‐driven models to enable AI innovation. A broad range of domain areas is covered by the funded efforts, spanning across healthcare and medicine, to climate change and disaster, and civil/built infrastructure. The projects are addressing sharing of open as well as sensitive/private data. In September 2021, six of the eighteen projects described here were selected for phase II of the program, as noted in this article. [ABSTRACT FROM AUTHOR]

Key Point: The editors thank the 2020 peer reviewers [ABSTRACT FROM AUTHOR]

Scientific workflows are powerful tools for the management of scalable experiments, often composed of complex tasks running on distributed resources. Existing cyberinfrastructure provides components that can be utilized within repeatable workflows. However, data and computing advances continuously change the way scientific workflows get developed and executed, pushing the scientific activity to be more data-driven, heterogeneous, and collaborative. Workflow development today depends on the effective collaboration and communication of a cross-disciplinary team, not only with humans but also with analytical systems and infrastructure. This paper presents a collaboration-centered reference architecture to extend workflow systems with dynamic, predictable, and programmable interfaces to systems and infrastructure while bridging the exploratory and scalable activities in the scientific process. We present a conceptual design toward the development of methodologies and services for effective workflow-driven collaborations, namely the PPoDS methodology for collaborative workflow development and the SmartFlows Services for smart execution in a rapidly evolving cyberinfrastructure ecosystem. [ABSTRACT FROM AUTHOR]

Today’s computational, experimental, and observational sciences rely on computations that involve many related tasks. The success of a scientific mission often hinges on the computer automation of these workflows. In April 2015, the US Department of Energy (DOE) invited a diverse group of domain and computer scientists from national laboratories supported by the Office of Science, the National Nuclear Security Administration, from industry, and from academia to review the workflow requirements of DOE’s science and national security missions, to assess the current state of the art in science workflows, to understand the impact of emerging extreme-scale computing systems on those workflows, and to develop requirements for automated workflow management in future and existing environments. This article is a summary of the opinions of over 50 leading researchers attending this workshop. We highlight use cases, computing systems, workflow needs and conclude by summarizing the remaining challenges this community sees that inhibit large-scale scientific workflows from becoming a mainstream tool for extreme-scale science. [ABSTRACT FROM AUTHOR]

Modern web technologies facilitate the creation of high-quality data visualizations, and rich, interactive components across a wide variety of devices. Scientific workflow systems can greatly benefit from these technologies by giving scientists a better understanding of their data or model leading to new insights. While several projects have enabled web access to scientific workflow systems, they are primarily organized as a large portal server encapsulating the workflow engine. In this vision paper, we propose the design for Kepler WebView, a lightweight framework that integrates web technologies with the Kepler Scientific Workflow System. By embedding a web server in the Kepler process, Kepler WebView enables a wide variety of usage scenarios that would be difficult or impossible using the portal model. [ABSTRACT FROM AUTHOR]

We present a method to integrate multiple implementations of a machine learning algorithm in Kepler actors. This feature enables the user to compare accuracy and scalability of various implementations of a machine learning technique without having to change the workflow. These actors are based on the Execution Choice actor. They can be incorporated into any workflow to provide machine learning functionality. We describe a use case where actors that provide several implementations of k-means clustering can be used in a workflow to process sensor data from weather stations for predicting wildfire risks. [ABSTRACT FROM AUTHOR]

This paper extends FARSITE (a software used for wildfire modeling and simulation) to incorporate data assimilation techniques based on noisy and limited spatial resolution observations of the fire perimeter to improve the accuracy of wildfire spread predictions. To include data assimilation in FARSITE, uncertainty on both the simulated wildfire perimeter and the measured wildfire perimeter is used to formulate optimal updates for the prediction of the spread of the wildfire. For data assimilation, Wildfire perimeter measurements with limited spatial resolution and a known uncertainty are used to to formulate an optimal adjustment in the fire perimeter prediction. The adjustment is calculated from the Kalman filter gain in an Ensemble Kalman filter that exploit the uncertainty information on both the simulated wildfire perimeter and the measured wildfire perimeter. The approach is illustated on a wildfire simulation representing the 2014 Cocos fire and presents comparison results for hourly data assimilation results. [ABSTRACT FROM AUTHOR]

As more and more public and private Cloud resources are becoming available, it is common for a user to have access to multiple Cloud resources at the same time. Cloud federation dynamically aggregates multiple Cloud resources into a federated one. This paper explores how to build and run scientific workflows on top of a federated Cloud by integrating Kepler scientific workflow platform with CometCloud platform. Our integration can leverage capabilities of the two plat- forms: 1) dynamic resource federation, provisioning and allocation from CometCloud; 2) Easy workflow composition from Kepler; 3) Dynamic workflow scheduling and execution from the integration. We apply our integration to a bioinformatics workflow with three Cloud resources to evaluate its capabilities. We also discuss possible future directions from the integration. [ABSTRACT FROM AUTHOR]

The BBDTC ( https://biobigdata.ucsd.edu ) is a community-oriented platform to encourage high-quality knowledge dissemination with the aim of growing a well-informed biomedical big data community through collaborative efforts on training and education. The BBDTC collaborative is an e-learning platform that supports the biomedical community to access, develop and deploy open training materials. The BBDTC supports Big Data skill training for biomedical scientists at all levels, and from varied backgrounds. The natural hierarchy of courses allows them to be broken into and handled as modules. Modules can be reused in the context of multiple courses and reshuffled, producing a new and different, dynamic course called a playlist. Users may create playlists to suit their learning requirements and share it with individual users or the wider public. BBDTC leverages the maturity and design of the HUBzero content-management platform for delivering educational content. To facilitate the migration of existing content, the BBDTC supports importing and exporting course material from the edX platform. Migration tools will be extended in the future to support other platforms. Hands-on training software packages, i.e., toolboxes, are supported through Amazon EC2 and Virtualbox virtualization technologies, and they are available as: (i) downloadable lightweight Virtualbox Images providing a standardized software tool environment with software packages and test data on their personal machines, and (ii) remotely accessible Amazon EC2 Virtual Machines for accessing biomedical big data tools and scalable big data experiments. At the moment, the BBDTC site contains three open Biomedical big data training courses with lecture contents, videos and hands-on training utilizing VM toolboxes, covering diverse topics. The courses have enhanced the hands-on learning environment by providing structured content that users can use at their own pace. A four course biomedical big data series is planned for development in early 2016. [ABSTRACT FROM AUTHOR]

Scientific community across many disciplines is exploring new ways to extract knowledge from all available sources. Historically, written manuscripts have been the media of choice for recording experimental findings. Many disciplines such as social science, medical science are exploring ways to automate knowledge discovery from a vast repository of published scientific work. This work attempts to accelerate the process of information extraction by extending Kepler, a graphical workflow management tool. Kepler provides a simple way of designing and executing complex workflows in the form of directed graphs. This work presents a scalable approach to convert published research as PDF documents into indexable XML documents using Kepler. This conversion is a critical step in the Natural Language Processing pipeline. Kepler's distributed data processing capability enables scientists to scale this critical computation by simply adding more computing resources over the cloud. [ABSTRACT FROM AUTHOR]

Wildfires are critical for ecosystems in many geographical regions. However, our current urbanized existence in these environments is inducing the ecological balance to evolve into a different dynamic leading to the biggest fires in history. Wildfire wind speeds and directions change in an instant, and first responders can only be effective if they take action as quickly as the conditions change. What is lacking in disaster management today is a system integration of real-time sensor networks, satellite imagery, near-real time data management tools, wildfire simulation tools, and connectivity to emergency command centers before, during and after a wildfire. As a first time example of such an integrated system, the WIFIRE project is building an end-to-end cyberinfrastructure for real-time and data-driven simulation, prediction and visualization of wildfire behavior. This paper summarizes the approach and early results of the WIFIRE project to integrate networked observations, e.g., heterogeneous satellite data and real-time remote sensor data with computational techniques in signal processing, visualization, modeling and data assimilation to provide a scalable, technological, and educational solution to monitor weather patterns to predict a wildfire's Rate of Spread. [ABSTRACT FROM AUTHOR]

In the Big Data era, workflow systems need to embrace data parallel computing techniques for efficient data analysis and analytics. Here, the authors present an easy-to-use, scalable approach to build and execute Big Data applications using actor-oriented modeling in data parallel computing. They use two bioinformatics use cases for next-generation sequencing data analysis to verify the feasibility of their approach. [ABSTRACT FROM PUBLISHER]

Background: Mandatory deposit of raw microarray data files for public access, prior to study publication, provides significant opportunities to conduct new bioinformatics analyses within and across multiple datasets. Analysis of raw microarray data files (e.g. Affymetrix CEL files) can be time consuming, complex, and requires fundamental computational and bioinformatics skills. The development of analytical workflows to automate these tasks simplifies the processing of, improves the efficiency of, and serves to standardize multiple and sequential analyses. Once installed, workflows facilitate the tedious steps required to run rapid intra- and inter-dataset comparisons. Results: We developed a workflow to facilitate and standardize Meta-Analysis of Affymetrix Microarray Data analysis (MAAMD) in Kepler. Two freely available stand-alone software tools, R and AltAnalyze were embedded in MAAMD. The inputs of MAAMD are user-editable csv files, which contain sample information and parameters describing the locations of input files and required tools. MAAMD was tested by analyzing 4 different GEO datasets from mice and drosophila. MAAMD automates data downloading, data organization, data quality control assesment, differential gene expression analysis, clustering analysis, pathway visualization, gene-set enrichment analysis, and cross-species orthologous-gene comparisons. MAAMD was utilized to identify gene orthologues responding to hypoxia or hyperoxia in both mice and drosophila. The entire set of analyses for 4 datasets (34 total microarrays) finished in ~ one hour. Conclusions: MAAMD saves time, minimizes the required computer skills, and offers a standardized procedure for users to analyze microarray datasets and make new intra- and inter-dataset comparisons. [ABSTRACT FROM AUTHOR]

Abstract: Scientific workflows integrate data and computing interfacesas configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiKworkflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing andfuture extensibility. [Copyright &y& Elsevier]

The size and frequency of wildland fires in the western United States have dramatically increased in recent years. On high-fire-risk days, a small fire ignition can rapidly grow and become out of control. Early detection of fire ignitions from initial smoke can assist the response to such fires before they become difficult to manage. Past deep learning approaches for wildfire smoke detection have suffered from small or unreliable datasets that make it difficult to extrapolate performance to real-world scenarios. In this work, we present the Fire Ignition Library (FIgLib), a publicly available dataset of nearly 25,000 labeled wildfire smoke images as seen from fixed-view cameras deployed in Southern California. We also introduce SmokeyNet, a novel deep learning architecture using spatiotemporal information from camera imagery for real-time wildfire smoke detection. When trained on the FIgLib dataset, SmokeyNet outperforms comparable baselines and rivals human performance. We hope that the availability of the FIgLib dataset and the SmokeyNet architecture will inspire further research into deep learning methods for wildfire smoke detection, leading to automated notification systems that reduce the time to wildfire response. [ABSTRACT FROM AUTHOR]