Cloud computing platforms to support cryo-EM structure determination.

Leveraging the power of single-particle cryo-electron microscopy (cryo-EM) requires robust and accessible computational infrastructure. Here, we summarize the cloud computing landscape and picture the outlook of a hybrid cryo-EM computing workflow, and make suggestions to the community to facilitate a future for cryo-EM that integrates into cloud computing infrastructure.

A cloud-based learning module for biomarker discovery.

This manuscript describes the development of a resource module that is part of a learning platform named "NIGMS Sandbox for Cloud-based Learning" https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox at the beginning of this Supplement. This module delivers learning materials on basic principles in biomarker discovery in an interactive format that uses appropriate cloud resources for data access and analyses. In collaboration with Google Cloud, Deloitte Consulting and NIGMS, the Rhode Island INBRE Molecular Informatics Core developed a cloud-based training module for biomarker discovery. The module consists of nine submodules covering various topics on biomarker discovery and assessment and is deployed on the Google Cloud Platform and available for public use through the NIGMS Sandbox. The submodules are written as a series of Jupyter Notebooks utilizing R and Bioconductor for biomarker and omics data analysis. The submodules cover the following topics: 1) introduction to biomarkers; 2) introduction to R data structures; 3) introduction to linear models; 4) introduction to exploratory analysis; 5) rat renal ischemia-reperfusion injury case study; (6) linear and logistic regression for comparison of quantitative biomarkers; 7) exploratory analysis of proteomics IRI data; 8) identification of IRI biomarkers from proteomic data; and 9) machine learning methods for biomarker discovery. Each notebook includes an in-line quiz for self-assessment on the submodule topic and an overview video is available on YouTube (https://www.youtube.com/watch?v=2-Q9Ax8EW84). This manuscript describes the development of a resource module that is part of a learning platform named ``NIGMS Sandbox for Cloud-based Learning'' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.

A cloud-based training module for efficient de novo transcriptome assembly using Nextflow and Google cloud.

This study describes the development of a resource module that is part of a learning platform named "NIGMS Sandbox for Cloud-based Learning" (https://github.com/NIGMS/NIGMS-Sandbox). The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox at the beginning of this Supplement. This module delivers learning materials on de novo transcriptome assembly using Nextflow in an interactive format that uses appropriate cloud resources for data access and analysis. Cloud computing is a powerful new means by which biomedical researchers can access resources and capacity that were previously either unattainable or prohibitively expensive. To take advantage of these resources, however, the biomedical research community needs new skills and knowledge. We present here a cloud-based training module, developed in conjunction with Google Cloud, Deloitte Consulting, and the NIH STRIDES Program, that uses the biological problem of de novo transcriptome assembly to demonstrate and teach the concepts of computational workflows (using Nextflow) and cost- and resource-efficient use of Cloud services (using Google Cloud Platform). Our work highlights the reduced necessity of on-site computing resources and the accessibility of cloud-based infrastructure for bioinformatics applications.

Cloud-based introduction to BASH programming for biologists.

This manuscript describes the development of a resource module that is part of a learning platform named 'NIGMS Sandbox for Cloud-based Learning', https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial authored by National Institute of General Medical Sciences: NIGMS Sandbox: A Learning Platform toward Democratizing Cloud Computing for Biomedical Research at the beginning of this supplement. This module delivers learning materials introducing the utility of the BASH (Bourne Again Shell) programming language for genomic data analysis in an interactive format that uses appropriate cloud resources for data access and analyses. The next-generation sequencing revolution has generated massive amounts of novel biological data from a multitude of platforms that survey an ever-growing list of genomic modalities. These data require significant downstream computational and statistical analyses to glean meaningful biological insights. However, the skill sets required to generate these data are vastly different from the skills required to analyze these data. Bench scientists that generate next-generation data often lack the training required to perform analysis of these datasets and require support from bioinformatics specialists. Dedicated computational training is required to empower biologists in the area of genomic data analysis, however, learning to efficiently leverage a command line interface is a significant barrier in learning how to leverage common analytical tools. Cloud platforms have the potential to democratize access to the technical tools and computational resources necessary to work with modern sequencing data, providing an effective framework for bioinformatics education. This module aims to provide an interactive platform that slowly builds technical skills and knowledge needed to interact with genomics data on the command line in the Cloud. The sandbox format of this module enables users to move through the material at their own pace and test their grasp of the material with knowledge self-checks before building on that material in the next sub-module. This manuscript describes the development of a resource module that is part of a learning platform named ``NIGMS Sandbox for Cloud-based Learning'' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.

CCPA: cloud-based, self-learning modules for consensus pathway analysis using GO, KEGG and Reactome.

This manuscript describes the development of a resource module that is part of a learning platform named 'NIGMS Sandbox for Cloud-based Learning' (https://github.com/NIGMS/NIGMS-Sandbox). The module delivers learning materials on Cloud-based Consensus Pathway Analysis in an interactive format that uses appropriate cloud resources for data access and analyses. Pathway analysis is important because it allows us to gain insights into biological mechanisms underlying conditions. But the availability of many pathway analysis methods, the requirement of coding skills, and the focus of current tools on only a few species all make it very difficult for biomedical researchers to self-learn and perform pathway analysis efficiently. Furthermore, there is a lack of tools that allow researchers to compare analysis results obtained from different experiments and different analysis methods to find consensus results. To address these challenges, we have designed a cloud-based, self-learning module that provides consensus results among established, state-of-the-art pathway analysis techniques to provide students and researchers with necessary training and example materials. The training module consists of five Jupyter Notebooks that provide complete tutorials for the following tasks: (i) process expression data, (ii) perform differential analysis, visualize and compare the results obtained from four differential analysis methods (limma, t-test, edgeR, DESeq2), (iii) process three pathway databases (GO, KEGG and Reactome), (iv) perform pathway analysis using eight methods (ORA, CAMERA, KS test, Wilcoxon test, FGSEA, GSA, SAFE and PADOG) and (v) combine results of multiple analyses. We also provide examples, source code, explanations and instructional videos for trainees to complete each Jupyter Notebook. The module supports the analysis for many model (e.g. human, mouse, fruit fly, zebra fish) and non-model species. The module is publicly available at https://github.com/NIGMS/Consensus-Pathway-Analysis-in-the-Cloud. This manuscript describes the development of a resource module that is part of a learning platform named ``NIGMS Sandbox for Cloud-based Learning'' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.

Whole-genome bisulfite sequencing data analysis learning module on Google Cloud Platform.

This study describes the development of a resource module that is part of a learning platform named 'NIGMS Sandbox for Cloud-based Learning' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox at the beginning of this Supplement. This module is designed to facilitate interactive learning of whole-genome bisulfite sequencing (WGBS) data analysis utilizing cloud-based tools in Google Cloud Platform, such as Cloud Storage, Vertex AI notebooks and Google Batch. WGBS is a powerful technique that can provide comprehensive insights into DNA methylation patterns at single cytosine resolution, essential for understanding epigenetic regulation across the genome. The designed learning module first provides step-by-step tutorials that guide learners through two main stages of WGBS data analysis, preprocessing and the identification of differentially methylated regions. And then, it provides a streamlined workflow and demonstrates how to effectively use it for large datasets given the power of cloud infrastructure. The integration of these interconnected submodules progressively deepens the user's understanding of the WGBS analysis process along with the use of cloud resources. Through this module, we can enhance the accessibility and adoption of cloud computing in epigenomic research, speeding up the advancements in the related field and beyond. This manuscript describes the development of a resource module that is part of a learning platform named ``NIGMS Sandbox for Cloud-based Learning'' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.

Reusable tutorials for using cloud-based computing environments for the analysis of bacterial gene expression data from bulk RNA sequencing.

This manuscript describes the development of a resource module that is part of a learning platform named "NIGMS Sandbox for Cloud-based Learning" https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox at the beginning of this Supplement. This module delivers learning materials on RNA sequencing (RNAseq) data analysis in an interactive format that uses appropriate cloud resources for data access and analyses. Biomedical research is increasingly data-driven, and dependent upon data management and analysis methods that facilitate rigorous, robust, and reproducible research. Cloud-based computing resources provide opportunities to broaden the application of bioinformatics and data science in research. Two obstacles for researchers, particularly those at small institutions, are: (i) access to bioinformatics analysis environments tailored to their research; and (ii) training in how to use Cloud-based computing resources. We developed five reusable tutorials for bulk RNAseq data analysis to address these obstacles. Using Jupyter notebooks run on the Google Cloud Platform, the tutorials guide the user through a workflow featuring an RNAseq dataset from a study of prophage altered drug resistance in Mycobacterium chelonae. The first tutorial uses a subset of the data so users can learn analysis steps rapidly, and the second uses the entire dataset. Next, a tutorial demonstrates how to analyze the read count data to generate lists of differentially expressed genes using R/DESeq2. Additional tutorials generate read counts using the Snakemake workflow manager and Nextflow with Google Batch. All tutorials are open-source and can be used as templates for other analysis.

NeuronBridge: an intuitive web application for neuronal morphology search across large data sets.

BACKGROUND: Neuroscience research in Drosophila is benefiting from large-scale connectomics efforts using electron microscopy (EM) to reveal all the neurons in a brain and their connections. To exploit this knowledge base, researchers relate a connectome's structure to neuronal function, often by studying individual neuron cell types. Vast libraries of fly driver lines expressing fluorescent reporter genes in sets of neurons have been created and imaged using confocal light microscopy (LM), enabling the targeting of neurons for experimentation. However, creating a fly line for driving gene expression within a single neuron found in an EM connectome remains a challenge, as it typically requires identifying a pair of driver lines where only the neuron of interest is expressed in both. This task and other emerging scientific workflows require finding similar neurons across large data sets imaged using different modalities. RESULTS: Here, we present NeuronBridge, a web application for easily and rapidly finding putative morphological matches between large data sets of neurons imaged using different modalities. We describe the functionality and construction of the NeuronBridge service, including its user-friendly graphical user interface (GUI), extensible data model, serverless cloud architecture, and massively parallel image search engine. CONCLUSIONS: NeuronBridge fills a critical gap in the Drosophila research workflow and is used by hundreds of neuroscience researchers around the world. We offer our software code, open APIs, and processed data sets for integration and reuse, and provide the application as a service at http://neuronbridge.janelia.org .

Serverless computing in omics data analysis and integration.

A comprehensive analysis of omics data can require vast computational resources and access to varied data sources that must be integrated into complex, multi-step analysis pipelines. Execution of many such analyses can be accelerated by applying the cloud computing paradigm, which provides scalable resources for storing data of different types and parallelizing data analysis computations. Moreover, these resources can be reused for different multi-omics analysis scenarios. Traditionally, developers are required to manage a cloud platform's underlying infrastructure, configuration, maintenance and capacity planning. The serverless computing paradigm simplifies these operations by automatically allocating and maintaining both servers and virtual machines, as required for analysis tasks. This paradigm offers highly parallel execution and high scalability without manual management of the underlying infrastructure, freeing developers to focus on operational logic. This paper reviews serverless solutions in bioinformatics and evaluates their usage in omics data analysis and integration. We start by reviewing the application of the cloud computing model to a multi-omics data analysis and exposing some shortcomings of the early approaches. We then introduce the serverless computing paradigm and show its applicability for performing an integrative analysis of multiple omics data sources in the context of the COVID-19 pandemic.

Interactive Quantum Chemistry Enabled by Machine Learning, Graphical Processing Units, and Cloud Computing.

Modern quantum chemistry algorithms are increasingly able to accurately predict molecular properties that are useful for chemists in research and education. Despite this progress, performing such calculations is currently unattainable to the wider chemistry community, as they often require domain expertise, computer programming skills, and powerful computer hardware. In this review, we outline methods to eliminate these barriers using cutting-edge technologies. We discuss the ingredients needed to create accessible platforms that can compute quantum chemistry properties in real time, including graphical processing units-accelerated quantum chemistry in the cloud, artificial intelligence-driven natural molecule input methods, and extended reality visualization. We end by highlighting a series of exciting applications that assemble these components to create uniquely interactive platforms for computing and visualizing spectra, 3D structures, molecular orbitals, and many other chemical properties.

Fractional social optimization-based migration and replica management algorithm for load balancing in distributed file system for cloud computing.

Effective management of data is a major issue in Distributed File System (DFS), like the cloud. This issue is handled by replicating files in an effective manner, which can minimize the time of data access and elevate the data availability. This paper devises a Fractional Social Optimization Algorithm (FSOA) for replica management along with balancing load in DFS in the cloud stage. Balancing the workload for DFS is the main objective. Here, the chunk creation is done by partitioning the file into a different number of chunks considering Deep Fuzzy Clustering (DFC) and then in the round-robin manner the Virtual machine (VM) is assigned. In that case for balancing the load considering certain objectives like resource use, energy consumption and migration cost thereby the load balancing is performed with the proposed FSOA. Here, the FSOA is formulated by uniting the Social optimization algorithm (SOA) and Fractional Calculus (FC). The replica management is done in DFS using the proposed FSOA by considering the various objectives. The FSOA has the smallest load of 0.299, smallest cost of 0.395, smallest energy consumption of 0.510, smallest overhead of 0.358, and smallest throughput of 0.537.

SJFO: Sail Jelly Fish Optimization enabled VM migration with DRNN-based prediction for load balancing in cloud computing.

The dynamic workload is evenly distributed among all nodes using balancing methods like hosts or VMs. Load Balancing as a Service (LBaaS) is another name for load balancing in the cloud. In this research work, the load is balanced by the application of Virtual Machine (VM) migration carried out by proposed Sail Jelly Fish Optimization (SJFO). The SJFO is formed by combining Sail Fish Optimizer (SFO) and Jellyfish Search (JS) optimizer. In the Cloud model, many Physical Machines (PMs) are present, where these PMs are comprised of many VMs. Each VM has many tasks, and these tasks depend on various parameters like Central Processing Unit (CPU), memory, Million Instructions per Second (MIPS), capacity, total number of processing entities, as well as bandwidth. Here, the load is predicted by Deep Recurrent Neural Network (DRNN) and this predicted load is compared with a threshold value, where VM migration is done based on predicted values. Furthermore, the performance of SJFO-VM is analysed using the metrics like capacity, load, and resource utilization. The proposed method shows better performance with a superior capacity of 0.598, an inferior load of 0.089, and an inferior resource utilization of 0.257.

Hybrid deep learning and optimized clustering mechanism for load balancing and fault tolerance in cloud computing.

Cloud services are one of the most quickly developing technologies. Furthermore, load balancing is recognized as a fundamental challenge for achieving energy efficiency. The primary function of load balancing is to deliver optimal services by releasing the load over multiple resources. Fault tolerance is being used to improve the reliability and accessibility of the network. In this paper, a hybrid Deep Learning-based load balancing algorithm is developed. Initially, tasks are allocated to all VMs in a round-robin method. Furthermore, the Deep Embedding Cluster (DEC) utilizes the Central Processing Unit (CPU), bandwidth, memory, processing elements, and frequency scaling factors while determining if a VM is overloaded or underloaded. The task performed on the overloaded VM is valued and the tasks accomplished on the overloaded VM are assigned to the underloaded VM for cloud load balancing. In addition, the Deep Q Recurrent Neural Network (DQRNN) is proposed to balance the load based on numerous factors such as supply, demand, capacity, load, resource utilization, and fault tolerance. Furthermore, the effectiveness of this model is assessed by load, capacity, resource consumption, and success rate, with ideal values of 0.147, 0.726, 0.527, and 0.895 are achieved.

An Analytical Model of IaaS Architecture for Determining Resource Utilization.

Cloud computing has become a major component of the modern IT ecosystem. A key contributor to this has been the development of Infrastructure as a Service (IaaS) architecture, in which users' virtual machines (VMs) are run on the service provider's physical infrastructure, making it possible to become independent of the need to purchase one's own physical machines (PMs). One of the main aspects to consider when designing such systems is achieving the optimal utilization of individual resources, such as processor, RAM, disk, and available bandwidth. In response to these challenges, the authors developed an analytical model (the ARU method) to determine the average utilization levels of the aforementioned resources. The effectiveness of the proposed analytical model was evaluated by comparing the results obtained by utilizing the model with those obtained by conducting a digital simulation of the operation of a cloud system according to the IaaS paradigm. The results show the effectiveness of the model regardless of the structure of the emerging requests, the variability of the capacity of individual resources, and the number of physical machines in the system. This translates into the applicability of the model in the design process of cloud systems.

A Review and Comparative Analysis of Relevant Approaches of Zero Trust Network Model.

The Zero Trust safety architecture emerged as an intriguing approach for overcoming the shortcomings of standard network security solutions. This extensive survey study provides a meticulous explanation of the underlying principles of Zero Trust, as well as an assessment of the many strategies and possibilities for effective implementation. The survey begins by examining the role of authentication and access control within Zero Trust Architectures, and subsequently investigates innovative authentication, as well as access control solutions across different scenarios. It more deeply explores traditional techniques for encryption, micro-segmentation, and security automation, emphasizing their importance in achieving a secure Zero Trust environment. Zero Trust Architecture is explained in brief, along with the Taxonomy of Zero Trust Network Features. This review article provides useful insights into the Zero Trust paradigm, its approaches, problems, and future research objectives for scholars, practitioners, and policymakers. This survey contributes to the growth and implementation of secure network architectures in critical infrastructures by developing a deeper knowledge of Zero Trust.

Network Slicing in 6G: A Strategic Framework for IoT in Smart Cities.

The emergence of 6G communication technologies brings both opportunities and challenges for the Internet of Things (IoT) in smart cities. In this paper, we introduce an advanced network slicing framework designed to meet the complex demands of 6G smart cities' IoT deployments. The framework development follows a detailed methodology that encompasses requirement analysis, metric formulation, constraint specification, objective setting, mathematical modeling, configuration optimization, performance evaluation, parameter tuning, and validation of the final design. Our evaluations demonstrate the framework's high efficiency, evidenced by low round-trip time (RTT), minimal packet loss, increased availability, and enhanced throughput. Notably, the framework scales effectively, managing multiple connections simultaneously without compromising resource efficiency. Enhanced security is achieved through robust features such as 256-bit encryption and a high rate of authentication success. The discussion elaborates on these findings, underscoring the framework's impressive performance, scalability, and security capabilities.

Trust Management and Resource Optimization in Edge and Fog Computing Using the CyberGuard Framework.

The growing importance of edge and fog computing in the modern IT infrastructure is driven by the rise of decentralized applications. However, resource allocation within these frameworks is challenging due to varying device capabilities and dynamic network conditions. Conventional approaches often result in poor resource use and slowed advancements. This study presents a novel strategy for enhancing resource allocation in edge and fog computing by integrating machine learning with the blockchain for reliable trust management. Our proposed framework, called CyberGuard, leverages the blockchain's inherent immutability and decentralization to establish a trustworthy and transparent network for monitoring and verifying edge and fog computing transactions. CyberGuard combines the Trust2Vec model with conventional machine-learning models like SVM, KNN, and random forests, creating a robust mechanism for assessing trust and security risks. Through detailed optimization and case studies, CyberGuard demonstrates significant improvements in resource allocation efficiency and overall system performance in real-world scenarios. Our results highlight CyberGuard's effectiveness, evidenced by a remarkable accuracy, precision, recall, and F1-score of 98.18%, showcasing the transformative potential of our comprehensive approach in edge and fog computing environments.

Smart Resource Allocation in Mobile Cloud Next-Generation Network (NGN) Orchestration with Context-Aware Data and Machine Learning for the Cost Optimization of Microservice Applications.

Mobile cloud computing (MCC) provides resources to users to handle smart mobile applications. In MCC, task scheduling is the solution for mobile users' context-aware computation resource-rich applications. Most existing approaches have achieved a moderate service reliability rate due to a lack of instance-centric resource estimations and task offloading, a statistical NP-hard problem. The current intelligent scheduling process cannot address NP-hard problems due to traditional task offloading approaches. To address this problem, the authors design an efficient context-aware service offloading approach based on instance-centric measurements. The revised machine learning model/algorithm employs task adaptation to make decisions regarding task offloading. The proposed MCVS scheduling algorithm predicts the usage rates of individual microservices for a practical task scheduling scheme, considering mobile device time, cost, network, location, and central processing unit (CPU) power to train data. One notable feature of the microservice software architecture is its capacity to facilitate the scalability, flexibility, and independent deployment of individual components. A series of simulation results show the efficiency of the proposed technique based on offloading, CPU usage, and execution time metrics. The experimental results efficiently show the learning rate in training and testing in comparison with existing approaches, showing efficient training and task offloading phases. The proposed system has lower costs and uses less energy to offload microservices in MCC. Graphical results are presented to define the effectiveness of the proposed model. For a service arrival rate of 80%, the proposed model achieves an average 4.5% service offloading rate and 0.18% CPU usage rate compared with state-of-the-art approaches. The proposed method demonstrates efficiency in terms of cost and energy savings for microservice offloading in mobile cloud computing (MCC).

Application of Deep Learning and Intelligent Sensing Analysis in Smart Home.

Deep learning technology can improve sensing efficiency and has the ability to discover potential patterns in data; the efficiency of user behavior recognition in the field of smart homes has been further improved, making the recognition process more intelligent and humanized. This paper analyzes the optical sensors commonly used in smart homes and their working principles through case studies and explores the technical framework of user behavior recognition based on optical sensors. At the same time, CiteSpace (Basic version 6.2.R6) software is used to visualize and analyze the related literature, elaborate the main research hotspots and evolutionary changes of optical sensor-based smart home user behavior recognition, and summarize the future research trends. Finally, fully utilizing the advantages of cloud computing technology, such as scalability and on-demand services, combining typical life situations and the requirements of smart home users, a smart home data collection and processing technology framework based on elderly fall monitoring scenarios is designed. Based on the comprehensive research results, the application and positive impact of optical sensors in smart home user behavior recognition were analyzed, and inspiration was provided for future smart home user experience research.

Dynamic Privacy-Preserving Anonymous Authentication Scheme for Condition-Matching in Fog-Cloud-Based VANETs.

Secure group communication in Vehicle Ad hoc Networks (VANETs) over open channels remains a challenging task. To enable secure group communications with conditional privacy, it is necessary to establish a secure session using Authenticated Key Agreement (AKA). However, existing AKAs suffer from problems such as cross-domain dynamic group session key negotiation and heavy computational burdens on the Trusted Authority (TA) and vehicles. To address these challenges, we propose a dynamic privacy-preserving anonymous authentication scheme for condition matching in fog-cloud-based VANETs. The scheme employs general Elliptic Curve Cryptosystem (ECC) technology and fog-cloud computing methods to decrease computational overhead for On-Board Units (OBUs) and supports multiple TAs for improved service quality and robustness. Furthermore, certificateless technology alleviates TAs of key management burdens. The security analysis indicates that our solution satisfies the communication security and privacy requirements. Experimental simulations verify that our method achieves optimal overall performance with lower computational costs and smaller communication overhead compared to state-of-the-art solutions.