BrainForge is a cloud-enabled, web-based analysis platform for neuroimaging research. This website allows users to archive data from a study and effortlessly process data on a high-performance computing cluster. After analyses are completed, results can be quickly shared with colleagues. BrainForge solves multiple problems for researchers who want to analyze neuroimaging data, including issues related to software, reproducibility, computational resources, and data sharing. BrainForge can currently process structural, functional, diffusion, and arterial spin labeling MRI modalities, including preprocessing and group level analyses. Additional pipelines are currently being added, and the pipelines can accept the BIDS format. Analyses are conducted completely inside of Singularity containers and utilize popular software packages including Nipype, Statistical Parametric Mapping, the Group ICA of fMRI Toolbox, and FreeSurfer. BrainForge also features several interfaces for group analysis, including a fully automated adaptive ICA approach.

The high-performance computing (HPC) platform for large-scale drug discovery simulation demands significant investment in speciality hardware, maintenance, resource management, and running costs. The rapid growth in computing hardware has made it possible to provide cost-effective, robust, secure, and scalable alternatives to the on-premise (on-prem) HPC via Cloud, Fog, and Edge computing. It has enabled recent state-of-the-art machine learning (ML) and artificial intelligence (AI)-based tools for drug discovery, such as BERT, BARD, AlphaFold2, and GPT. This chapter attempts to overview types of software architectures for developing scientific software or application with deployment agnostic (on-prem to cloud and hybrid) use cases. Furthermore, the chapter aims to outline how the innovation is disrupting the orthodox mindset of monolithic software running on on-prem HPC and provide the paradigm shift landscape to microservices driven application programming (API) and message parsing interface (MPI)-based scientific computing across the distributed, high-available infrastructure. This is coupled with agile DevOps, and good coding practices, low code and no-code application development frameworks for cost-efficient, secure, automated, and robust scientific application life cycle management.

There is a rapid increase in the number of edge devices in IoT solutions, generating vast amounts of data that need to be processed and analyzed efficiently. Traditional cloud-based architectures can face latency, bandwidth, and privacy challenges when dealing with this data flood. There is currently no unified approach to the creation of edge computing solutions. This work addresses this problem by exploring containerization for data processing solutions at the network\'s edge. The current approach involves creating a specialized application compatible with the device used. Another approach involves using containerization for deployment and monitoring. The heterogeneity of edge environments would greatly benefit from a universal modular platform. Our proposed edge computing-based framework implements a streaming extract, transform, and load pipeline for data processing and analysis using ZeroMQ as the communication backbone and containerization for scalable deployment. Results demonstrate the effectiveness of the proposed framework, making it suitable for time-sensitive IoT applications.

With the advent of high-throughput biotechnological platforms and their ever-growing capacity, life science has turned into a digitized, computational and data-intensive discipline. As a consequence, standard analysis with a bioinformatics pipeline in the context of routine production has become a challenge such that the data can be processed in real-time and delivered to the end-users as fast as possible. The usage of workflow management systems along with packaging systems and containerization technologies offer an opportunity to tackle this challenge. While very powerful, they can be used and combined in many multiple ways which may differ from one developer to another. Therefore, promoting the homogeneity of the workflow implementation requires guidelines and protocols which detail how the source code of the bioinformatics pipeline should be written and organized to ensure its usability, maintainability, interoperability, sustainability, portability, reproducibility, scalability and efficiency. Capitalizing on Nextflow, Conda, Docker, Singularity and the nf-core initiative, we propose a set of best practices along the development life cycle of the bioinformatics pipeline and deployment for production operations which target different expert communities including i) the bioinformaticians and statisticians ii) the software engineers and iii) the data managers and core facility engineers. We implemented Geniac (Automatic Configuration GENerator and Installer for nextflow pipelines) which consists of a toolbox with three components: i) a technical documentation available at https://geniac.readthedocs.io to detail coding guidelines for the bioinformatics pipeline with Nextflow, ii) a command line interface with a linter to check that the code respects the guidelines, and iii) an add-on to generate configuration files, build the containers and deploy the pipeline. The Geniac toolbox aims at the harmonization of development practices across developers and automation of the generation of configuration files and containers by parsing the source code of the Nextflow pipeline.

UNASSIGNED: Neuroimaging technology has experienced explosive growth and transformed the study of neural mechanisms across health and disease. However, given the diversity of sophisticated tools for handling neuroimaging data, the field faces challenges in method integration, particularly across multiple modalities and species. Specifically, researchers often have to rely on siloed approaches which limit reproducibility, with idiosyncratic data organization and limited software interoperability.
UNASSIGNED: To address these challenges, we have developed Quantitative Neuroimaging Environment & Toolbox (QuNex), a platform for consistent end-to-end processing and analytics. QuNex provides several novel functionalities for neuroimaging analyses, including a \"turnkey\" command for the reproducible deployment of custom workflows, from onboarding raw data to generating analytic features.
UNASSIGNED: The platform enables interoperable integration of multi-modal, community-developed neuroimaging software through an extension framework with a software development kit (SDK) for seamless integration of community tools. Critically, it supports high-throughput, parallel processing in high-performance compute environments, either locally or in the cloud. Notably, QuNex has successfully processed over 10,000 scans across neuroimaging consortia, including multiple clinical datasets. Moreover, QuNex enables integration of human and non-human workflows via a cohesive translational platform.
UNASSIGNED: Collectively, this effort stands to significantly impact neuroimaging method integration across acquisition approaches, pipelines, datasets, computational environments, and species. Building on this platform will enable more rapid, scalable, and reproducible impact of neuroimaging technology across health and disease.

Cloud computing is a commercial and economic paradigm that has gained traction since 2006 and is presently the most significant technology in IT sector. From the notion of cloud computing to its energy efficiency, cloud has been the subject of much discussion. The energy consumption of data centres alone will rise from 200 TWh in 2016 to 2967 TWh in 2030. The data centres require a lot of power to provide services, which increases CO2 emissions. In this survey paper, software-based technologies that can be used for building green data centers and include power management at individual software level has been discussed. The paper discusses the energy efficiency in containers and problem-solving approaches used for reducing power consumption in data centers. Further, the paper also gives details about the impact of data centers on environment that includes the e-waste and the various standards opted by different countries for giving rating to the data centers. This article goes beyond just demonstrating new green cloud computing possibilities. Instead, it focuses the attention and resources of academia and society on a critical issue: long-term technological advancement. The article covers the new technologies that can be applied at the individual software level that includes techniques applied at virtualization level, operating system level and application level. It clearly defines different measures at each level to reduce the energy consumption that clearly adds value to the current environmental problem of pollution reduction. This article also addresses the difficulties, concerns, and needs that cloud data centres and cloud organisations must grasp, as well as some of the factors and case studies that influence green cloud usage.

Lately, the software development industry is going through a slow but real transformation. Software is increasingly a part of everything, and, software developers, are trying to cope with this exploding demand through more automation. The pipelining technique of continuous integration (CI) and continuous delivery (CD) has developed considerably due to the overwhelming demand for the deployment and deliverability of new features and applications. As a result, DevOps approaches and Agile principles have been developed, in which developers collaborate closely with infrastructure engineers to guarantee that their applications are deployed quickly and reliably. Thanks to pipeline approach thinking, the efficiency of projects has greatly improved. Agile practices represent the introduction to the system of new features in each sprint delivery. Those practices may contain well-developed features or can contain bugs or failures which impact the delivery. The pipeline approach, depicted in this paper, overcomes the problems of delivery, improving the delivery timeline, the test load steps, and the benchmarking tasks. It decreases system interruption by integrating multiple test steps and adds stability and deliverability to the entire process. It provides standardization which means having an established, time-tested process to use, and can also decrease ambiguity and guesswork, guarantee quality and boost productivity. This tool is developed with an interpreted language, namely Bash, which offers an easier method to integrate it into any platform. Based on the experimental results, we demonstrate the value that this solution currently creates. This solution provides an effective and efficient way to generate, manage, customize, and automate Agile-based CI and CD projects through automated pipelines. The suggested system acts as a starting point for standard CI/CD processes, caches Docker layers for subsequent usage, and implements highly available deliverables in a Kubernetes cluster using Helm. Changing the principles of this solution and expanding it into multiple platforms (windows) will be addressed in a future discussion.

Information systems used by platform trials should handle changes that are not predefined. Unfortunately, the technical architecture of most existing clinical data management systems (CDMS) do not support changes to be incorporated into an ongoing trial. Adaptive clinical trials need advanced architectural solutions setup to enable biomarker stratification and enrichment strategy necessary for the adaptive clinical trial operation. This short paper presents the microservices-based architecture solution that is used to run and support the adaptive RECORDS-Trial.

Kubernetes (K8s) is expected to be a key container orchestration tool for edge computing infrastructures owing to its various features for supporting container deployment and dynamic resource management. For example, its horizontal pod autoscaling feature provides service availability and scalability by increasing the number of replicas. kube-proxy provides traffic load-balancing between replicas by distributing client requests equally to all pods (replicas) of an application in a K8s cluster. However, this approach can result in long delays when requests are forwarded to remote workers, especially in edge computing environments where worker nodes are geographically dispersed. Moreover, if the receiving worker is overloaded, the request-processing delay can increase significantly. To overcome these limitations, this paper proposes an enhanced load balancer called resource adaptive proxy (RAP). RAP periodically monitors the resource status of each pod and the network status among worker nodes to aid in load-balancing decisions. Furthermore, it preferentially handles requests locally to the maximum extent possible. If the local worker node is overloaded, RAP forwards its requests to the best node in the cluster while considering resource availability. Our experimental results demonstrated that RAP could significantly improve throughput and reduce request latency compared with the default load-balancing mechanism of K8s.

The use of monitoring systems based on cloud computing has become common for smart buildings. However, the dilemma of centralization versus decentralization, in terms of gathering information and making the right decisions based on it, remains. Performance, dependent on the system design, does matter for emergency detection, where response time and loading behavior become very important. We studied several design options based on edge computing and containers for a smart building monitoring system that sends alerts to the responsible personnel when necessary. The study evaluated performance, including a qualitative analysis and load testing, for our experimental settings. From 700+ edge nodes, we obtained response times that were 30% lower for the public cloud versus the local solution. For up to 100 edge nodes, the values were better for the latter, and in between, they were rather similar. Based on an interpretation of the results, we developed recommendations for five real-world configurations, and we present the design choices adopted in our development for a complex of smart buildings.