In the last decades, we have witnessed a spectacular information explosion over the Internet. Millions of users are consuming the Internet through various services, such as mobile applications, and online games. The service providers, at the back-end side, are supported by state-of-art infrastructures. Targeting on providing the services at scale, virtualization is one of the emerging technologies used in data centers and cloud environments to improve the quality of services. In this project, we aim to develop a dynamic resource management scheme based on virtual containers. It collects the runtime job progress from the running tasks and allocates the resources dynamically to improve the overall system performance.

Cloud computing nowadays is not an emerging topic, and virtualization is an indispensable technology to expedite cloud computing to become the next sign of the coming Internet revolution. In real life, scientists never stop at exploring the possibilities from such technology by investigating millions of experiments and applications to enhance the quality of virtual services. However, isolated construction for the virtual machine doesn’t save the technology from unwanted data volumes or insensitive processing time. Containers are created to address such problems, by distributing applications without initiating the entire virtual machine. Docker, as an important player in this game, is an open-source application of the container family. The management tool from Docker containers, Swamskit, does not take heterogeneities in either virtualized containers or physical nodes. There are different nodes in the cluster, and each node is different in configurations, resource availability, or concerning resource, etc. Furthermore, the requirements initiated by different services change all the time. The demand might be CPU-intensive (e.g. Clustering services) and also memory-intensive (e.g. Web services), or completely at the opposite. In this paper, we focus on exploring the Docker container cluster and designing, DRAPS, a resource-aware placement scheme, to improve the system performance in a heterogeneous cluster.

In the past decade, we have witnessed a dramatically increasing volume of data collected from varied sources. The explosion of data has transformed the world as more information is available for collection and analysis than ever before. To maximize the utilization, various machine and deep learning models have been developed, e.g. CNN [1] and RNN [2], to study data and extract valuable information from different perspectives. While data-driven applications improve countless products, training models for hyperparameter tuning are still time-consuming and resource-intensive. Cloud computing provides infrastructure support for the training of deep learning applications. The cloud service providers, such as Amazon Web Services [3], create an isolated virtual environment (virtual machines and containers) for clients, who share physical resources, e.g., CPU and memory. On the cloud, resource management schemes are implemented to enable better sharing among users and boost the system-wide performance. However, general scheduling approaches, such as spread priority and balanced resource schedulers, do not work well with deep learning workloads. In this project, we propose SpeCon, a novel container scheduler that is optimized for shortlived deep learning applications. Based on virtualized containers, such as Kubernetes [4] and Docker [5], SpeCon analyzes the common characteristics of training processes. We design a suite of algorithms to monitor the progress of the training and speculatively migrate the slow-growing models to release resources for fast-growing ones. Specifically, the extensive experiments demonstrate that SpeCon improves the completion time of an individual job by up to 41.5%, 14.8% system-wide and 24.7% in terms of makespan.

Recently the increased cost-effectiveness of high-throughput technologies has made available a large number of RNA sequencing datasets to identify circular RNAs (circRNAs). However, despite many computational tools were developed to predict circRNAs, a limited number of workflows exists to predict and to characterize circRNAs. Moreover, to the best of our knowledge, these available workflows do not ensure computational reproducibility and require advanced bash scripting skills to be correctly installed and used. To cope with these critical aspects we present Docker4Circ, a new computational framework designed for a comprehensive analysis of circRNAs composed of: circRNAs prediction, classification and annotation using public databases, the back-splicing sequence reconstruction; the internal alternative splicing of circularizing exons; the alignment-free circRNAs quantification from RNA-Seq reads, and, finally, their differential expression analysis. Docker4Circ was specifically designed for making easier and more accessible circRNAs analysis thanks to the following features: (i) its R interface; (ii) the encapsulation of its computational tasks into a docker image; (iii) an available user-friendly Java GUI Interface. Furthermore, Docker4Circ ensures a reproducible analysis because all its tasks were embedded into a docker image following the guidelines provided by Reproducible Bioinformatics Project (RBP, http://reproducible-bioinformatics.org/). The effectiveness of Docker4Circ was demonstrated on a real case study whose goal is to characterize the circRNAs predicted in colorectal cancer cell lines and quantified in public RNA-Seq experiments performed on primary tumor tissues. In conclusion, we propose Docker4Circ as a framework for reproducible and comprehensive analyses of circRNAs to efficiently exploit their biological role.

This paper thoroughly assesses the ARM and RISC-V architectures in the context of High-Performance Computing (HPC). It includes an analysis of Docker, Kubernetes, and KVM virtualization integration. Our study aims to evaluate and compare these systems' performance, scalability, and practicality in a general context and then assess the impact that might have on special use cases, like HPC. ARM-based systems exhibited better performance and seamless integration with Docker and Kubernetes, underscoring their advanced development and effectiveness in managing high-performance computing workloads. On the other hand, despite their open-source architecture, RISC-V platforms presented considerable intricacy and difficulties in coordinating with Kubernetes, which hurt their overall effectiveness and ease of management. The results of our study offer valuable insights into the practical consequences of implementing these architectures for HPC, highlighting ARM's preparedness and the potential of RISC-V while acknowledging the increased complexity involved and significant trade-offs at this point.

: In the realm of data management, data preservation stands as a critical undertaking aimed at preserving and upholding the integrity of data. Regardless of whether it concerns personal or enterprise data, the detrimental effects of malicious alterations implemented by attackers cannot be overlooked. Particularly in conventional industrial control environments, the prevalent practice involves the transmission of data from sensors to databases for storage purposes. However, it is essential to recognize that this process exposes the data to various vulnerabilities. Thus, to ensure the long-term security and reliability of the data, it becomes imperative to implement robust data preservation strategies within these industrial control systems. However, the reliance of these databases on physical hard disks introduces inherent vulnerabilities, including the potential for data loss due to disk damage or targeted malicious attacks. Consequently, it becomes imperative to prioritize the implementation of robust data preservation measures. These measures are crucial in mitigating the risk of disruptions and protecting critical data from compromise. By establishing effective data backup systems, employing advanced security protocols, and implementing proactive monitoring mechanisms, organizations can bolster their data preservation capabilities and safeguard against potential threats to data integrity and availability. As a result, many enterprises opt to store their data with third-party providers to ensure data integrity. However, this approach carries inherent risks. If the third-party service experiences an attack or if the data is tampered with, it becomes challenging to verify the integrity of the data. To address these concerns and ensure data preservation within the context of the Internet of Things (IoT), a growing number of individuals are integrating IoT with Distributed Ledger Technology (DLT). By leveraging DLT, the integrity of data can be ensured, reducing reliance on centralized third-party storage and enhancing security in the IoT ecosystem. In this article, IOTA is the DLT, which employs Directed Acyclic Graph (DAG) to store transaction information. Compared to Ethereum or other blockchain technologies, IOTA offers notable advantages in terms of transaction verification speed, making it highly suitable for real-time IoT environments. However, the conventional transmission path from sensors to IOTA nodes entails a complex route, involving multiple hardware devices before reaching the intended destination. This complexity poses challenges in ensuring data integrity during transmission and introduces vulnerabilities such as man-in-the-middle attacks or SQL injection attacks. To address these issues, we propose a method to streamline the transmission path between sensors and IOTA, specifically tailored for industrial fields with numerous IoT devices. Our approach involves preprocessing the data stored on the server using our method before uploading, ensuring data confidentiality, and leveraging IOTA to guarantee data integrity. To achieve the shortest path between IoT and DLT nodes, it becomes necessary to establish IOTA nodes on lower-level devices, such as Raspberry Pi or IoT controllers. By simplifying the transmission path, we can reduce the potential for tampering and enhance overall data security. Implementing our proposed method enables the assurance of data confidentiality and integrity during both transmission and storage on the server, strengthening the trustworthiness of the IoT, and IOTA integration.

With the advent of microservice-based software architectures, an increasing number of modern cloud environments and enterprises use operating system level virtualization, often referred to as containers. Docker Swarm is one of the most popular container orchestration infrastructures, providing high availability and fault tolerance. Occasionally discovered container escape vulnerabilities allow adversaries to execute code on the host operating system and operate within the cloud infrastructure. We show that docker swarm is currently not secured against misbehaving manager nodes and allows a high impact, high probability privilege escalation attack that we refer to as leadership hijacking. Cloud lateral movement and defense evasion payloads allow an adversary to leverage the docker swarm functionality to control each and every host in the underlying cluster. We demonstrate an end-to-end attack, in which an adversary with access to an application running on the cluster achieves full control of the cluster. To reduce the probability of a successful high impact attack, container orchestration infrastructures must reduce the trust level of participating nodes and in particular, incorporate adversary immune leader election algorithms.

In the era of DevOps, developing new toolsets and frameworks that leverage DevOps principles is crucial. This paper demonstrates how Ansible’s powerful automation capabilities can be harnessed to manage the complexity of Kubernetes environments. This paper evaluates efficiency across various CNI (Container Network Interface) plugins by orchestrating performance analysis tools across multiple power profiles. Our methodology, which involves managing numerous components, dependencies, and configurations, requires high expertise and precision. Our performance evaluations across network interfaces with different theoretical bandwidths gave us a comprehensive understanding of CNI performance and overall efficiency. Our research confirms that certain CNIs are better suited for specific use cases, mainly when tuning our environment for smaller or larger network packages and workload types, but also that there are configuration changes we can make to mitigate that. This paper also provides research into how to use performance tuning to optimize the performance and efficiency of our CNI infrastructure, with practical implications for improving the performance of Kubernetes environments in real-world scenarios, particularly in more demanding scenarios such as High-Performance Computing (HPC) and Artificial Intelligence (AI).

NMR spectroscopy, which is based on the phenomenon of nuclear magnetic resonance, has been widely popularized by its application in medical imaging under the name of MRI. In the organic laboratory, the 13C NMR spectrum of a newly synthetized compound remains an essential step in elucidating its structure. For the chemist, the interpretation of such a spectrum, which is a set of chemical shift values, is made easier if he has a tool capable of predicting with sufficient accuracy the carbon shift values from the structure he intends to prepare. As there are few open source methods for accurately estimating this property, we applied our graph machine approach to build models capable of predicting the chemical shifts of carbons. For this study, we have focused on benzene compounds building an optimized model derived from training a database of 10577 chemical shifts originating from 2026 structures which contain up to ten types of atoms other than carbon, namely H, O, N, S, P, Si and halogens. It provides a training root mean squared relative error (RMSRE) of 0.5 %, i.e. a root mean squared error (RMSE) of 0.6 ppm, and a mean absolute error (MAE) of 0.4 ppm for estimating the chemical shifts of the 10k carbons. The predictive capability of the graph machine model is also compared with that of three commercial software on a data set of 171 original benzenic structures (1012 chemical shifts). The graph machine model proves very efficient in predicting chemical shifts with an RMSE of 0.9 ppm, and compares favorably with the RMSEs of 3.4, 1.8 and 1.9 ppm computed with ChemDraw, ACD and MestReNova softwares respectively. Finally, a Docker-based tool is proposed to predict the carbon chemical shifts of benzenic compounds solely from their SMILES codes.

In the future, smart cities will provide key services including seamless communication, intelligent transport systems, advanced healthcare platforms, urban and infrastructure management, and digital services for local and regional government. Therefore, a new service and networking paradigm, called the Intelligent Edge Environment, has been specified. and is known as the Intelligent Edge Environment. As a key part of this system, a new secure service ecosystem must be developed to provide the secure realtime movement of services on different High-Performance Edge Cloud Systems. This paper explores these issues by introducing the following mechanisms: the Resource Allocation Algorithm, the Resource Allocation Secure Protocol and finally the Secure Service Protocols. These systems were integrated into the Basic Capabilities System Library and a multithreaded FUSE client connected to the Service Management Framework. Docker was used as a migration mechanism. A prototype was developed and implemented using a FUSE-Network Memory System in which the Network Memory Server was migrated as users move around. The result shows that this approach was safe and could be used to develop new applications and services for smart cities.

The third trimester of pregnancy is the most critical period for human brain development, during which significant changes occur in the morphology of the brain. The development of sulci and gyri allows considerable increase of the brain surface. In premature childrens, these alterations take place outside the womb that may cause a disruption of the normal brain maturation process. We hypothesize that a normalized atlas of brain maturation with cerebral ultrasound images from birth to term equivalent age will help clinicians assess these changes. This work proposes a semi-automatic GUI platform for segmenting the main cerebral sulci in the clinical setting from ultrasound images. This platform has been obtained from images of a cerebral ultrasound neonatal database images provided by two clinical researchers from the Hospital Sant Joan de Déu in Barcelona, Spain. The primary objective is to provide a user-friendly design platform for clinicians, for running and visualizing an atlas of images validated by medical experts. This GUI offers different segmentation approaches, pre-processing tools, and is friendly designed for running, visualizing images, and segmenting the principal sulci. The presented results are discussed in detail in this paper, providing an exhaustive analysis of the proposed approach’s effectiveness.

During our digital transition, Docker containers have become essential for adaptable application deployment, although posing inherent security threats. This study utilizes Trivy for static analysis and Falco for dynamic analysis to identify and address vulnerabilities in Docker environments before deployment and in real-time. The IoT sector is now dealing with security issues that are made more severe by extensive connectivity and the prevalence of WiFi. This research promotes the use of AWS cloud security technologies such as IoT Core, CloudWatch, and GuardDuty to protect IoT devices from threats, with the goal of maintaining user privacy and ensuring safety in our interconnected digital world. This comprehensive strategy aims to enhance security measures in both Docker and IoT sectors, strengthening the security framework in our interconnected world.

This study analyses some of the leading technologies for the construction and configuration of IT infrastructures to provide services to users. For modern applications, guaranteeing service continuity even in very high computational load or network problems is essential. Our configuration has among the main objectives of being highly available (HA) and horizontally scalable, that is, able to increase the computational resources that can be delivered when needed and reduce them when they are no longer necessary. Various architectural possibilities are analysed, and the central schemes used to tackle problems of this type are also described in terms of disaster recovery. The benefits offered by virtualisation technologies are highlighted and are bought with modern techniques for managing Docker containers that will be used to build the back-end of a sample infrastructure related to a use-case we have developed. In addition to this, an in-depth analysis is reported on the central autoscaling policies that can help manage high loads of requests from users to the services provided by the infrastructure. The results we have presented show an average response time of 21.7 milliseconds with a standard deviation of 76.3 milliseconds showing excellent responsiveness. Some peaks are associated with high-stress events for the infrastructure, but the response time does not exceed 2 seconds even in this case. The results of the considered use case studied for nine months are presented and discussed. In the study period, we improved the back-end configuration and defined the main metrics to deploy the web application efficiently.

Mincle, a C-type lectin, is expressed predominantly in macrophages, where it plays a role in the macrophage response to various microorganisms such as mycobacteria. Docking is a computational procedure in which various software packages generate different positions at which ligands bind to their receptors. Discovery Studio docking was used in Molegro Virtual Studios. ChemDraw and ChemDraw3D were used for ligand preparation and construction because the protein preparation performed using docking software was a very lengthy process. Mincle plays a novel and non-redundant role in the induction of inflammatory signaling in response to mycobacteria. One disadvantage of Molegro studio docking is that it does not show the metallic atoms with which it interacts but rather shows hydrogen bonding and amino acid interactions. Hypothetically, trehalose dimycolate (TDM) and trehalose dibenzenate (TDB) detected by macrophages ultimately lead to CARD9 signaling, thereby producing pro-inflammatory cytokines and chemokines that have the potential to be used therapeutically.