MOTIVATION: Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific workflows and executed using the Kubernetes container orchestrator. RESULTS: We developed a Virtual Research Environment (VRE) which facilitates rapid integration of new tools and developing scalable and interoperable workflows for performing metabolomics data analysis. The environment can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry, one nuclear magnetic resonance spectroscopy and one fluxomics study. We showed that the method scales dynamically with increasing availability of computational resources. We demonstrated that the method facilitates interoperability using integration of the major software suites resulting in a turn-key workflow encompassing all steps for mass-spectrometry-based metabolomics including preprocessing, statistics and identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science. AVAILABILITY AND IMPLEMENTATION: The PhenoMeNal consortium maintains a web portal (https://portal.phenomenal-h2020.eu) providing a GUI for launching the Virtual Research Environment. The GitHub repository https://github.com/phnmnl/ hosts the source code of all projects. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Motivation: TranSMART has a wide range of functionalities for translational research and a large user community, but it does not support imaging data. In this context, imaging data typically includes 2D or 3D sets of magnitude data and metadata information. Imaging data may summarise complex feature descriptions in a less biased fashion than user defined plain texts and numeric numbers. Imaging data also is contextualised by other data sets and may be analysed jointly with other data that can explain features or their variation. Results: Here we describe the tranSMART-XNAT Connector we have developed. This connector consists of components for data capture, organisation and analysis. Data capture is responsible for imaging capture either from PACS system or directly from an MRI scanner, or from raw data files. Data are organised in a similar fashion as tranSMART and are stored in a format that allows direct analysis within tranSMART. The connector enables selection and download of DICOM images and associated resources using subjects' clinical phenotypic and genotypic criteria. Availability and Implementation: tranSMART-XNAT connector is written in Java/Groovy/Grails. It is maintained and available for download at https://github.com/sh107/transmart-xnat-connector.git. Contact: [email protected].

We present a novel security monitoring framework for intrusion detection in IaaS cloud infrastructures. The framework uses statistical anomaly detection techniques over data monitored both inside and outside each Virtual Machine instance. We present the architecture of our monitoring framework and describe the implementation of the real-time monitors and detectors. We also describe how the framework is used in three different attack scenarios. For each of the three attack scenarios, we describe how the attack itself works and how it could be detected. We describe what data is monitored in our framework and how the detection is conducted using anomaly detection methods. We also present evaluation of the detection using synthetic and real data sets. Our experimental evaluation across all three scenarios shows that our tools perform well in practical situations and provide a promising direction for future research.

Resource provisioning based on virtual machine (VM) has been widely accepted and adopted in cloud computing environments. A key problem resulting from using static scheduling approaches for allocating VMs on different physical machines (PMs) is that resources tend to be not fully utilised. Although some existing cloud reconfiguration algorithms have been developed to address the problem, they normally result in high migration costs and low resource utilisation due to ignoring the multi-dimensional characteristics of VMs and PMs. In this paper we present and evaluate a new algorithm for improving resource utilisation for cloud providers. By using a multivariate probabilistic model, our algorithm selects suitable PMs for VM re-allocation which are then used to generate a reconfiguration plan. We also describe two heuristics metrics which can be used in the algorithm to capture the multi-dimensional characteristics of VMs and PMs. By combining these two heuristics metrics in our experiments, we observed that our approach improves the resource utilisation level by around 8% for cloud providers, such as IC Cloud, which accept user-defined VM configurations and 14% for providers, such as Amazon EC2, which only provide limited types of VM configurations.

Virtual machine (VM) based virtual infrastructure has been adopted widely in cloud computing environment for elastic resource provisioning. Performing resource management using VMs, however, is a heavyweight task. In practice, we have identified two scenarios where VM based resource management is less feasible and less resource-efficient. In this paper, we propose a lightweight resource management model that is called Elastic Application Container (EAC). EAC is a virtual resource unit for delivering better resource efficiency and more scalable cloud applications. We describe the EAC system architecture and components, and also present an algorithm for EAC resource provisioning. We also describe an implementation of the EAC-oriented platform to support multi-tenant cloud use. To evaluate our approach and implementation, we conducted experiments and collected performance data by comparing VM-based and EAC-based resource management with regards to their feasibility and resource-efficiency. The experiment results show that our proposed EAC-based resource management approach outperforms the VM-based approach in terms of feasibility and resource-efficiency.

An Infrastructure-as-a-Service (IaaS) provider is usually assumed to own a large data centre with significant computational resources. For a small or medium sized Internet Data Centre (IDC), offering cloud computing service is a nature of business model but there are technical barriers which need to be resolved. One of the key issues is ineffective resource management given such an IDC usually has only limited resource. In this paper, we propose an efficient resource management solution specially designed for helping small and medium sized IaaS cloud providers to better utilise their hardware resources with minimum operational cost. Such an optimised resource utilisation is achieved by a well-designed underlying hardware infrastructure, an efficient resource scheduling algorithm and a set of migrating operations of VMs.

Simplifying the process of deploying applications is almost essential in the cloud. However, existing techniques can automate applications' initial deployment but have not yet adequately addressed their scaling problem. In this paper, a deployment platform to enable a novel dynamic scaling technique is introduced. This platform employs: (i) an extensible specification that describes all aspects of applications, (ii) a flexible analytical model that determines how many servers to be deployed for an application in each scaling. The platform's ability to handle dynamic workloads and to scale applications quickly enough to maintain the response time target is demonstrated.