KheOps: Cost-effective Repeatability, Reproducibility, and Replicability of Edge-to-Cloud Experiments

Distributed infrastructures for computation and analytics are now evolving towards an interconnected ecosystem allowing complex scientific workflows to be executed across hybrid systems spanning from IoT Edge devices to Clouds, and sometimes to supercomputers (the Computing Continuum). Understanding the performance trade-offs of large-scale workflows deployed on such complex Edge-to-Cloud Continuum is challenging. To achieve this, one needs to systematically perform experiments, to enable their reproducibility and allow other researchers to replicate the study and the obtained conclusions on different infrastructures. This breaks down to the tedious process of reconciling the numerous experimental requirements and constraints with low-level infrastructure design choices.To address the limitations of the main state-of-the-art approaches for distributed, collaborative experimentation, such as Google Colab, Kaggle, and Code Ocean, we propose KheOps, a collaborative environment specifically designed to enable cost-effective reproducibility and replicability of Edge-to-Cloud experiments. KheOps is composed of three core elements: (1) an experiment repository; (2) a notebook environment; and (3) a multi-platform experiment methodology.We illustrate KheOps with a real-life Edge-to-Cloud application. The evaluations explore the point of view of the authors of an experiment described in an article (who aim to make their experiments reproducible) and the perspective of their readers (who aim to replicate the experiment). The results show how KheOps helps authors to systematically perform repeatable and reproducible experiments on the Grid5000 + FIT IoT LAB testbeds. Furthermore, KheOps helps readers to cost-effectively replicate authors experiments in different infrastructures such as Chameleon Cloud + CHI@Edge testbeds, and obtain the same conclusions with high accuracies (> 88% for all performance metrics)

The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web

Research in life sciences is increasingly being conducted in a digital and online environment. In particular, life scientists have been pioneers in embracing new computational tools to conduct their investigations. To support the sharing of digital objects produced during such research investigations, we have witnessed in the last few years the emergence of specialized repositories, e.g., DataVerse and FigShare. Such repositories provide users with the means to share and publish datasets that were used or generated in research investigations. While these repositories have proven their usefulness, interpreting and reusing evidence for most research results is a challenging task. Additional contextual descriptions are needed to understand how those results were generated and/or the circumstances under which they were concluded. Because of this, scientists are calling for models that go beyond the publication of datasets to systematically capture the life cycle of scientific investigations and provide a single entry point to access the information about the hypothesis investigated, the datasets used, the experiments carried out, the results of the experiments, the people involved in the research, etc. In this paper we present the Research Object (RO) suite of ontologies, which provide a structured container to encapsulate research data and methods along with essential metadata descriptions. Research Objects are portable units that enable the sharing, preservation, interpretation and reuse of research investigation results. The ontologies we present have been designed in the light of requirements that we gathered from life scientists. They have been built upon existing popular vocabularies to facilitate interoperability. Furthermore, we have developed tools to support the creation and sharing of Research Objects, thereby promoting and facilitating their adoption.Comment: 20 page

Digital Engineering Framework - A Systematic Review of What and How to Digitalize

Symposium PresentationApproved for public release; distribution is unlimited

A Real-Time Remote IDS Testbed for Connected Vehicles

Connected vehicles are becoming commonplace. A constant connection between vehicles and a central server enables new features and services. This added connectivity raises the likelihood of exposure to attackers and risks unauthorized access. A possible countermeasure to this issue are intrusion detection systems (IDS), which aim at detecting these intrusions during or after their occurrence. The problem with IDS is the large variety of possible approaches with no sensible option for comparing them. Our contribution to this problem comprises the conceptualization and implementation of a testbed for an automotive real-world scenario. That amounts to a server-side IDS detecting intrusions into vehicles remotely. To verify the validity of our approach, we evaluate the testbed from multiple perspectives, including its fitness for purpose and the quality of the data it generates. Our evaluation shows that the testbed makes the effective assessment of various IDS possible. It solves multiple problems of existing approaches, including class imbalance. Additionally, it enables reproducibility and generating data of varying detection difficulties. This allows for comprehensive evaluation of real-time, remote IDS.Comment: Peer-reviewed version accepted for publication in the proceedings of the 34th ACM/SIGAPP Symposium On Applied Computing (SAC'19

ENGINEERING ENVIRONMENT AND AVIONICS VIRTUAL PROTOTYPING

Specialized system engineering tools, although capable of supporting specific tasks or functions, have limited use in most organizations and do not dearly fit into a broader project data architecture. Attempts by either tool users or developers to integrate applications outside of a bundled tool set have generally been limited to various forms of data import which creates recurring manual administrative effort and related configuration management problems by having data in multiple places. Collaborative engineering and virtual prototyping Is the application of advanced distributed modeling and simulation and engineering tools in an integrated environment to support technology development, system design, performance, cost, and producibility trade-off analyses throughout the entire product and system engineering life-cycle

Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools

Stoichiometric models of metabolism, such as flux balance analysis (FBA), are classically applied to predicting steady state rates - or fluxes - of metabolic reactions in genome-scale metabolic networks. Here we revisit the central assumption of FBA, i.e. that intracellular metabolites are at steady state, and show that deviations from flux balance (i.e. flux imbalances) are informative of some features of in vivo metabolite concentrations. Mathematically, the sensitivity of FBA to these flux imbalances is captured by a native feature of linear optimization, the dual problem, and its corresponding variables, known as shadow prices. First, using recently published data on chemostat growth of Saccharomyces cerevisae under different nutrient limitations, we show that shadow prices anticorrelate with experimentally measured degrees of growth limitation of intracellular metabolites. We next hypothesize that metabolites which are limiting for growth (and thus have very negative shadow price) cannot vary dramatically in an uncontrolled way, and must respond rapidly to perturbations. Using a collection of published datasets monitoring the time-dependent metabolomic response of Escherichia coli to carbon and nitrogen perturbations, we test this hypothesis and find that metabolites with negative shadow price indeed show lower temporal variation following a perturbation than metabolites with zero shadow price. Finally, we illustrate the broader applicability of flux imbalance analysis to other constraint-based methods. In particular, we explore the biological significance of shadow prices in a constraint-based method for integrating gene expression data with a stoichiometric model. In this case, shadow prices point to metabolites that should rise or drop in concentration in order to increase consistency between flux predictions and gene expression data. In general, these results suggest that the sensitivity of metabolic optima to violations of the steady state constraints carries biologically significant information on the processes that control intracellular metabolites in the cell.Published versio

The Development of an Assault Directed Infrared Countermeasures (DIRCM) Program

The purpose of this thesis is to document the history of the development of an Assault Directed Infrared Countermeasures (DIRCM) Program as well as Navy Program Office (PMA272) efforts to date, to initiate a new start ACAT II Program for Navy and Marine Corps helicopters starting in Fiscal Year (FY) 2006. It concentrates on the programmatic aspects of Assault DIRCM and does not go into detail on the design or technical aspects of the development of the system. This thesis will introduce emerging threats to helicopters operating in theater and describe the requirement for a DIRCM technology. It will also highlight program issues based on observations made over the past year as well as provide a recommended path forward for immediate program execution considering internal and external program and acquisition constraints both real and perceived