Flexible modeling and execution of choreographies

Approaches to address domain specific problems often share overlapping requirements but typically satisfy them in a unique manner for example using service-oriented concepts. The notion of Collaborative, Dynamic & Complex (CDC) systems has been proposed in literature to address the requirements of application domains such as eScience and Collective Adaptive Systems in a unified, generic manner. CDC systems are characterized by dealing with potentially large amounts of data and/or participating applications which engage in complex interactions specified by some collaboration protocol. Furthermore, the need for adaptation mechanisms is a common requirement and users from these application domains are typically no IT experts. The choreography concept originally known from collaborations in the business domain captures the interaction between independent parties from a global perspective. Each party is denoted as a choreography participant, which is implemented by a workflow or a service. This concept provides a way to model and execute for example complex eScience experiments involving multiple scientific fields, scientific methods, and time and/or length scales as a set of coupled workflows. However, typical choreography concepts as described in literature do not provide the desired level of flexibility and ease of use in both modeling and execution to address the requirements of users in CDC system application domains such as eScience. Thus, existing choreography concepts have to be considerably extended by introducing the Model-as-you-go for Choreographies approach in this thesis as a central notion providing capabilities for the flexible modeling and execution of choreographies. In the context of this approach, we provide a concept for fostering reuse in choreography modeling in the form of so-called choreography fragments. Such fragments can be extracted from existing and inserted into new choreography models in order to save time as well as reuse established and approved logic by inexperienced modelers in a less error-prone manner. Furthermore, we provide support for the user-driven control of the complete choreography life cycle. This effectively allows users to automatically deploy the workflow models implementing a choreography as well as starting, pausing, resuming, and terminating a choreography instance, which is formed through the collective execution of workflow instances. Most importantly, the underlying complexity of managing a set of coupled workflow instances is completely hidden from the users. Additional flexibility is given by a concept that allows to re-run already executed choreography logic in order to enforce the convergence of a calculation towards a particular result or to react to errors with parameter changes. The proposed concepts are implemented in a message-based system, the ChorSystem, which is able to handle the challenges of choreography life cycle management from deployment, to run time control and the re-run of logic. Furthermore, the modeling and run time monitoring are integrated into one graphical tool supporting the seamless transition from modeling to execution of choreographies. The concepts, their supporting algorithms, and the prototypical ChorSystem are validated by a set of case studies from different CDC system application domains and evaluated by performance measurements showing the practical applicability

Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

© 2019 Author(s). As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn potential energy functions, biomolecular conformational sampling, protein-ligand binding, reaction discovery using "on-the-fly" quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances and outline how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies such as iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures

Danceroom spectroscopy: At the frontiers of physics, performance, interactive art and technology

© 2016 ISAST. Danceroom Spectroscopy is an interactive audiovisual art installation and performance system driven by rigorous algorithms commonly used to simulate and analyze nanoscale atomic dynamics. danceroom Spectroscopy interprets humans as “energy landscapes,” resulting in an interactive system in which human energy fields are embedded within a simulation of thousands of atoms. Users are able to sculpt the atomic dynamics using their movements and experience their interactions visually and sonically in real time. danceroom Spectroscopy has so far been deployed as both an interactive sci-art installation and as the platform for a dance performance called Hidden Fields

Integrated CHOReOS middleware - Enabling large-scale, QoS-aware adaptive choreographies

This document describes the final implementation and the evaluation of the CHOReOS middleware. Evaluation is achieved both via the use of the middleware on CHOReOS use-cases and via synthetic experiments and simulation. The conclusion was that the implementation of the CHOReOS middleware has achieved a good level of maturity for an open source project and it is ready to be used in real-world, complex choreographies

Survey of scientific programming techniques for the management of data-intensive engineering environments

The present paper introduces and reviews existing technology and research works in the field of scientific programming methods and techniques in data-intensive engineering environments. More specifically, this survey aims to collect those relevant approaches that have faced the challenge of delivering more advanced and intelligent methods taking advantage of the existing large datasets. Although existing tools and techniques have demonstrated their ability to manage complex engineering processes for the development and operation of safety-critical systems, there is an emerging need to know how existing computational science methods will behave to manage large amounts of data. That is why, authors review both existing open issues in the context of engineering with special focus on scientific programming techniques and hybrid approaches. 1193 journal papers have been found as the representative in these areas screening 935 to finally make a full review of 122. Afterwards, a comprehensive mapping between techniques and engineering and nonengineering domains has been conducted to classify and perform a meta-analysis of the current state of the art. As the main result of this work, a set of 10 challenges for future data-intensive engineering environments have been outlined.The current work has been partially supported by the Research Agreement between the RTVE (the Spanish Radio and Television Corporation) and the UC3M to boost research in the field of Big Data, Linked Data, Complex Network Analysis, and Natural Language. It has also received the support of the Tecnologico Nacional de Mexico (TECNM), National Council of Science and Technology (CONACYT), and the Public Education Secretary (SEP) through PRODEP

Architecture-based Evolution of Dependable Software-intensive Systems

This cumulative habilitation thesis, proposes concepts for (i) modelling and analysing dependability based on architectural models of software-intensive systems early in development, (ii) decomposition and composition of modelling languages and analysis techniques to enable more flexibility in evolution, and (iii) bridging the divergent levels of abstraction between data of the operation phase, architectural models and source code of the development phase

Changing Time - Shaping World: Changemakers in Arts & Education

A World of Changemakers - how can a hybrid arts lecture series concept in e-learning create attitudes and shape skills as a playful and critical thinking navigator in an uncertain world? To re-create meaning is an interdisciplinary cross-sectional task of our zeitgeist in a civil society. The international contributors represent key roles in relevant philosophical, technical or economic debates, non-university community art & design projects or companies

Changing Time - Shaping World

A World of Changemakers - how can a hybrid arts lecture series concept in e-learning create attitudes and shape skills as a playful and critical thinking navigator in an uncertain world? To re-create meaning is an interdisciplinary cross-sectional task of our zeitgeist in a civil society. The international contributors represent key roles in relevant philosophical, technical or economic debates, non-university community art & design projects or companies

Aktualisierung und Änderungsweitergabe in Workflow-Choreographien

Das Forschungsfeld e-Science beschäftigt sich unter anderem mit Simulationen in der Wissenschaft. Eine Strategie besteht darin, die etablierten Standards, aus der Geschäftswelt, auf die Anforderungen von Wissenschaftlern, für Scientific-Workflows, zu übertragen. Die angebotene Werkzeuge für Wissenschaftler sollten das Modellieren mit der Trial and Error Methode unterstützen, da dies eine natürliche Vorgehensweise bei der Erstellung von Experimenten darstellt. Die Experimente werden als Workflow-Choreographien beschrieben. Diese Arbeit beschäftigt sich damit, wie Aktualisierungen von Workflow-Choreographien an die beteiligten Partner propagiert und gleichzeitig diese Aktualisierungen automatisch in das bestehende Modell des Partners übernommen werden können. Dazu wird ein Model-Integration-Konzept erarbeitet und anschließend in einem Proof of Concept die Funktionalität innerhalb eines wissenschaftlichen Prototyps bereitgestellt

CHOReOS Middleware Specification (D3.1)

This deliverable specifies the main concepts of the CHOReOS middleware architecture. Starting from the Future Internet (FI) challenges for scalability, heterogeneity, mobility, awareness, and adaptation that have been investigated in prior work done in WP1, we introduce the aforementioned concepts to deal with the requirements derived from the FI challenges. In particular, we propose an extensible and scalable service discovery approach for the organization and discovery of services that relies on multiple service discovery protocols. Moreover, we introduce an extensible and scalable approach, based on the service bus paradigm, for service access that features the integration and adaptation of multiple interaction protocols. Furthermore, we propose solutions that enable the execution of FI service compositions that range from compositions of choreographed services, developed according to the CHOReOS development process, to massive compositions of things. Finally, we detail the Cloud & Grid middleware facilities that support the overall middleware and the choreographies that are built on it, via a unified API that provides access to multiple cloud infrastructures (e.g., Amazon EC2, HP Open Cirrus, private clouds)