Achieving User Interface Heterogeneity in a Distributed Environment

The introduction of distribution into the field of computing has enhanced the possibilities of information processing and interchange on scales which could not previously be achieved with stand-alone machines. However, the successful distribution of a process across a distributed system requires three problems to be considered; how the functionality of a process is distributed, how the data set on which the process works is distributed and how the interface that allows the process to communicate with the outside world is distributed. The focus of the work in this paper lies in describing a model that attempts to provide a solution to the latter problem. The model that has been developed allows the functionality of a process to be separated from and to exist independently from its interface and employs user interface independent display languages to provide distributed and heterogeneous user interfaces to processes. This separation also facilitates access to a service from diverse platforms and can support user interface mobility and third-party application integration. The goals and advantages of this model are partially realised in a prototype that has been designed around the WWW and its associated protocols, and it is predicted how the model could be fully realised by adopting a modular and object-oriented approach, as advocated by the Java programming environment

Molecular docking with Raccoon2 on clouds: extending desktop applications with cloud computing

Molecular docking is a computer simulation that predicts the binding affinity between two molecules, a ligand and a receptor. Large-scale docking simulations, using one receptor and many ligands, are known as structure-based virtual screening. Often used in drug discovery, virtual screening can be very computationally demanding. This is why user-friendly domain-specific web or desktop applications that enable running simulations on powerful computing infrastructures have been created. Cloud computing provides on-demand availability, pay-per-use pricing, and great scalability which can improve the performance and efficiency of scientific applications. This paper investigates how domain-specific desktop applications can be extended to run scientific simulations on various clouds. A generic approach based on scientific workflows is proposed, and a proof of concept is implemented using the Raccoon2 desktop application for virtual screening, WS-PGRADE workflows, and gUSE services with the CloudBroker platform. The presented analysis illustrates that this approach of extending a domain-specific desktop application can run workflows on different types of clouds, and indeed makes use of the on-demand scalability provided by cloud computing. It also facilitates the execution of virtual screening simulations by life scientists without requiring them to abandon their favourite desktop environment and providing them resources without major capital investment

Building Science Gateways for Analysing Molecular Docking Results Using a Generic Framework and Methodology

Molecular docking and virtual screening experiments require large computational and data resources and high-level user interfaces in the form of science gateways. While science gateways supporting such experiments are relatively common, there is a clearly identified need to design and implement more complex environments for further analysis of docking results. This paper describes a generic framework and a related methodology that supports the efficient development of such environments. The framework is modular enabling the reuse of already existing components. The methodology, which proposes three techniques that the development team can use, is agile and encourages active participation of end-users. Based on the framework and methodology, two prototype implementations of science-gateway-based docking environments are presented and evaluated. The first system recommends a receptor-ligand pair for the next docking experiment, and the second filters docking results based on ligand properties

Community-Aware Event Dissemination

This paper presents a distributed algorithm to disseminate events in a publish/subscribe system, where processes publish events of certain topics, organized in a hierarchy, and expect events of topics they subscribed to. Every topic defines a dynamic notion of ``community'', gathering the processes which publish on that topic or subscribe to it. Our algorithm is completely decentralized (no brokers), yet does not require from any process to ever receive, store or forward, events from a community it is not part of. We order the communities according to the topic inclusion relationships to efficiently manage the flow of information within, and between the communities, as well as limit the memory consumption of each process. Processes can control, for each of their communities, the trade-off between the message complexity and the reliability of event dissemination. We convey this trade-off through analysis, simulations and measurements obtained with a full implementation of our algorithm

Extending Molecular Docking Desktop Applications with Cloud Computing Support and Analysis of Results

Structure-based virtual screening simulations, which are often used in drug discovery, can be very computationally demanding. This is why user-friendly domain-specific web or desktop applications that enable running simulations on powerful computing infrastructures have been created. This article investigates how domain-specific desktop applications can be extended to use cloud computing and how they can be part of scenarios that require sharing and analysing previous molecular docking results. A generic approach based on interviews with scientists and analysis of existing systems is proposed. A proof of concept is implemented using the Raccoon2 desktop application for virtual screening, WS-PGRADE workflows, gUSE services with the CloudBroker Platform, the structural alignment tool DeepAlign, and the ligand similarity tool LIGSIFT. The presented analysis illustrates that this approach of extending a domainspecific desktop application can use different types of clouds, thus facilitating the execution of virtual screening simulations by life scientists without requiring them to abandon their favourite desktop environment and providing them resources without major capital investment. It also shows that storing and sharing molecular docking results can produce additional conclusions such as viewing similar docking input files for verification or learning

The DAMA Protocol, an Introduction: Finding Pathogens before They Find Us

Globally, humanity is coming to recognize the magnitude of the interactive crisis for emerging infectious disease (EID). Strategies for coping with EID have been largely in the form of reactive measures for crisis response. The DAMA protocol (Document, Assess, Monitor, Act), the operational policy extension of the Stockholm paradigm, constitutes a preventive/proactive dimension to those efforts. DAMA is aimed at focusing and extending human and material resources devoted to coping with the accelerating wave of EID. DAMA is integrative, combining efforts to strategically document the distribution of complex pathogen and host assemblages in the biosphere in the context of dynamic environmental interfaces that provide the opportunities for pathogen exchange and emergence. Movement of habitats and animals (a breakdown in ecological isolation) catalyzed by climate change and broader anthropogenic trajectories of environmental disruption provide the landscape of opportunity for emergence. Evolutionarily and ecologically conserved capacities for exploitation of host-based resources allow pathogens to persist in one place or among a particular spectrum of hosts and provide insights to predict outcomes of persistence and emergence in novel conditions and across changing ecological interfaces. DAMA trajectories combine “boots on the ground” contributions of citizen scientists working with field biologists in development and application of sophisticated archival repositories, bioinformatics, molecular biology, and satellite surveillance. DAMA is a focus for anticipation, mitigation, and prevention of EID through knowledge of pathogens present in the environment and actions necessary to diminish risk space for their emergence. DAMA can be an effective strategy for buying time in the arena of accelerating environmental and socioeconomic disturbance and expanding EID linked to a future of climate change. Information + action = prediction and lives saved in a realm of EID. This article has been produced in support of and with appreciation for the efforts by Gábor Földvári of the Institute of Evolution, Centre for Ecological Research, and the Centre for Eco-Epidemiology, National Laboratory for Health Security (both located at 1121 Budapest, Konkoly-Thege Miklós út 29-33, Hungary). Through his untiring efforts, team building, and leadership, he has secured the first EU-wide team research grant. This work was supported by the National Research, Development and Innovation Office in Hungary (RRF-2.3.1-21-2022-00006) and the COST Action CA21170 “Prevention, anticipation and mitigation of tick-borne disease risk applying the DAMA protocol (PRAGMATICK),” which represent the first funded efforts to apply the principles of the DAMA protocol

Defining the Placental Barrier during Toxoplasma gondii Infection

Toxoplasma gondii is a major source of congenital disease worldwide, but the cellular and molecular factors associated with its vertical transmission are largely unknown. In humans, the placenta forms the key interface between the maternal and fetal compartments and forms the primary barrier that restricts the hematogenous spread of microorganisms. This dissertation describes both the identification of two mechanisms of placental syncytiotrophoblast resistance to T. gondii infection and a preliminary understanding of the CCL22 response induced by the Toxoplasma dense granule protein GRA28. Collectively, these findings provide new insights into (1) protective role of the syncytiotrophoblast during T. gondii infection, (2) interferon-gamma independent restriction of T. gondii growth, and (3) parasite-directed manipulation of the intercellular communication between the placenta and components of the maternal immune system