Application Plugins for Distributed Simulations on the Grid

Computing grids are today still underexploited by scientific computing communities. The main reasons for this are, on the one hand, the complexity and variety of tools and services existent in the grid middleware ecosystem, and, on the other hand, the complexity of the development of applications capable to exploit the grids. We address in this work the challenge of developing grid applications that keep pace with the rapid evolution of grid middleware. For that, we propose an approach based on plugins for grid applications that encapsulate a set of commonly used type of grid operations. We further propose more complex high-level functionalities, such as the plugins for remote exploration of simulation scenarios and for monitoring of the behavior of end-user applications in grids. We provide an example of a grid application constructed with these software components and evaluate based on it the performance of our approach in the context of the simulation of biological neurons. The results obtained on test and production grids demonstrate the usefulness of the proposed plugins, with a small performance overhead compared to traditional grid tools

extending wenmr e infrastructure outside europe

WeNMR (Worldwide e-Infrastructure for Nuclear Magnetic Resonance and Structural Biology) is a EU FP7 project that brings together research teams in the Structural Biology area into a Virtual Research Community at a worldwide level, focusing on bio-molecular Nuclear Magnetic Resonance (NMR) and Small Angle X-ray Scattering (SAXS). This has been achieved through the implementation of a grid based e-Infrastructure, now fully integrated into EGI, aimed at providing the user community with a platform integrating and streamlining the computational approaches necessary for NMR and SAXS data analysis and structural modelling. Nowadays more than 20% of the users come from outside Europe. Therefore, in the last year the WeNMR team has worked to extend the e-Infrastructure with new resource centres from South Africa, Latin America, North America, Mediterranean and Asia-Pacific areas, with the goal of involving their NGIs to support their local NMR/SAXS community. In particular, a program to interoperate with the OSG grid in US in collaboration with their SBGrid Virtual Organisation has started, and the first tests of WeNMR job submission to OSG have been successfully carried out in the last months. WeNMR is also involved, through its collaboration with the EU FP7 project CHAIN (Coordination & Harmonisation of Advanced e-INfrastructures) in the effort to foster interoperability among EGI and those other grid infrastructures in China and India, which are not based on the EMI/gLite middleware

Information Technology Standards in eResearch: A Conceptual Model of the Primary Adoption Process in Higher Education Organizations

Current research on IT standards tends to focus on their lifecycle: from the development and selection, to their implementation and use. This work proposed an interdisciplinary perspective to analyze primary adoption process in the eResearch domain. As organizations are the core entities in the innovation process, the analysis of IT standards adoption was applied to eResearch infrastructures within higher education organizations. The core argument was built on the adopter s viewpoint as it provides the most explanatory process about adoption. Two international case studies probed the suitability of a model to identify the determinant role of factors like external and internal networks, top management support and organization structure. This dissertation delivers new insights that contribute to bring certainty about one relevant context of standards adoption

Využití tenchnologie GRID při zpracování medicínské informace

Práce se soustředí na vybrané oblasti biomedicínského výzkumu, které mohou profitovat ze současných výpočetních infrastruktur vybudovaných ve vědecké komunitě v evropském a světovém prostoru. Teorie výpočtu, paralelismu a distribuovaného počítání je stručně uvedena s ohledem na počítání v gridech a cloudech. Práce se zabývá oblastí výměny medicínských snímků a představuje propojení Gridového PACS systému s existujícími distribuovanými systémy pro sdílení DICOM snímků. Práce se dál zaměřuje na studium vědy týkající se lidského hlasu. Práce představuje vzdálený způsob přístupu k aplikaci pro analýzu hlasu v reálném čase pomocí úpravy protokolů pro vzdálenou plochu a pro přenos zvukových nahrávek. Tento dílčí výsledek ukazuje možnost využití stávajících aplikací na dálku specialisty na hlas. Oblast lidské fyziologie a patofyziologie byla studována pomocí přístupu tzv. systémové biologie. Práce přispívá v oblasti metodologie modelování lidské fyziologie pro tvorbu komplexních modelů založených na akauzálním a objektově orientovaném modelovacím přístupu. Metody pro studium parametrů byly představeny pomocí technologie počítání v gridech a v cloudech. Práce ukazuje, že proces identifikaci parametrů středně komplexních modelů kardiovasculárního systému a komplexního modelu lidské fyziologie lze významně zrychlit...This thesis focuses on selected areas of biomedical research in order to benefit from current computational infrastructures established in scientific community in european and global area. The theory of computation, parallelism and distributed computing, with focus on grid computing and cloud computing, is briefly introduced. Exchange of medical images was studied and a seamless integration of grid-based PACS system was established with the current distributed system in order to share DICOM medical images. Voice science was studied and access to real-time voice analysis application via remote desktop technology was introduced using customized protocol to transfer sound recording. This brings a possibility to access current legacy application remotely by voice specialists. The systems biology approach within domain of human physiology and pathophysiology was studied. Modeling methodology of human physiology was improved in order to build complex models based on acausal and object-oriented modeling techniques. Methods for conducting a parameter study (especially parameter estimation and parameter sweep) were introduced using grid computing and cloud computing technology. The identification of parameters gain substantial speedup by utilizing cloud computing deployment when performed on medium complex models of...nezařazení_neaktivníFirst Faculty of Medicine1. lékařská fakult

Interoperation of world-wide production e-Science infrastructures

Many production Grid and e-Science infrastructures have begun to offer services to end-users during the past several years with an increasing number of scientific applications that require access to a wide variety of resources and services in multiple Grids. Therefore, the Grid Interoperation Now-Community Group of the Open Grid Forum-organizes and manages interoperation efforts among those production Grid infrastructures to reach the goal of a world-wide Grid vision on a technical level in the near future. This contribution highlights fundamental approaches of the group and discusses open standards in the context of production e-Science infrastructures. Copyright (C) 2009 John Wiley & Sons, Ltd

Interoperation of world-wide production e-Science infrastructures

Many production Grid and e-Science infrastructures have begun to offer services to end-users during the past several years with an increasing number of scientific applications that require access to a wide variety of resources and services in multiple Grids. Therefore, the Grid Interoperation Now-Community Group of the Open Grid Forum-organizes and manages interoperation efforts among those production Grid infrastructures to reach the goal of a world-wide Grid vision on a technical level in the near future. This contribution highlights fundamental approaches of the group and discusses open standards in the context of production e-Science infrastructures. © 2009 John Wiley and Sons, Ltd