5,181 research outputs found
E-BioFlow: Different Perspectives on Scientific Workflows
We introduce a new type of workflow design system called\ud
e-BioFlow and illustrate it by means of a simple sequence alignment workflow. E-BioFlow, intended to model advanced scientific workflows, enables the user to model a workflow from three different but strongly coupled perspectives: the control flow perspective, the data flow perspective, and the resource perspective. All three perspectives are of\ud
equal importance, but workflow designers from different domains prefer different perspectives as entry points for their design, and a single workflow designer may prefer different perspectives in different stages of workflow design. Each perspective provides its own type of information, visualisation and support for validation. Combining these three perspectives in a single application provides a new and flexible way of modelling workflows
Plasma Edge Kinetic-MHD Modeling in Tokamaks Using Kepler Workflow for Code Coupling, Data Management and Visualization
A new predictive computer simulation tool targeting the development of the H-mode pedestal at the plasma edge in tokamaks and the triggering and dynamics of edge localized modes (ELMs) is presented in this report. This tool brings together, in a coordinated and effective manner, several first-principles physics simulation codes, stability analysis packages, and data processing and visualization tools. A Kepler workflow is used in order to carry out an edge plasma simulation that loosely couples the kinetic code, XGC0, with an ideal MHD linear stability analysis code, ELITE, and an extended MHD initial value code such as M3D or NIMROD. XGC0 includes the neoclassical ion-electron-neutral dynamics needed to simulate pedestal growth near the separatrix. The Kepler workflow processes the XGC0 simulation results into simple images that can be selected and displayed via the Dashboard, a monitoring tool implemented in AJAX allowing the scientist to track computational resources, examine running and archived jobs, and view key physics data, all within a standard Web browser. The XGC0 simulation is monitored for the conditions needed to trigger an ELM crash by periodically assessing the edge plasma pressure and current density profiles using the ELITE code. If an ELM crash is triggered, the Kepler workflow launches the M3D code on a moderate-size Opteron cluster to simulate the nonlinear ELM crash and to compute the relaxation of plasma profiles after the crash. This process is monitored through periodic outputs of plasma fluid quantities that are automatically visualized with AVS/Express and may be displayed on the Dashboard. Finally, the Kepler workflow archives all data outputs and processed images using HPSS, as well as provenance information about the software and hardware used to create the simulation. The complete process of preparing, executing and monitoring a coupled-code simulation of the edge pressure pedestal buildup and the ELM cycle using the Kepler scientific workflow system is described in this paper
Workflow Partitioning and Deployment on the Cloud using Orchestra
Orchestrating service-oriented workflows is typically based on a design model
that routes both data and control through a single point - the centralised
workflow engine. This causes scalability problems that include the unnecessary
consumption of the network bandwidth, high latency in transmitting data between
the services, and performance bottlenecks. These problems are highly prominent
when orchestrating workflows that are composed from services dispersed across
distant geographical locations. This paper presents a novel workflow
partitioning approach, which attempts to improve the scalability of
orchestrating large-scale workflows. It permits the workflow computation to be
moved towards the services providing the data in order to garner optimal
performance results. This is achieved by decomposing the workflow into smaller
sub workflows for parallel execution, and determining the most appropriate
network locations to which these sub workflows are transmitted and subsequently
executed. This paper demonstrates the efficiency of our approach using a set of
experimental workflows that are orchestrated over Amazon EC2 and across several
geographic network regions.Comment: To appear in Proceedings of the IEEE/ACM 7th International Conference
on Utility and Cloud Computing (UCC 2014
Enhancing Workflow with a Semantic Description of Scientific Intent
Peer reviewedPreprin
High-Performance Cloud Computing: A View of Scientific Applications
Scientific computing often requires the availability of a massive number of
computers for performing large scale experiments. Traditionally, these needs
have been addressed by using high-performance computing solutions and installed
facilities such as clusters and super computers, which are difficult to setup,
maintain, and operate. Cloud computing provides scientists with a completely
new model of utilizing the computing infrastructure. Compute resources, storage
resources, as well as applications, can be dynamically provisioned (and
integrated within the existing infrastructure) on a pay per use basis. These
resources can be released when they are no more needed. Such services are often
offered within the context of a Service Level Agreement (SLA), which ensure the
desired Quality of Service (QoS). Aneka, an enterprise Cloud computing
solution, harnesses the power of compute resources by relying on private and
public Clouds and delivers to users the desired QoS. Its flexible and service
based infrastructure supports multiple programming paradigms that make Aneka
address a variety of different scenarios: from finance applications to
computational science. As examples of scientific computing in the Cloud, we
present a preliminary case study on using Aneka for the classification of gene
expression data and the execution of fMRI brain imaging workflow.Comment: 13 pages, 9 figures, conference pape
Work flows in life science
The introduction of computer science technology in the life science domain has resulted in a new life science discipline called bioinformatics. Bioinformaticians are biologists who know how to apply computer science technology to perform computer based experiments, also known as in-silico or dry lab experiments. Various tools, such as databases, web applications and scripting languages, are used to design and run in-silico experiments. As the size and complexity of these experiments grow, new types of tools are required to design and execute the experiments and to analyse the results. Workflow systems promise to fulfill this role. The bioinformatician composes an experiment by using tools and web services as building blocks, and connecting them, often through a graphical user interface. Workflow systems, such as Taverna, provide access to up to a few thousand resources in a uniform way. Although workflow systems are intended to make the bioinformaticians' work easier, bioinformaticians experience difficulties in using them. This thesis is devoted to find out which problems bioinformaticians experience using workflow systems and to provide solutions for these problems.\u
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