Introduce: An Open Source Toolkit for Rapid Development of Strongly Typed Grid Services
TL;DR: It is expected that enabling strongly typed Grid services while lowering the difficulty of entry to the Grid via toolkits like Introduce will have a major impact to the success of the Grid and its wider adoption as a viable technology of choice in the commercial sector as well as in academic, medical, and government research.
Abstract: Service-oriented architectures and applications have gained wide acceptance in the Grid computing community. A number of tools and middleware systems have been developed to support application development using Grid Services architectures. Most of these efforts, however, have focused on low-level support for management and execution of Grid services, management of Grid-enabled resources, and deployment and execution of applications that make use of Grid services. Simple-to-use service development tools, which would allow a Grid service developer to leverage Grid technologies without needing to know low-level details, are becoming increasingly important for wider application of the Grid. In this paper, we describe an open-source, extensible toolkit, called Introduce, that supports easy development and deployment of Web Services Resource Framework (WSRF) compliant services. Introduce is designed to reduce the service development and deployment effort by hiding low level details of the Globus Toolkit and to enable the implementation of strongly typed services. In strongly typed services, a service produces and consumes data types that are well-defined and published in the Grid. This enables data-level syntactic interoperability so that clients and services can access and consume data elements programmatically and correctly. We expect that enabling strongly typed Grid services while lowering the difficulty of entry to the Grid via toolkits like Introduce will have a major impact to the success of the Grid and its wider adoption as a viable technology of choice in the commercial sector as well as in academic, medical, and government research.
Citations
More filters
TL;DR: While caGrid 1.0 is designed to address use cases in cancer research, the requirements associated with discovery, analysis and integration of large scale data, and coordinated studies are common in other biomedical fields.
119 citations
Cites methods from "Introduce: An Open Source Toolkit f..."
...It provides a unified service authoring toolkit, called Introduce,...
[...]
TL;DR: GeWorkbench leverages standards-based middleware technologies to provide seamless access to remote data, annotation and computational servers, thus, enabling researchers with limited local resources to benefit from available public infrastructure.
Abstract: Summary: geWorkbench (genomics Workbench) is an open source Java desktop application that provides access to an integrated suite of tools for the analysis and visualization of data from a wide range of genomics domains (gene expression, sequence, protein structure and systems biology) More than 70 distinct plug-in modules are currently available implementing both classical analyses (several variants of clustering, classification, homology detection, etc) as well as state of the art algorithms for the reverse engineering of regulatory networks and for protein structure prediction, among many others geWorkbench leverages standards-based middleware technologies to provide seamless access to remote data, annotation and computational servers, thus, enabling researchers with limited local resources to benefit from available public infrastructure
Availability: The project site (http://wwwgeworkbenchorg) includes links to self-extracting installers for most operating system (OS) platforms as well as instructions for building the application from scratch using the source code [which is freely available from the project's SVN (subversion) repository] geWorkbench support is available through the end-user and developer forums of the caBIG® Molecular Analysis Tools Knowledge Center, https://cabig-kcncinihgov/Molecular/forums/
Contact: udeaibmuloc2b2c@hcnebkroweg
Supplementary Information: Supplementary data are available at Bioinformatics online
91 citations
26 Nov 2014
TL;DR: Tracking the aberrations that drive cancers, identifying biomarkers unique to each individual for molecular-level di- nosis and treatment response, monitoring adverse events and complex dosing schedules, and providing annotated molecular data for ongoing research to improve treatments comprise a major biomedical informatics need.
Abstract: view, showing that multiple molecular pathways must be affected for cancer to develop, but with different specific proteins in each pathway mutated or differentially expressed in a given tumor (The Cancer Genome Atlas Research Network 2008; Parsons et al. 2008). Different studies demonstrated that while widespread mutations exist in cancer, not all mutations drive cancer development (Lin et al. 2007). This suggests a need to target only a deleterious subset of aberrant proteins, since any tre- ment must aim to improve health to justify its potential side effects. Treatment for cancer must become highly individualized, focusing on the specific aberrant driver proteins in an individual. This drives a need for informatics in cancer far beyond the need in other diseases. For instance, routine treatment with statins has become widespread for minimizing heart disease, with most patients responding to standard doses (Wilt et al. 2004). In contrast, standard treatment for cancer must become tailored to the molecular phenotype of an individual tumor, with each patient receiving a different combination of therapeutics aimed at the specific aberrant proteins driving the cancer. Tracking the aberrations that drive cancers, identifying biomarkers unique to each individual for molecular-level di- nosis and treatment response, monitoring adverse events and complex dosing schedules, and providing annotated molecular data for ongoing research to improve treatments comprise a major biomedical informatics need.
49 citations
01 Mar 2010
TL;DR: The Ontology of Clinical Research (OCRe) is developed to model study features such as design type, interventions, and outcomes to support scientific query and analysis in human studies.
Abstract: Human studies, encompassing interventional and observational studies, are the most important source of evidence for advancing our understanding of health, disease, and treatment options. To promote discovery, the design and results of these studies should be made machine-readable for large-scale data mining, synthesis, and re-analysis. The Human Studies Database Project aims to define and implement an informatics infrastructure for institutions to share the design of their human studies. We have developed the Ontology of Clinical Research (OCRe) to model study features such as design type, interventions, and outcomes to support scientific query and analysis. We are using OCRe as the reference semantics for federated data sharing of human studies over caGrid, and are piloting this implementation with several Clinical and Translational Science Award (CTSA) institutions.
35 citations
Cites methods from "Introduce: An Open Source Toolkit f..."
...HSDBgrid accommodates both platforms (Figure 1). caGrid databases that are built using the caCORE SDK are directly grid-accessible. i2b2 databases can be exposed on caGrid using the Introduce Toolkit (10)....
[...]
...i2b2 databases can be exposed on caGrid using the Introduce Toolkit (10)....
[...]
20 Jun 2011
TL;DR: The Cloud4Home project and approach is presented, which enables and explores the aggregate use of @home and @datacenter computational and storage capabilities, and uses virtualization technologies to create content storage, access, and sharing services that are fungible both in terms of where stored objects are located and in termsof where they are manipulated.
Abstract: Mobile devices, net books and laptops, and powerful home PCs are creating ever-growing computational capacity at the periphery of the Internet, and this capacity is supporting an increasingly rich set of services, including media-rich entertainment and social networks, gaming, home security applications, flexible data access and storage, and others. Such 'at the edge' capacity raises the question, however, about how to combine it with the capabilities present in the cloud computing infrastructures residing in data center systems and reachable via the Internet. The Cloud4Home project and approach presented in this paper addresses this topic, by enabling and exploring the aggregate use of @home and @datacenter computational and storage capabilities. Cloud4Home uses virtualization technologies to create content storage, access, and sharing services that are fungible both in terms of where stored objects are located and in terms of where they are manipulated. In this fashion, data services can provide low latency response to @home events as well as high throughput response when the higher and less predictable latencies of data center access can be tolerated. Cloud4Home is implemented with the Xen open source hyper visors for standard x86-based mobile to server platforms, and is evaluated using sample applications based on home security and video conversion services.
31 citations
Cites methods from "Introduce: An Open Source Toolkit f..."
...We avoid using all 6 home devices so as to limit the contention for the scarce bandwidth resource between home and remote cloud devices....
[...]
References
More filters
01 Aug 2001
TL;DR: The authors present an extensible and open Grid architecture, in which protocols, services, application programming interfaces, and software development kits are categorized according to their roles in enabling resource sharing.
Abstract: "Grid" computing has emerged as an important new field, distinguished from conventional distributed computing by its focus on large-scale resource sharing, innovative applications, and, in some cases, high performance orientation. In this article, the authors define this new field. First, they review the "Grid problem," which is defined as flexible, secure, coordinated resource sharing among dynamic collections of individuals, institutions, and resources--what is referred to as virtual organizations. In such settings, unique authentication, authorization, resource access, resource discovery, and other challenges are encountered. It is this class of problem that is addressed by Grid technologies. Next, the authors present an extensible and open Grid architecture, in which protocols, services, application programming interfaces, and software development kits are categorized according to their roles in enabling resource sharing. The authors describe requirements that they believe any such mechanisms must satisfy and discuss the importance of defining a compact set of intergrid protocols to enable interoperability among different Grid systems. Finally, the authors discuss how Grid technologies relate to other contemporary technologies, including enterprise integration, application service provider, storage service provider, and peer-to-peer computing. They maintain that Grid concepts and technologies complement and have much to contribute to these other approaches.
6,716 citations
"Introduce: An Open Source Toolkit f..." refers methods in this paper
...The most widely used reference implementations of OGSA, as realized by OGSI (Open Grid Services Infrastructure), and WSRF are the Globus Toolkit (GT; http://www.globus.org) version 3.2 (GT 3.2) and version 4.0 (GT 4.0), respectively....
[...]
...Morohoshi and Huang [33] propose a toolkit designed to support service development on top of the GT3 platform, which is based on the OGSA standards....
[...]
...The Open Grid Services Architecture (OGSA) [23, 24] has been developed through standardization efforts coordinated mainly by the Global Grid Forum (http:// www....
[...]
...The OGSA and WSRF enable architecture-level interoperability by defining standards for data and information exchange protocols, service creation and management, and service invocation....
[...]
...The OGSA, WSRF, and GT provide a foundation upon which domain specific secure services, tools, and applications can be developed....
[...]
01 Jan 2002
TL;DR: This presentation complements an earlier foundational article, “The Anatomy of the Grid,” by describing how Grid mechanisms can implement a service-oriented architecture, explaining how Grid functionality can be incorporated into a Web services framework, and illustrating how the architecture can be applied within commercial computing as a basis for distributed system integration.
Abstract: In both e-business and e-science, we often need to integrate services across distributed, heterogeneous, dynamic “virtual organizations” formed from the disparate resources within a single enterprise and/or from external resource sharing and service provider relationships. This integration can be technically challenging because of the need to achieve various qualities of service when running on top of different native platforms. We present an Open Grid Services Architecture that addresses these challenges. Building on concepts and technologies from the Grid and Web services communities, this architecture defines a uniform exposed service semantics (the Grid service); defines standard mechanisms for creating, naming, and discovering transient Grid service instances; provides location transparency and multiple protocol bindings for service instances; and supports integration with underlying native platform facilities. The Open Grid Services Architecture also defines, in terms of Web Services Description Language (WSDL) interfaces and associated conventions, mechanisms required for creating and composing sophisticated distributed systems, including lifetime management, change management, and notification. Service bindings can support reliable invocation, authentication, authorization, and delegation, if required. Our presentation complements an earlier foundational article, “The Anatomy of the Grid,” by describing how Grid mechanisms can implement a service-oriented architecture, explaining how Grid functionality can be incorporated into a Web services framework, and illustrating how our architecture can be applied within commercial computing as a basis for distributed system integration—within and across organizational domains. This is a DRAFT document and continues to be revised. The latest version can be found at http://www.globus.org/research/papers/ogsa.pdf. Please send comments to foster@mcs.anl.gov, carl@isi.edu, jnick@us.ibm.com, tuecke@mcs.anl.gov Physiology of the Grid 2
3,455 citations
01 Jun 1997
TL;DR: The Globus system is intended to achieve a vertically integrated treatment of application, middleware, and net work, an integrated set of higher level services that enable applications to adapt to heteroge neous and dynamically changing metacomputing environ ments.
Abstract: The Globus system is intended to achieve a vertically integrated treatment of application, middleware, and net work. A low-level toolkit provides basic mechanisms such as communication, authentication, network information, and data access. These mechanisms are used to con struct various higher level metacomputing services, such as parallel programming tools and schedulers. The long- term goal is to build an adaptive wide area resource environment AWARE, an integrated set of higher level services that enable applications to adapt to heteroge neous and dynamically changing metacomputing environ ments. Preliminary versions of Globus components were deployed successfully as part of the I-WAY networking experiment.
3,450 citations
"Introduce: An Open Source Toolkit f..." refers background in this paper
...These include middleware and tools for service deployment and remote service invocation [1], security [2–4], resource monitoring and scheduling [5–8], high-speed data transfer [9–11], metadata and replica management [12–16], component based application composition [17–19], and workflow management [20–22]....
[...]
TL;DR: The current implementation of the NWS for Unix and TCP/IP sockets is described and examples of its performance monitoring and forecasting capabilities are provided.
1,414 citations
"Introduce: An Open Source Toolkit f..." refers methods in this paper
...P-GRADE, ASKALON, FORTE HPC, and GEMLCA as well as tools for highperformance bulk data transfer [10, 11], job scheduling and monitoring [5, 7], could be used in the Introduce framework to support services that involve parallel application execution, legacy programs, job scheduling, and large data transfer....
[...]
07 Aug 2001
TL;DR: It is asserted that Condor-G can serve as a general-purpose interface to Grid resources, for use by both end users and higher-level program development tools.
Abstract: In recent years, there has been a dramatic increase in the amount of available computing and storage resources, yet few have been able to exploit these resources in an aggregated form. We present the Condor-G system, which leverages software from Globus and Condor to allow users to harness multi-domain resources as if they all belong to one personal domain. We describe the structure of Condor-G and how it handles job management, resource selection, security and fault tolerance.
1,343 citations