The Telescience Portal for advanced tomography applications

Peltier, Steven T.; Lin, Abel W.; Lee, David; Mock, Stephen; LaMont, S. P.; Molina, Tomas; Wong, Mona; Dai, Lu; Martone, Maryann E.; Ellisman, Mark H.

doi:10.1016/s0743-7315(03)00061-3

Cited by 45 publications

(15 citation statements)

References 15 publications

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“…Many EM laboratories therefore have clusters of workstations as part of their facilities, and use parallel computing for the most time-consuming stages of structure determination Marinescu et al, 2001;Peltier et al, 2003). The current implementation of Xmipp includes parallel support for 3D reconstruction by iterative real-space techniques (SIRT, SART, CAV, BICAV, and Averaging Strings) of both single-particles and single-tilt electron tomography data.…”

Section: Parallel Computing In 3d Reconstructionmentioning

confidence: 99%

XMIPP: a new generation of an open-source image processing package for electron microscopy

Sorzano

Marabini

Velázquez-Muriel

et al. 2004

Journal of Structural Biology

454

366

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Section: Parallel Computing In 3d Reconstructionmentioning

confidence: 99%

XMIPP: a new generation of an open-source image processing package for electron microscopy

Sorzano

Marabini

Velázquez-Muriel

et al. 2004

Journal of Structural Biology

454

366

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“…The CCDB utilized the basic architecture developed by the Biomedical Informatics Research Network (BIRN; Grethe et al, 2005) and Telescience (Peltier et al, 2003) projects for distributed file storage and access. The BIRN project is an example of a so-called ''grid'' project, predicated on a model of distributed hardware and software.…”

Section: Current Architecture Of the Ccdbmentioning

confidence: 99%

“…This uniformity is provided by software layers, ''middleware'', that sit between the physical resource and the programs required to access it. The CCDB utilizes both the distributed collections manager called the Storage Resource Broker (SRB; Grethe et al, 2005) and the authentication mechanisms for CCDB files (Peltier et al, 2003).…”

Section: Current Architecture Of the Ccdbmentioning

confidence: 99%

“…However, we have deployed a set of input forms through a custom portal developed for the National Center for Microscopy and Imaging Research (NCMIR), the P41 technology development center that hosts the CCDB. The Telescience Multiscale Imaging Portal (https://.telescience.ucsd.edu), a Gridsphere-based portal, provides secure access to high voltage electron microscopes, computational resources and tools for electron tomography, all using a single user account (Peltier et al, 2003). The CCDB accepts the authentication certificate issued by Telescience, so that users logged into Telescience are also authorized to enter data into the CCDB.…”

Section: Data Input To Ccdbmentioning

confidence: 99%

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The Cell Centered Database project: An update on building community resources for managing and sharing 3D imaging data

Martone

Tran

Wong

et al. 2008

Journal of Structural Biology

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Databases have become integral parts of data management, dissemination, and mining in biology. At the Second Annual Conference on Electron Tomography, held in Amsterdam in 2001, we proposed that electron tomography data should be shared in a manner analogous to structural data at the protein and sequence scales. At that time, we outlined our progress in creating a database to bring together cell level imaging data across scales, The Cell Centered Database (CCDB). The CCDB was formally launched in 2002 as an on-line repository of high-resolution 3D light and electron microscopic reconstructions of cells and subcellular structures. It contains 2D, 3D, and 4D structural and protein distribution information from confocal, multiphoton, and electron microscopy, including correlated light and electron microscopy. Many of the data sets are derived from electron tomography of cells and tissues. In the 5 years since its debut, we have moved the CCDB from a prototype to a stable resource and expanded the scope of the project to include data management and knowledge engineering. Here, we provide an update on the CCDB and how it is used by the scientific community. We also describe our work in developing additional knowledge tools, e.g., ontologies, for annotation and query of electron microscopic data.

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“…In order to provide users with transparent and easy access to these resources, the NGS Portal has been developed and deployed for production usage. Many Web-based portals have been set up for distributed environments to improve the usability of the Grid; for example, the Telescience Portal [13], the HotPage Grid Computing Portal [14] and the Cambridge CFD Grid Portal [15]. Work in the Grid Technology Group at the CCLRC Daresbury Laboratory has focused on integrating Grid services and collaboration tools into a familiar Web portal environment.…”

Section: The Uk Ngsmentioning

confidence: 99%

CCLRC Portal infrastructure to support research facilities

Akram

Chohan

Meredith

et al. 2006

Concurrency and Computation

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SUMMARYThe emergence of portal technology is providing benefits in developing portlet interfaces to applications to meet the current and future requirements of CCLRC facilities support. Portlets can be reused by different projects, e.g. the high-profile Integrative Biology project (with the University of Oxford), and in different Java Specification Request 168 Portlet Specification (JSR 168) compliant portal frameworks. Deployment and maintenance of applications developed as portlets becomes easier and manageable. A community process is already beginning and many portal frameworks come with free-to-use useful portlets. As rendering is carried out in the framework, applications can be easily accessible and internationalized. Portlets are compatible with J2EE, thus providing additional capabilities required in the service-oriented architecture (SOA). We also describe how Web service gateways can be used to provide many of the functionalities encapsulated in a portal server in a way to support Grid applications. Portals used as a rich client can allow users to customize or personalize their user interfaces and even their workflow and application access. CCLRC facilities will be able to leverage the work so far carried out on the National Grid Service (NGS) and e-HTPX portals, as they are fully functional and have received detailed user feedback. This demonstrates the usefulness of providing advanced capabilities for e-Research and having the associated business logic in a SOA loosely coupled from the presentation layer for an Integrated e-Science Environment.

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The Telescience Portal for advanced tomography applications

Cited by 45 publications

References 15 publications

XMIPP: a new generation of an open-source image processing package for electron microscopy

XMIPP: a new generation of an open-source image processing package for electron microscopy

The Cell Centered Database project: An update on building community resources for managing and sharing 3D imaging data

CCLRC Portal infrastructure to support research facilities

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