The Community Authorization Service: Status and Future

Virtual organizations (VOs) are communities of resource providers and users distributed over multiple policy domains. These VOs often wish to define and enforce consistent policies in addition to the policies of their underlying domains. This is challenging, not only because of the problems in distributing the policy to the domains, but also because of the fact that those domains may each have different capabilities for enforcing the policy. The Community Authorization Service (CAS) solves this problem by allowing resource providers to delegate some policy authority to the VO while maintaining ultimate control over their resources. In this paper we describe CAS and our past and current implementations of CAS, and we discuss our plans for CAS-related research.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003. 9 Pages, PD

The Cost of Stability in Coalitional Games

A key question in cooperative game theory is that of coalitional stability, usually captured by the notion of the \emph{core}--the set of outcomes such that no subgroup of players has an incentive to deviate. However, some coalitional games have empty cores, and any outcome in such a game is unstable. In this paper, we investigate the possibility of stabilizing a coalitional game by using external payments. We consider a scenario where an external party, which is interested in having the players work together, offers a supplemental payment to the grand coalition (or, more generally, a particular coalition structure). This payment is conditional on players not deviating from their coalition(s). The sum of this payment plus the actual gains of the coalition(s) may then be divided among the agents so as to promote stability. We define the \emph{cost of stability (CoS)} as the minimal external payment that stabilizes the game. We provide general bounds on the cost of stability in several classes of games, and explore its algorithmic properties. To develop a better intuition for the concepts we introduce, we provide a detailed algorithmic study of the cost of stability in weighted voting games, a simple but expressive class of games which can model decision-making in political bodies, and cooperation in multiagent settings. Finally, we extend our model and results to games with coalition structures.Comment: 20 pages; will be presented at SAGT'0

Montage: a grid portal and software toolkit for science-grade astronomical image mosaicking

Montage is a portable software toolkit for constructing custom, science-grade mosaics by composing multiple astronomical images. The mosaics constructed by Montage preserve the astrometry (position) and photometry (intensity) of the sources in the input images. The mosaic to be constructed is specified by the user in terms of a set of parameters, including dataset and wavelength to be used, location and size on the sky, coordinate system and projection, and spatial sampling rate. Many astronomical datasets are massive, and are stored in distributed archives that are, in most cases, remote with respect to the available computational resources. Montage can be run on both single- and multi-processor computers, including clusters and grids. Standard grid tools are used to run Montage in the case where the data or computers used to construct a mosaic are located remotely on the Internet. This paper describes the architecture, algorithms, and usage of Montage as both a software toolkit and as a grid portal. Timing results are provided to show how Montage performance scales with number of processors on a cluster computer. In addition, we compare the performance of two methods of running Montage in parallel on a grid.Comment: 16 pages, 11 figure

Collaboration in the Semantic Grid: a Basis for e-Learning

The CoAKTinG project aims to advance the state of the art in collaborative mediated spaces for the Semantic Grid. This paper presents an overview of the hypertext and knowledge based tools which have been deployed to augment existing collaborative environments, and the ontology which is used to exchange structure, promote enhanced process tracking, and aid navigation of resources before, after, and while a collaboration occurs. While the primary focus of the project has been supporting e-Science, this paper also explores the similarities and application of CoAKTinG technologies as part of a human-centred design approach to e-Learning

High performance computing and communications grand challenges program

The so-called protein folding problem has numerous aspects, however it is principally concerned with the {ital de novo} prediction of three-dimensional (3D) structure from the protein primary amino acid sequence, and with the kinetics of the protein folding process. Our current project focuses on the 3D structure prediction problem which has proved to be an elusive goal of molecular biology and biochemistry. The number of local energy minima is exponential in the number of amino acids in the protein. All current methods of 3D structure prediction attempt to alleviate this problem by imposing various constraints that effectively limit the volume of conformational space which must be searched. Our Grand Challenge project consists of two elements: (1) a hierarchical methodology for 3D protein structure prediction; and (2) development of a parallel computing environment, the Protein Folding Workbench, for carrying out a variety of protein structure prediction/modeling computations. During the first three years of this project, we are focusing on the use of two proteins selected from the Brookhaven Protein Data Base (PDB) of known structure to provide validation of our prediction algorithms and their software implementation, both serial and parallel. Both proteins, protein L from {ital peptostreptococcus magnus}, and {ital streptococcal} protein G, are known to bind to IgG, and both have an {alpha} {plus} {beta} sandwich conformation. Although both proteins bind to IgG, they do so at different sites on the immunoglobin and it is of considerable biological interest to understand structurally why this is so. 12 refs., 1 fig

Reproducible big data science: A case study in continuous FAIRness.

Big biomedical data create exciting opportunities for discovery, but make it difficult to capture analyses and outputs in forms that are findable, accessible, interoperable, and reusable (FAIR). In response, we describe tools that make it easy to capture, and assign identifiers to, data and code throughout the data lifecycle. We illustrate the use of these tools via a case study involving a multi-step analysis that creates an atlas of putative transcription factor binding sites from terabytes of ENCODE DNase I hypersensitive sites sequencing data. We show how the tools automate routine but complex tasks, capture analysis algorithms in understandable and reusable forms, and harness fast networks and powerful cloud computers to process data rapidly, all without sacrificing usability or reproducibility-thus ensuring that big data are not hard-to-(re)use data. We evaluate our approach via a user study, and show that 91% of participants were able to replicate a complex analysis involving considerable data volumes

Reproducible big data science: A case study in continuous FAIRness

Big biomedical data create exciting opportunities for discovery, but make it difficult to capture analyses and outputs in forms that are findable, accessible, interoperable, and reusable (FAIR). In response, we describe tools that make it easy to capture, and assign identifiers to, data and code throughout the data lifecycle. We illustrate the use of these tools via a case study involving a multi-step analysis that creates an atlas of putative transcription factor binding sites from terabytes of ENCODE DNase I hypersensitive sites sequencing data. We show how the tools automate routine but complex tasks, capture analysis algorithms in understandable and reusable forms, and harness fast networks and powerful cloud computers to process data rapidly, all without sacrificing usability or reproducibility—thus ensuring that big data are not hard-to-(re)use data. We evaluate our approach via a user study, and show that 91% of participants were able to replicate a complex analysis involving considerable data volumes

MultiCellDS : a community-developed standard for curating microenvironment-dependent multicellular data

Exchanging and understanding scientific data and their context represents a significant barrier to advancing research, especially with respect to information siloing. Maintaining information provenance and providing data curation and quality control help overcome common concerns and barriers to the effective sharing of scientific data. To address these problems in and the unique challenges of multicellular systems, we assembled a panel composed of investigators from several disciplines to create the MultiCellular Data Standard (MultiCellDS) with a use-case driven development process. The standard includes (1) digital cell lines, which are analogous to traditional biological cell lines, to record metadata, cellular microenvironment, and cellular phenotype variables of a biological cell line, (2) digital snapshots to consistently record simulation, experimental, and clinical data for multicellular systems, and (3) collections that can logically group digital cell lines and snapshots. We have created a MultiCellular DataBase (MultiCellDB) to store digital snapshots and the 200+ digital cell lines we have generated. MultiCellDS, by having a fixed standard, enables discoverability, extensibility, maintainability, searchability, and sustainability of data, creating biological applicability and clinical utility that permits us to identify upcoming challenges to uplift biology and strategies and therapies for improving human health

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types.

Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human tissues. We validate that these footprints overlap true-positive TF binding sites from ChIP-seq. We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits