The Graph Rewriting and Transformation Language: GReAT

In this paper, we describe the language and features of our graph transformation tool, GReAT.We begin with a brief introduction and motivation, followed by an overview of the actual language, the modeling framework, and the tools that were written to support transformations. Finally, we compare GReAT to other similar tools, discuss additional functionality we are currently implementing, and describe some of our experiences with the tool thus far

Enabling Self-Management by Using Model-Based Design Space Exploration

Abstract—Reconfiguration and self-management are important properties for systems that operate in hazardous and uncontrolled environments, such as inter-planetary space. These systems need a reconfiguration mechanism that provides recovery from individual component failures as well as the ability to dynamically adapt to evolving mission goals. One way to provide this functionality is to define a model of alternative system configurations and allow the system to choose the current configuration based on its current state, including environmental parameters and goals. The primary difficulties with this approach are (1) the state space of configurations can grow very large, which can make explicit enumeration infeasible, and (2) the component failures and evolving system goals must be somehow encoded in the system configuration model. This paper describes an online reconfiguration method based on model-based designspace exploration. We symbolically encode the set of valid system configurations and assert the current system state and goals as symbolic constraints. Our initial work indicates that this method scales and is capable of providing effective online dynamic reconfiguration. I

Gravitational waves from inspiraling compact binaries: Validity of the stationary-phase approximation to the Fourier transform

We prove that the oft-used stationary-phase method gives a very accurate expression for the Fourier transform of the gravitational-wave signal produced by an inspiraling compact binary. We give three arguments. First, we analytically calculate the next-order correction to the stationary-phase approximation, and show that it is small. This calculation is essentially an application of the steepest-descent method to evaluate integrals. Second, we numerically compare the stationary-phase expression to the results obtained by Fast Fourier Transform. We show that the differences can be fully attributed to the windowing of the time series, and that they have nothing to do with an intrinsic failure of the stationary-phase method. And third, we show that these differences are negligible for the practical application of matched filtering.Comment: 8 pages, ReVTeX, 4 figure

Formins Determine the Functional Properties of Actin Filaments in Yeast

The actin cytoskeleton executes a broad range of essential functions within a living cell. The dynamic nature of the actin polymer is modulated to facilitate specific cellular processes at discrete locations by actin-binding proteins (ABPs), including the formins and tropomyosins (Tms). Formins nucleate actin polymers, while Tms are conserved dimeric proteins that form polymers along the length of actin filaments. Cells possess different Tm isoforms, each capable of differentially regulating the dynamic and func- tional properties of the actin polymer. However, the mecha- nism by which a particular Tm localizes to a specific actin polymer is unknown. Here we show that specific formin family members dictate which Tm isoform will associate with a particular actin filament to modulate its dynamic and functional properties at specific cellular locations. Exchanging the localization of the fission yeast formins For3 and Cdc12 results in an exchange in localizations of Tm forms on actin polymers. This nucleator-driven switch in filament composition is reflected in a switch in actin dynamics, together with a corresponding change in the filament’s ability to regulate ABPs and myosin motor activity. These data establish a role for formins in dictating which specific Tm variant will associate with a growing actin filament and therefore specify the functional capacity of the actin filaments that they create

A Subgraph Operator for Graph Transformation Languages

In practical applications of graph transformation techniques to model transformations one often has the need for copying, deleting, or moving entire subgraphs that match a certain graph pattern. While this can be done using elementary node and edge operations, the transformation is rather cumbersome to write. To simplify the transformation, we have recently developed a novel approach that allows selecting subgraphs from the matched portion of the host graph, applying a filter condition to the selection, and performing a delete, move, or copy operation on the filtered result in the context of a transformation rule. The approach has been implemented in the GReAT language and tested on examples that show the practical efficacy of the technique. The paper describes the technique in detail and illustrates its use on a real-life example

Software for Distributed Computation on Medical Databases: A Demonstration Project

Bringing together the information latent in distributed medical databases promises to personalize medical care by enabling reliable, stable modeling of outcomes with rich feature sets (including patient characteristics and treatments received). However, there are barriers to aggregation of medical data, due to lack of standardization of ontologies, privacy concerns, proprietary attitudes toward data, and a reluctance to give up control over end use. Aggregation of data is not always necessary for model fitting. In models based on maximizing a likelihood, the computations can be distributed, with aggregation limited to the intermediate results of calculations on local data, rather than raw data. Distributed fitting is also possible for singular value decomposition. There has been work on the technical aspects of shared computation for particular applications, but little has been published on the software needed to support the "social networking" aspect of shared computing, to reduce the barriers to collaboration. We describe a set of software tools that allow the rapid assembly of a collaborative computational project, based on the flexible and extensible R statistical software and other open source packages, that can work across a heterogeneous collection of database environments, with full transparency to allow local officials concerned with privacy protections to validate the safety of the method. We describe the principles, architecture, and successful test results for the site-stratified Cox model and rank-k Singular Value Decomposition (SVD)