2779311
The immune system as a reactive system: modeling T cell activation with statecharts
The construction of reliable reactive systems is considered to be one of the most challenging goals in the fields of software and system engineering. The definition of a reactive system suits biological systems at different levels, ranging from gene networks, developing embryos and the immune system. We report here the application of a tool developed for constructing computerized systems to the modeling and analysis of a biological system, the immune system. We use the language of statecharts within the framework of object-oriented modeling. The results described here indicate that this modeling strategy can contribute to the transition of biology from the phase of analysis to the phase of synthesis.
10640301
Smart play-out
We describe "smart play-out", a new method for executing and analyzing scenario based behavior, which is part of the Play-In/Play-Out methodology and the Play-Engine tool. Behavior is "played in" directly from the system's GUI, and as this is being done the Play-Engine continuously constructs Live Sequence Charts (LSCs), a powerful extension of sequence diagrams. Later, behavior can be "played out" freely from the GUI, and the tool executes the LSCs directly, thus driving the system's behavior. An inherent difficulty in constructing a ``play-out" mechanism is how to resolve the nondeterminism allowed by the LSC specification in order to obtain an executable model. Smart play-out, is a recent strengthening of the play-out mechanism, which addresses this problem by using powerful verification methods, mainly model-checking, to execute and analyze the LSCs, helping the execution to avoid deadlocks and violations. Thus, smart play-out utilizes verification techniques to run programs, rather than to verify a program with respect to given requirements, as in traditional verification approaches. The ideas appear to be relevant in various stages of system development, including requirements specification and analysis, implementation and testing.
122739950
Graph Drawing by High-Dimensional Embedding
346060
A Multi-scale Algorithm for the Linear Arrangement Problem
Finding a linear ordering of the vertices of a graph is a common problem arising in diverse applications. In this paper we present a linear-time algorithm for this problem, based on the multi-scale paradigm. Experimental results are similar to those of the best known approaches, while the running time is significantly better, enabling it to deal with much larger graphs. The paper contains a general multi-scale construction, which may be used for a broader range of ordering problems.
8837470
Reactive Animation
Software engineers use system visualization mainly in two domains: algorithm visualization and system visualization, and both of these are often animated. In this paper we provide a generic link between the specification and animation of complex object-oriented reactive systems, which constitute one of the most important and difficult classes of systems. The link and its methodology form a basis for communication between standard reactive specification tools and standard animation tools. Reactive Animation can be used in a wide range of applications: computer games, navigation and traffic systems, interactive scientific visualization. Reactive Animation helps make the programming of such applications more reliable, expeditious and natural to observe and comprehend. We illustrate two examples: a complex biological model of thymic T-cell behavior and a traffic simulation. 3
1037525
Graph Drawing by High-Dimensional Embedding
We present a novel approach to the aesthetic drawing of undirected graphs. The method has two phases: first embed the graph in a very high dimension and then project it into the 2-D plane using principal components analysis. Running time is linear in the graph size, and experiments we have carried out show the ability of the method to draw graphs of 105 nodes in few seconds. The new method appears to have several advantages over classical methods, including a significantly better running time, a useful inherent capability to exhibit the graph in various dimensions, and an effective means for interactive exploration of large graphs.
14408974
Towards an odor communication system
We propose a setup for an odor communication system. Its different parts are described, and ways to realize them are outlined. Our scheme enables an output device-the whiffer-to release an imitation of an odorant read in by an input device-the sniffer-upon command. The heart of the system is the novel algorithmic scheme that makes the scheme feasible. We are currently at work researching and developing some of the components that constitute the algorithm, and we hope that the description of the overall scheme in this paper will help to get other groups to join in this effort.