Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

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Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

THE DESIGN AND ANALYSIS OF EXPERIMENTS. By Oscar Kempthorne. New York, John Wiley and Sons, Inc., 1952. 631 pp. $8.50. This book by a teacher of statistics (as well as a consultant for \"experimenters\") is a comprehensive study of the philosophical background for the statistical design of experiment. It is necessary to have some facility with algebraic notation and manipulation to be able to use the volume intelligently. The problems are presented from the theoretical point of view, without such practical examples as would be helpful for those not acquainted with mathematics. The mathematical justification for the techniques is given. As a somewhat advanced treatment of the design and analysis of experiments, this volume will be interesting and helpful for many who approach statistics theoretically as well as practically. With emphasis on the \"why,\" and with description given broadly, the author relates the subject matter to the general theory of statistics and to the general problem of experimental inference. MARGARET J. ROBERTSON

The Design and Analysis of Experiments

1 GAs: What Are They?.- 2 GAs: How Do They Work?.- 3 GAs: Why Do They Work?.- 4 GAs: Selected Topics.- 5 Binary or Float?.- 6 Fine Local Tuning.- 7 Handling Constraints.- 8 Evolution Strategies and Other Methods.- 9 The Transportation Problem.- 10 The Traveling Salesman Problem.- 11 Evolution Programs for Various Discrete Problems.- 12 Machine Learning.- 13 Evolutionary Programming and Genetic Programming.- 14 A Hierarchy of Evolution Programs.- 15 Evolution Programs and Heuristics.- 16 Conclusions.- Appendix A.- Appendix B.- Appendix C.- Appendix D.- References.

Genetic Algorithms + Data Structures = Evolution Programs

Planning algorithms are impacting technical disciplines and industries around the world, including robotics, computer-aided design, manufacturing, computer graphics, aerospace applications, drug design, and protein folding. This coherent and comprehensive book unifies material from several sources, including robotics, control theory, artificial intelligence, and algorithms. The treatment is centered on robot motion planning but integrates material on planning in discrete spaces. A major part of the book is devoted to planning under uncertainty, including decision theory, Markov decision processes, and information spaces, which are the “configuration spaces” of all sensor-based planning problems. The last part of the book delves into planning under differential constraints that arise when automating the motions of virtually any mechanical system. Developed from courses taught by the author, the book is intended for students, engineers, and researchers in robotics, artificial intelligence, and control theory as well as computer graphics, algorithms, and computational biology.

Planning Algorithms: Introductory Material

SUMMARY We present a modification of the spring-embedder model of Eades [ Congresses Numerantium, 42, 149–160, (1984)] for drawing undirected graphs with straight edges. Our heuristic strives for uniform edge lengths, and we develop it in analogy to forces in natural systems, for a simple, elegant, conceptuallyintuitive, and efficient algorithm.

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Graph drawing by force-directed placement

From the Publisher:
This book is designed to describe fundamental algorithmic techniques for constructing drawings of graphs. Suitable as a book or reference manual, its chapters offer an accurate, accessible reflection of the rapidly expanding field of graph drawing.

Graph Drawing: Algorithms for the Visualization of Graphs

Several data presentation problems involve drawing graphs so that they are easy to read and understand. Examples include circuit schematics and diagrams for information systems analysis and design. In this paper we present a bibliographic survey on algorithms whose goal is to produce aesthetically pleasing drawings of graphs. Research on this topic is spread over the broad spectrum of computer science. This bibliography constitutes a first attempt to encompass both theoretical and application-oriented papers from disparate areas.

Algorithms for drawing graphs: an annotated bibliography

We consider the problem of efficiently proving the integrity of data stored at untrusted servers. In the provable data possession (PDP) model, the client preprocesses the data and then sends it to an untrusted server for storage, while keeping a small amount of meta-data. The client later asks the server to prove that the stored data has not been tampered with or deleted (without downloading the actual data). However, the original PDP scheme applies only to static (or append-only) files.We present a definitional framework and efficient constructions for dynamic provable data possession (DPDP), which extends the PDP model to support provable updates to stored data. We use a new version of authenticated dictionaries based on rank information. The price of dynamic updates is a performance change from O(1) to O(logn) (or O(nelog n), for a file consisting of n blocks, while maintaining the same (or better, respectively) probability of misbehavior detection. Our experiments show that this slowdown is very low in practice (e.g. 415KB proof size and 30ms computational overhead for a 1GB file). We also show how to apply our DPDP scheme to outsourced file systems and version control systems (e.g. CVS).

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Dynamic provable data possession

Given a planar graph G together with a planar representation P, a region preserving grid embedding of G is a planar embedding of G in the rectilinear grid that has planar representation isomorphic to P. In this paper, an algorithm is presented that computes a region preserving grid embedding with the minimum number of bends in edges. This algorithm makes use of network flow techniques, and runs in time $O(n^2 \log n)$, where n is the number of vertices of the graph. Constrained versions of the problem are also considered, and most results are extended to k-gonal graphs, i.e., graphs whose edges are sequences of segments with slope multiple of ${{180} / k}$ degrees. Applications of the above results can be found in several areas: VLSI circuit layout, architectural design, communication by light or microwave, transportation problems, and automatic layout of graphlike diagrams.

On embedding a graph in the grid with the minimum number of bends

The state of the art in automatic graph drawing is reviewed, with special attention to the readability of information system diagrams. Existing results in the literature are compared, and a comprehensive algorithmic approach to the problem is proposed. The algorithm presented draws graphs on a grid and is suitable for both undirected graphs and mixed graphs that contain as subgraphs hierarchic structures. Several applications of GIOTTO, a graphic tool that embodies the aforementioned facility, are shown. >

Roberto Tamassia

Papers

Graph Drawing: Algorithms for the Visualization of Graphs

Algorithms for drawing graphs: an annotated bibliography

Dynamic provable data possession

On embedding a graph in the grid with the minimum number of bends

Automatic graph drawing and readability of diagrams