Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.

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Features and development of Coot.

This paper provides a theoretical framework for analysis of consensus algorithms for multi-agent networked systems with an emphasis on the role of directed information flow, robustness to changes in network topology due to link/node failures, time-delays, and performance guarantees. An overview of basic concepts of information consensus in networks and methods of convergence and performance analysis for the algorithms are provided. Our analysis framework is based on tools from matrix theory, algebraic graph theory, and control theory. We discuss the connections between consensus problems in networked dynamic systems and diverse applications including synchronization of coupled oscillators, flocking, formation control, fast consensus in small-world networks, Markov processes and gossip-based algorithms, load balancing in networks, rendezvous in space, distributed sensor fusion in sensor networks, and belief propagation. We establish direct connections between spectral and structural properties of complex networks and the speed of information diffusion of consensus algorithms. A brief introduction is provided on networked systems with nonlocal information flow that are considerably faster than distributed systems with lattice-type nearest neighbor interactions. Simulation results are presented that demonstrate the role of small-world effects on the speed of consensus algorithms and cooperative control of multivehicle formations

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Consensus and Cooperation in Networked Multi-Agent Systems

In this article we discuss our experience designing and implementing a statistical computing language. In developing this new language, we sought to combine what we felt were useful features from two existing computer languages. We feel that the new language provides advantages in the areas of portability, computational efficiency, memory management, and scoping.

R: A Language for Data Analysis and Graphics

In this paper we present a new data structure for representing Boolean functions and an associated set of manipulation algorithms. Functions are represented by directed, acyclic graphs in a manner similar to the representations introduced by Lee [1] and Akers [2], but with further restrictions on the ordering of decision variables in the graph. Although a function requires, in the worst case, a graph of size exponential in the number of arguments, many of the functions encountered in typical applications have a more reasonable representation. Our algorithms have time complexity proportional to the sizes of the graphs being operated on, and hence are quite efficient as long as the graphs do not grow too large. We present experimental results from applying these algorithms to problems in logic design verification that demonstrate the practicality of our approach.

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Graph-Based Algorithms for Boolean Function Manipulation

The primary purpose of a programming language is to assist the programmer in the practice of her art. Each language is either designed for a class of problems or supports a different style of programming. In other words, a programming language turns the computer into a ‘virtual machine’ whose features and capabilities are unlimited. In this article, we illustrate these aspects through a language similar tologo. Programs are developed to draw geometric pictures using this language.

Introduction to algorithms: 4. Turtle graphics

From the Publisher:
With an analytical and rigorous approach to problem solving and programming techniques,this book is oriented toward engineering. Structure and Interpretation of Computer Programs emphasizes the central role played by different approaches to dealing with time in computational models. Its unique approach makes it appropriate for an introduction to computer science courses,as well as programming languages and program design.

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Structure and Interpretation of Computer Programs

Turtle Geometry presents an innovative program of mathematical discovery that demonstrates how the effective use of personal computers can profoundly change the nature of a student's contact with mathematics. Using this book and a few simple computer programs, students can explore the properties of space by following an imaginary turtle across the screen.The concept of turtle geometry grew out of the Logo Group at MIT. Directed by Seymour Papert, author of Mindstorms, this group has done extensive work with preschool children, high school students and university undergraduates. Harold Abelson is an associate professor in the Department of Electrical Engineering and Computer Science at MIT. Andrea diSessa is an associate professor in the Graduate School of Education, University of California, Berkeley.

Turtle Geometry: The Computer as a Medium for Exploring Mathematics

ion to Continuous Space and Time The amorphous model postulates computing particles distributed throughout a space. If the particles are dense, one can imagine the particles as actually filling the space, and create programming abstractions that view the space itself as the object being programmed, rather than the collection of particles. Beal and Bachrach [10, 4] pursued this approach by creating a language, Proto, where programmers specify the behavior of an amorphous computer as though it were a continuous material filling the space it occupies. Proto programs manipulate fields of values spanning the entire space. Programming primitives are designed to make it simple to compile global operations to operations at each point of the continuum. These operations are approximated by having each device represent a nearby chunk of space. Programs are specified in space and time units that are independent of the distribution of particles and of the particulars of communication and execution on those particles (Figure 5). Programs are composed functionally, and many of the details of communication and composition are made implicit by Proto’s runtime system, allowing complex programs to be expressed simply. Proto has been applied to applications in sensor networks like target tracking and threat avoidance, to swarm robotics and to modular robotics, e.g., generating a planar wave for coordinated actuation. Newton’s language Regiment [45, 44] also takes a continuous view of space and time. Regiment is organized in terms of stream operations, where each stream represents a time-varying quantity over a part of space, for example, the average value of the temperature over a disc of a given radius centered at a designated point. Regiment, also a functional language, is designed to gather streams of data from regions of the amorphous computer and accumulate them at a single point. This assumption allows Regiment to provide region-wide summary functions that are difficult to implement in Proto.

Amorphous computing

The report gives a defining description of the programming language Scheme. Scheme is a statically scoped and properly tail-recursive dialect of the Lisp programming language invented by Guy Lewis Steele, Jr. and Gerald Jay Sussman. It was designed to have an exceptionally clear and simple semantics and few different ways to form expressions. A wide variety of programming paradigms, including imperative, functional, and message passing styles, find convenient expression in Scheme.

The introduction offers a brief history of the language and of the report.

The first three chapters present the fundamental ideas of the language and describe the notational conventions used for describing the language and for writing programs in the language.

Sections 5 and 6 describe the syntax and semantics of expressions, programs, and definitions.

Section 7 describes Scheme‘s built-in procedures, which include all of the language‘s data manipulation and input/output primitives.

Section 8 provides a formal syntax for Scheme written in extended BNF, along with a formal denotational semantics. An example of the use of the language follows the formal syntax and semantics.

The report concludes with a list of references and an alphabetic index and is followed by a short list of clarifications and corrections.

Revised Report on the Algorithmic Language Scheme

The report gives a defining description of the programming language Scheme. Scheme is a statically scoped and properly tail-recursive dialect of the Lisp programming language invented by Guy Lewis Steele Jr. and Gerald Jay Sussman. It was designed to have an exceptionally clear and simple semantics and few different ways to form expressions. A wide variety of programming paradigms, including imperative, functional, and message passing styles, find convenient expression in Scheme.

Harold Abelson

Papers

Structure and Interpretation of Computer Programs

Turtle Geometry: The Computer as a Medium for Exploring Mathematics

Amorphous computing

Revised Report on the Algorithmic Language Scheme

Revised4 report on the algorithmic language scheme