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

Structure et intérpretation des programmes informatiques

This chapter contains sections titled: Controlling Screen Output, Keyboard Input, Example: The Dynaturtle Program

Writing Interactive Programs

Logo for the Macintosh teaches the art of programming to first time programmers. It begins with Turtle Geometry, a series of exercises involving both Logo programming and geometric concepts. Later chapters illustrate more advanced topics, such as the famous DOCTOR program with its simulated psychotherapist and an INSTANT program that enables parents and teachers to create a programming environment for preschool children. A chapter is devoted to the topic of object-oriented programming, a key feature of the Object Logo implementation of Logo.Logo for the Macintosh is written primarily for use with Object Logo, a powerful implementation of the Logo language that greatly enhances its speed, capabilities, and overall usability in education and beyond. The book may also be used with other versions of Logo for the Macintosh.Harold Abelson is Professor of Computer Science at the Massachusetts Institute of Technology. He directed the first implementation of Logo for the Apple II, which made Logo widely available on personal computers beginning in 1981. Amanda Abelson, a high-school student, runs a nationwide Internet based multiuser simulation game.

Logo for the Macintosh: An Introduction Through Object Logo With the Student Edition of Object Logo

This instructor's manual and reader's guide accompanies the secondedition of Structure and Interpretation of Computer Programs,by Harold Abelson and Gerald Jay Sussman with Julie Sussman. This instructor's manual and reader's guide accompanies the second edition of Structure and Interpretation of Computer Programs, by Harold Abelson and Gerald Jay Sussman with Julie Sussman. It contains discussions of exercises and other material in the text as well as supplementary material, additional examples and exercises, and teaching suggestions. An appendix summarizes the Scheme programming language as used in the text, showing at what point in the text each element of Scheme is introduced.

Harold Abelson

Papers

Structure et intérpretation des programmes informatiques

Writing Interactive Programs

Logo for the Macintosh: An Introduction Through Object Logo With the Student Edition of Object Logo

Instructor's Manual to Accompany Structure and Interpretation of Computer Programs

Programming with Procedures