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.

A type system is a syntactic method for automatically checking the absence of certain erroneous behaviors by classifying program phrases according to the kinds of values they compute. The study of type systems -- and of programming languages from a type-theoretic perspective -- has important applications in software engineering, language design, high-performance compilers, and security.This text provides a comprehensive introduction both to type systems in computer science and to the basic theory of programming languages. The approach is pragmatic and operational; each new concept is motivated by programming examples and the more theoretical sections are driven by the needs of implementations. Each chapter is accompanied by numerous exercises and solutions, as well as a running implementation, available via the Web. Dependencies between chapters are explicitly identified, allowing readers to choose a variety of paths through the material.The core topics include the untyped lambda-calculus, simple type systems, type reconstruction, universal and existential polymorphism, subtyping, bounded quantification, recursive types, kinds, and type operators. Extended case studies develop a variety of approaches to modeling the features of object-oriented languages.

https://www.seas.upenn.edu/~bcpierce/tapl/contents.pdf

Types and Programming Languages

We present an interprocedural flow-insensitive points-to analysis based on type inference methods with an almost linear time cost complexity To our knowledge, this is the asymptotically fastest non-trivial interprocedural points-to analysis algorithm yet described The algorithm is based on a non-standard type system. The type inferred for any variable represents a set of locations and includes a type which in turn represents a set of locations possibly pointed to by the variable. The type inferred for a function variable represents a set of functions It may point to and includes a type signature for these functions The results are equivalent to those of a flow-insensitive alias analysis (and control flow analysis) that assumes alias relations are reflexive and transitive.This work makes three contributions. The first is a type system for describing a universally valid storage shape graph for a program in linear space. The second is a constraint system which often leads to better results than the "obvious" constraint system for the given type system The third is an almost linear time algorithm for points-to analysis by solving a constraint system.

/pdf/points-to-analysis-in-almost-linear-time-ziolc34o27.pdf

Points-to analysis in almost linear time

\"Some half dozen persons have written technically on combinatory logic, and most of these, including ourselves, have published something erroneous. Since some of our fellow sinners are among the most careful and competent logicians on the contemporary scene, we regard this as evidence that the subject is refractory. Thus fullness of exposition is necessory for accurary; and excessive condensation would be false economy here, even more than it is ordinarily.\

Report on the Programming Language Haskell, A Non-strict, Purely Functional Language.

In the last three decades a large number of compiler transformations for optimizing programs have been implemented. Most optimizations for uniprocessors reduce the number of instructions executed by the program using transformations based on the analysis of scalar quantities and data-flow techniques. In contrast, optimizations for high-performance superscalar, vector, and parallel processors maximize parallelism and memory locality with transformations that rely on tracking the properties of arrays using loop dependence analysis.This survey is a comprehensive overview of the important high-level program restructuring techniques for imperative languages, such as C and Fortran. Transformations for both sequential and various types of parallel architectures are covered in depth. We describe the purpose of each transformation, explain how to determine if it is legal, and give an example of its application.Programmers wishing to enhance the performance of their code can use this survey to improve their understanding of the optimizations that compilers can perform, or as a reference for techniques to be applied manually. Students can obtain an overview of optimizing compiler technology. Compiler writers can use this survey as a reference for most of the important optimizations developed to date, and as bibliographic reference for the details of each optimization. Readers are expected to be familiar with modern computer architecture and basic program compilation techniques.

Compiler transformations for high-performance 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.

Revised4 report on the algorithmic language scheme

Programming languages should be designed not by piling feature on top of feature, but by removing the weaknesses and restrictions that make additional features appear necessary. Scheme demonstrates that a very small number of rules for forming expressions, with no restrictions on how they are composed, are enough to form a practical and efficient programming language that is flexible enough to support most of the major programming paradigms in use today. This book contains the three parts comprising 'R6RS', the sixth revision of a series of reports describing the programming language Scheme. The book is divided into parts: a description of the language itself, a description of the standard libraries and non-normative appendices. Early chapters introduce Scheme and later chapters act as a reference manual. This is an important report for programmers that work with or want to learn about the Scheme language.

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Revised [6] Report on the Algorithmic Language Scheme

/pdf/revised-5-report-on-the-algorithmic-language-26r0nsx5sp.pdf

Revised 5 Report on the Algorithmic Language

Abstract The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal ( https://data.4dnucleome.org/ ), a repository for datasets generated in the 4DN network and relevant external datasets. Datasets were generated with a wide range of experiments, including chromosome conformation capture assays such as Hi-C and other innovative sequencing and microscopy-based assays probing chromosome architecture. All together, the 4DN data portal hosts more than 1800 experiment sets and 36000 files. Results of sequencing-based assays from different laboratories are uniformly processed and quality-controlled. The portal interface allows easy browsing, filtering, and bulk downloads, and the integrated HiGlass genome browser allows interactive visualization and comparison of multiple datasets. The 4DN data portal represents a primary resource for chromosome contact and other nuclear architecture data for the scientific community. 

/pdf/author-correction-the-4d-nucleome-data-portal-as-a-resource-1bxvr0oy.pdf

K. M. Pitman

Papers

Revised Report on the Algorithmic Language Scheme

Revised4 report on the algorithmic language scheme

Revised [6] Report on the Algorithmic Language Scheme

Revised 5 Report on the Algorithmic Language

Author Correction: The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data