The book is an introduction to the idea of design patterns in software engineering, and a catalog of twenty-three common patterns. The nice thing is, most experienced OOP designers will find out they've known about patterns all along. It's just that they've never considered them as such, or tried to centralize the idea behind a given pattern so that it will be easily reusable.

Design Patterns: Elements of Reusable Object-Oriented Software

AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user.

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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

SciPy is an open source scientific computing library for the Python programming language. SciPy 1.0 was released in late 2017, about 16 years after the original version 0.1 release. SciPy has become a de facto standard for leveraging scientific algorithms in the Python programming language, with more than 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories, and millions of downloads per year. This includes usage of SciPy in almost half of all machine learning projects on GitHub, and usage by high profile projects including LIGO gravitational wave analysis and creation of the first-ever image of a black hole (M87). The library includes functionality spanning clustering, Fourier transforms, integration, interpolation, file I/O, linear algebra, image processing, orthogonal distance regression, minimization algorithms, signal processing, sparse matrix handling, computational geometry, and statistics. In this work, we provide an overview of the capabilities and development practices of the SciPy library and highlight some recent technical developments.

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SciPy 1.0--Fundamental Algorithms for Scientific Computing in Python

Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.

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phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.

From the Publisher:
Written by Bjarne Stroustrup, the creator of C, this is the world's most trusted and widely read book on C.

For this special hardcover edition, two new appendixes on locales and standard library exception safety have been added. The result is complete, authoritative coverage of the C language, its standard library, and key design techniques. Based on the ANSI/ISO C standard, The C Programming Language provides current and comprehensive coverage of all C language features and standard library components.

For example: 
abstract classes as interfaces class hierarchies for object-oriented programming templates as the basis for type-safe generic software exceptions for regular error handling namespaces for modularity in large-scale software run-time type identification for loosely coupled systems the C subset of C for C compatibility and system-level work standard containers and algorithms standard strings, I/O streams, and numerics C compatibility, internationalization, and exception safety 
Bjarne Stroustrup makes C even more accessible to those new to the language, while adding advanced information and techniques that even expert C programmers will find invaluable.

The C++ Programming Language

The C++ programming language (2nd ed.)

Preface. 1. Introduction. Overview. Syntax Notation. Evolution of C++. Acknowledgements. 2. Lexical Conventions. Tokens. Comments. Identifiers. Keywords. Literals. Implementation Dependencies. 3. Basic Concepts. Declarations and Definitions. Scopes. Program and Linkage. Start and Termination. Storage Classes. Types. Lvalues. Name Spaces. Numerical Limits. 4. Standard Conversions. Integral Promotions. Integral Conversions. Float and Double. Floating and Integral. Arithmetic Conversions. Pointer Conversions. Reference Conversions. Pointers to Members. Arithmetic Conversions. 5. Expressions. Primary Expressions. Postfix Expressions. Unary Operators. Explicit Type Conversion. Pointer-to-Member Operators. Multiplicative Operators. Additive Operators. Shift Operators. Relational Operators. Equality Operators. Bitwise AND Operator. Bitwise Exclusive OR Operator. Bitwise Inclusive OR Operator. Logical AND Operator. Logical OR Operator. Conditional Operator. Assignment Operators. Comma Operator. Constant Expressions. 6. Statements. Labeled Statement. Expression Statement. Compound Statement, or Block. Selection Statements. Iteration Statements. Jump Statements. Declaration Statement. Ambiguity Resolution. 7. Declarations. Specifiers. Enumeration Declarations. Asm Declarations. Linkage Specifications. Linkage Specifications. Type-safe Linkage. Limitations. 8. Declarators. Type Names Meaning of Declarators. Function Definitions. Initializers. Pointers to Members. 9. Classes. Class Names. Class Members. Member Functions. Static Members. Unions. Bit-Fields. Nested Class Declarations. Local Class Declarations. Local Type Names. Interfaces. 10. Derived Classes. Multiple Base Classes. Virtual Functions. Abstract Classes. Summary of Scope Rules. Single Inheritance. Multiple Inheritance. Multiple Inheritance and Casting. Multiple Inheritance and Implicit Conversion. Virtual Base Classes. Virtual Base Classes and Casting. Single Inheritance and Virtual Functions. Multiple Inheritance and Virtual Functions. Instantiation of Virtual Functions. Virtual Base Classes with Virtual Functions. Renaming. 11. Member Access Control. Access Specifiers. Access Specifiers for Base Classes. Access Declarations. Friends. Protected Member Access. Access to Virtual Functions. Multiple Access. General Ideas. Per Class Protection. Access Control. 12. Special Member Functions. Constructors. Temporary Objects. Conversions. Destructors. Free Store. Initialization. Constructors and Destructors. Copying Class Objects. Temporary Elimination. Access Control and Special Functions. Summary of Member, Friend, and Special Functions. 13. Overloading. Declaration Matching. Argument Matching. Address of Overload Function. Overloaded Operators. 14. Templates. Templates. Class Templates. Type Equivalence. Function Templates. Declarations and Definitions. Member Function Templates. Friends. Static Members and Variables. 15. Exception Handling. Exception Handling. Throwing an Exception. Constructors and Destructors. Handling and Exception. Exception Specifications. Special Functions. Exceptions and Access. 16. Preprocessing. Phases of Preprocessing. Trigraph Sequences. Macro Definition and Expansion. File Inclusion. Conditional Compilation. Line Control. Error Directive. Pragmas. Null Directive. Predefined Names. C++ Constructs versus #define. Compatibility. Classic C Preprocessing. 17. Grammar Summary. Keywords. Expressions. Declarations. Declarators. Class. Statements. Preprocessor. Templates. Exception. 18. Compatibility. Extensions. C++ and ANSI C. Anachronisms. ANSI/ISO Resolutions. Index. 0201514591T04062001

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The Annotated C++ Reference Manual

The C++ programming language

From the Publisher:
This is a complete rewrite of the most widely read and most trusted book on C++. Based on the ANSI/ISO C++ final draft, this book covers the C++ language, its standard library, and key design techniques as an integrated whole. The C++ Programming Language provides comprehensive coverage of C++ language features and standard library components. With this third edition, Stroustrup makes C++ even more accessible to those new to the language while adding information and techniques that even expert C++ programmers will find invaluable.

Bjarne Stroustrup

Papers

The C++ Programming Language

The C++ programming language (2nd ed.)

The Annotated C++ Reference Manual

The C++ programming language

The C++ Programming Language, 4th Edition