1. Introduction Designing PCR and sequencing primers are essential activities for molecular biologists around the world. This chapter assumes acquaintance with the principles and practice of PCR, as outlined in, for example, refs. 1–4. Primer3 is a computer program that suggests PCR primers for a variety of applications, for example to create STSs (sequence tagged sites) for radiation hybrid mapping (5), or to amplify sequences for single nucleotide polymor-phism discovery (6). Primer3 can also select single primers for sequencing reactions and can design oligonucleotide hybridization probes. In selecting oligos for primers or hybridization probes, Primer3 can consider many factors. These include oligo melting temperature, length, GC content , 3′ stability, estimated secondary structure, the likelihood of annealing to or amplifying undesirable sequences (for example interspersed repeats), the likelihood of primer–dimer formation between two copies of the same primer, and the accuracy of the source sequence. In the design of primer pairs Primer3 can consider product size and melting temperature, the likelihood of primer– dimer formation between the two primers in the pair, the difference between primer melting temperatures, and primer location relative to particular regions of interest or to be avoided.

/pdf/primer3-on-the-www-for-general-users-and-for-biologist-pgzaqxkztz.pdf

Primer3 on the WWW for general users and for biologist programmers.

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.

/pdf/scipy-1-0-fundamental-algorithms-for-scientific-computing-in-111lr790ol.pdf

SciPy 1.0--Fundamental Algorithms for Scientific Computing in Python

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.

/pdf/bioconductor-open-software-development-for-computational-3fbxl4vnkq.pdf

Bioconductor: open software development for computational biology and bioinformatics

Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

/pdf/scipy-1-0-fundamental-algorithms-for-scientific-computing-in-45othhotbu.pdf

SciPy 1.0: fundamental algorithms for scientific computing in Python.

From the Publisher:
Written by the inventors of the technology, The Java(tm) Language Specification, Second Edition is the definitive technical reference for the Java(tm) programming language If you want to know the precise meaning of the language's constructs, this is the source for you 
The book provides complete, accurate, and detailed coverage of the syntax and semantics of the Java programming language It describes all aspects of the language, including the semantics of all types, statements, and expressions, as well as threads and binary compatibility

/pdf/the-java-language-specification-1s92cud0yi.pdf

The Java Language Specification

The defacto standard - a must-have for all LISP programmers. In this greatly expanded edition of the defacto standard, you'll learn about the nearly 200 changes already made since original publication - and find out about gray areas likely to be revised later. Written by the Vice- Chairman of X3J13 (the ANSI committee responsible for the standardization of Common Lisp) and co-developer of the language itself, the new edition contains the entire text of the first edition plus six completely new chapters. They cover: - CLOS, the Common Lisp Object System, with new features to support function overloading and object-oriented programming, plus complete technical specifications * Loops, a powerful control structure for multiple variables * Conditions, a generalization of the error signaling mechanism * Series and generators * Plus other subjects not part of the ANSI standards but of interest to professional programmers. Throughout, you'll find fresh examples, additional clarifications, warnings, and tips - all presented with the author's customary vigor and wit.

Common Lisp the Language

Parallel computers with tens of thousands of processors are typically programmed in a data parallel style, as opposed to the control parallel style used in multiprocessing. The success of data parallel algorithms—even on problems that at first glance seem inherently serial—suggests that this style of programming has much wider applicability than was previously thought.

Data parallel algorithms

Written by the inventors of the technology, The Java™ Language Specification, Third Edition, is the definitive technical reference for the Java™ programming language. If you want to know the precise meaning of the language's constructs, this is the source for you.The book provides complete, accurate, and detailed coverage of the Java programming language. It provides full coverage of all new features added since the previous edition, including generics, annotations, asserts, autoboxing, enums, for-each loops, variable arity methods, and static import clauses.

Java(TM) Language Specification, The (3rd Edition) (Java (Addison-Wesley))

From the Publisher:
High Performance Fortran (HPF) is a set of extensions to Fortran expressing parallel execution at a relatively high level. For the thousands of scientists, engineers, and others who wish to take advantage of the power of both vector and parallel supercomputers, five of the principal authors of HPF have teamed up here to write a tutorial for the language.
There is an increasing need for a common parallel Fortran that can serve as a programming interface with the new parallel machines that are appearing on the market. While HPF does not solve all the problems of parallel programming, it does provide a portable, high-level expression for data- parallel algorithms that brings the convenience of sequential Fortran a step closer to today's complex parallel machines.

Guy L. Steele

Papers

The Java Language Specification

Common Lisp the Language

Data parallel algorithms

Java(TM) Language Specification, The (3rd Edition) (Java (Addison-Wesley))

The High Performance Fortran Handbook