PD5: A General Purpose Library for Primer Design Software

Background

Complex PCR applications for large genome-scale projects require fast, reliable and often highly sophisticated primer design software applications. Presently, such applications use pipelining methods to utilise many third party applications and this involves file parsing, interfacing and data conversion, which is slow and prone to error. A fully integrated suite of software tools for primer design would considerably improve the development time, the processing speed, and the reliability of bespoke primer design software applications.

Results

The PD5 software library is an open-source collection of classes and utilities, providing a complete collection of software building blocks for primer design and analysis. It is written in object-oriented C⁺⁺ with an emphasis on classes suitable for efficient and rapid development of bespoke primer design programs. The modular design of the software library simplifies the development of specific applications and also integration with existing third party software where necessary. We demonstrate several applications created using this software library that have already proved to be effective, but we view the project as a dynamic environment for building primer design software and it is open for future development by the bioinformatics community. Therefore, the PD5 software library is published under the terms of the GNU General Public License, which guarantee access to source-code and allow redistribution and modification.

Conclusions

The PD5 software library is downloadable from Google Code and the accompanying Wiki includes instructions and examples: http://code.google.com/p/primer-design     

Problem Concepts in Evolution Part I: Purpose and Design

In 1999, Scott suggested that evolution has existential repercussions for some students because they confuse methodological naturalism with philosophical naturalism: conflating the incapacity of scientific explanations to appeal to the supernatural with the idea that God must not exist. Unfortunately, part of the reason for the confusion involves terms that are used in a technical sense by evolutionary biologists but that also convey existential meanings to the general public. Such terms therefore should be used carefully by teachers, and their scientific meanings distinguished from their common meanings. We revisit these problem concepts, particularly in light of recent papers in cognitive psychology as they relate to understanding evolution, in a two-part series of articles. Here, in part I, we address design and purpose.     

Purpose and Scope

Neurochemical Research -     

THE SCOPE AND RESPONSIBILITY OF MEDICINE-A Forum with a Purpose

To engender discussion of what the scope and responsibility of medicine ought to be in today's society, California Medicine printed in its June issue six essays by authors known to have keen if various interest in the subject.In presenting the essays the editors expressed hope that they would be the beginning of a forum from which a definition of our profession's responsibilities may be distilled. Readers were invited to take part in a continuation of the forum in succeeding issues. Following are three contributions selected from those received to date. Others will be published in the months ahead.If you have thoughts on the subject, just address them to the editors of California Medicine, 693 Sutter Street, San Francisco, California 94102. Keep your essays short, please.     

THE SCOPE AND RESPONSIBILITY OF MEDICINE-A Forum with a Purpose

To engender discussion of what the scope and responsibility of medicine ought to be in today's society, California Medicine printed in its June issue six essays by authors known to have keen if various interest in the subject.In presenting the essays the editors expressed hope that they would be the beginning of a forum from which a definition of our profession's responsibilities may be distilled. Readers were invited to take part in a continuation of the forum in succeeding issues. Following are three contributions selected from those received to date. Others will be published in the months ahead.If you have thoughts on the subject, just address them to the editors of California Medicine, 693 Sutter Street, San Francisco, California 94102. Keep your essays short, please.