Coffee Break is a collection of short reports on recent biological discoveries. Each report incorporates interactive tutorials that show how bioinformatics tools are used as a part of the research process.
Following the success of both molecular biology and information technology has risen a new and rapidly evolving discipline: bioinformatics, the process by which data is gathered, organized and computationally analyzed. Bioinformatics is really a theoretical approach to biology that makes use of computer algorithms and existing knowledge to mine nuggets of useful information from the mass of molecular data available. This approach can provide scientific investigators with new leads to solve biomedical problems - there are few, if any, experiments undertaken these days that do not involve some element of online data analysis, ranging from literature and DNA sequence searches to 3D molecular modeling.
The National Center for Biotechnology Information (NCBI) is a part of the National Library of Medicine, at the National Institutes of Health. Its mission is to organize DNA sequence and related data in such a way that it is available for investigators to use and analyze. This has involved the provision of tools such as BLAST, the sequence similarity search tool, and the design of search engines, such as PubMed, for mining the biomedical abstracts database, MEDLINE.
Coffee Break is a resource at NCBI that combines reports on recent biomedical discoveries with use of NCBI tools. The result is an interactive tutorial that tells a biological story. Each report is about 400 words, and is usually based on a discovery reported in one or more articles from the recently published peer-reviewed literature. After a brief introduction that sets the work described into a broader context, the report focuses on how a molecular understanding can provide explanations of observed biology and lead to therapies for diseases.
Each vignette is accompanied by a figure and hypertext links that lead to a series of pages that interactively show how NCBI tools and resources are used in the research process. The reader participates in a predefined search that demonstrates the functionality of a tool or search engine, and expands on the content within the article. Currently, the articles feature PubMed searches of MEDLINE, and searches of GenBank using BLAST. The demonstration sequence searches also include analysis of the BLAST result, usually in the form of a sequence alignment that illustrates the biological focus of the story.
The intended audience for Coffee Break is molecular biologists, clinicians and students. We hope that they will be informative and fun to read, and may serve as teaching aids for college and graduate students.