数据库

Mathematical models serve to explain complex biological phenomena and provide predictions that can be tested experimentally. They can provide plausible scenarios of a complex biological behavior when intuition is not sufficient anymore. The process from a biological hypothes ...

In the last 30 years, many of the mechanisms behind signal transduction, the process by which the cell takes extracellular signals as an input and converts them to a specific cellular phenotype, have been experimentally determined. With these discoveries, however, has come the realization t ...

The study of the interactome—the totality of the protein–protein interactions taking place in a cell—has experienced an enormous growth in the last few years. Biological networks representation and analysis has become an everyday tool for many biologists and bioinformatics, as these ...

Cytoscape is an open-source software for visualizing, analyzing, and modeling biological networks. This chapter explains how to use Cytoscape to analyze the functional effect of sequence variations in the context of biological networks such as protein–protein interaction netw ...

This chapter is split into two main sections; first, I will present an introduction to gene networks. Second, I will discuss various approaches to gene network modeling which will include some examples for using different data sources. Computational modeling has been used for many different ...

Workflows are useful to perform data analysis and integration in systems biology. Workflow management systems can help users create workflows without any previous knowledge in programming and web services. However the computational skills required to build such workflows are usu ...

Here we provide a broad overview of the definition of the term “systems biology” as well as pinpoint specific events in biological research and beyond that are consistently cited to have contributed and led to the current science of in silico systems biology. Since there have been many reviews and hi ...

A relatively large number of signaling databases available today have strongly contributed to our understanding of signaling pathway properties. However, pathway comparisons both within and across databases are currently severely hampered by the large variety of data sources a ...

The first steps of building a new model can be very time-consuming, involving consulting many research papers and then assembling a plausible network of reactions. In this chapter, tools for speeding up this process will be discussed. Reactome is a database containing extensive coverage of p ...

We consider the Bayesian analysis of mechanistic models describing the dynamic behavior of ligand-gated ion channels. The opening of the transmembrane pore in an ion channel is brought about by conformational changes in the protein, which results in a flow of ions through the pore. Remarkabl ...

Every cell in an organism essentially contains the same genome. However, the subset of genes expressed in one cell type is different from another and is determined by the functional role of that cell. It is also known that the protein coding regions in an eukaryotic genome only account for 10-20% of the DNA. R ...

Gel documentation is a broad term, ranging from a $300 film camera to a $15,000 complete gel-analysis station. We will focus here on the essential parts needed to assemble an entry level low-light gel image acquisition, computer archive, and analysis system. This consists of an illuminator, a came ...

The European Bioinformatics Institute (EBI) is an EMBL Outstation located at the Wellcome Trust Genome Campus in Hinxton (UK). The EBI maintains and distributes the EMBL Nucleotide Sequence database, Europe’s primary nucleotide sequence data resource, the SwissProt Protein Seque ...

The National Center for Biotechnology Information (NCBI) was established in November 1988, at the National Library of Medicine (NLM) in the United States. The NLM was chosen because it had experience in creating and maintaining biomedical databases and as part of the National Institutes of H ...

Over the course of the last decade, genetics has become one of the most rapidly expanding sciences. The overwhelming and evergrowing pool of knowledge makes it virtually impossible to follow new and recent discoveries using conventional methods such as reviewing journals or scientific t ...

You will find a large collection of free applications for molecular biology and chemistry through Internet servers and from other sources. Most of these are written by biologists, chemists, and software developers, sometimes as part of a university- or government-funded project, somet ...

A brief look at the history of humanity shows that since the earliest days people needed to count and compute, either for measuring the months and the seasons or for commerce and construction. The means used for performing calculations were whatever was available, and thus progressed gradually ...

This article describes the network computer (NC), an alternative to the standal one PC. By shifting data storage and most processing to the server, any user can do any task from any NC. NCs provide a reliable, consistent interface for all users, and make it easy to provide group access to resources such as lab ...

The worldwide embrace of the Internet has led to the development of an electronic marketplace for purchasing research laboratory supplies. The exponentia l growth of the World Wide Web has given suppliers cost-effective tools for continually providing up-to-date information on prod ...

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.