ComB: SNP calling and mapping analysis for color and nucleotide space platforms.

The determination of single nucleotide polymorphisms (SNPs) has become faster and more cost effective since the advent of short read data from next generation sequencing platforms such as Roche's 454 Sequencer, Illumina's Solexa platform, and Applied Biosystems SOLiD sequencer. The SOLiD sequencing platform, which is capable of producing more than 6 GB of sequence data in a single run, uses a unique encoding scheme where color reads represent transitions between adjacent nucleotides. The determination of SNPs from color reads usually involves the translation of color alignments to likely nucleotide strings to facilitate the use of tools designed for nucleotide reads.

The Bioverse API and web application.

The Bioverse is a framework for creating, warehousing and presenting biological information based on hierarchical levels of organisation. The framework is guided by a deeper philosophy of desiring to represent all relationships between all components of biological systems towards the goal of a wholistic picture of organismal biology. Data from various sources are combined into a single repository and a uniform interface is exposed to access it.

Computational representation of biological systems.

Integration of large and diverse biological data sets is a daunting problem facing systems biology researchers. Exploring the complex issues of data validation, integration, and representation, we present a systematic approach for the management and analysis of large biological data sets based on data warehouses. Our system has been implemented in the Bioverse, a framework combining diverse protein information from a variety of knowledge areas such as molecular interactions, pathway localization, protein structure, and protein function.

BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes.

We have made a number of enhancements to the previously described Bioverse web server and computational biology framework (http://bioverse.compbio.washington.