ABSTRACT
The effective control of tuberculosis (TB) has been thwarted by the need for prolonged, complex and potentially toxic drug regimens, by reliance on an inefficient vaccine and by the absence of biomarkers of clinical status. The promise of the genomics era for TB control is substantial, but has been hindered by the lack of a central repository that collects and integrates genomic and experimental data about this organism in a way that can be readily accessed and analyzed. The Tuberculosis Database (TBDB) is an integrated database providing access to TB genomic data and resources, relevant to the discovery and development of TB drugs, vaccines and biomarkers. The current release of TBDB houses genome sequence data and annotations for 28 different Mycobacterium tuberculosis strains and related bacteria. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives. TBDB currently hosts data for nearly 1500 public tuberculosis microarrays and 260 arrays for Streptomyces. In addition, TBDB provides access to a suite of comparative genomics and microarray analysis software. By bringing together M. tuberculosis genome annotation and gene-expression data with a suite of analysis tools, TBDB (http://www.tbdb.org/) provides a unique discovery platform for TB research.
Subject(s)
Databases, Genetic , Mycobacterium tuberculosis/genetics , Tuberculosis/microbiology , Biomedical Research , Computer Graphics , Gene Expression , Genome, Bacterial , Genomics , Humans , Mycobacterium tuberculosis/metabolism , Systems Integration , Tuberculosis/diagnosis , Tuberculosis/drug therapyABSTRACT
Recent advances in optical-sectioning microscopy, along with novel fluorescent proteins and probes, give us the tools to image molecules and their interactions in space and time. Investigators using these tools routinely collect multichannel three-dimensional (3D) images and time series, but analyzing such complex datasets requires sophisticated visualization techniques. We here provide an overview of the principles and practices of 3D visualization of multichannel microscopic data. We also describe ImageSurfer, a new software package for volume visualization and data analysis. ImageSurfer is freely available (www.imagesurfer.org) and provides powerful interactive tools to explore and analyze complex multichannel 3D datasets. Although ImageSurfer is designed with fluorescent microscopy in mind, it is also effective for other types of data, including 3D datasets acquired by functional magnetic resonance imaging and EM tomography.
