CbGRiTS: cerebellar gene regulation in time and space.

The mammalian CNS is one of the most complex biological systems to understand at the molecular level. The temporal information from time series transcriptome analysis can serve as a potent source of associative information between developmental processes and regulatory genes. Here, we introduce a new transcriptome database called, Cerebellar Gene Regulation in Time and Space (CbGRiTS). This dataset is populated with transcriptome data across embryonic and postnatal development from two standard mouse strains, C57BL/6J and DBA/2J, several recombinant inbred lines and cerebellar mutant strains. Users can evaluate expression profiles across cerebellar development in a deep time series with graphical interfaces for data exploration and link-out to anatomical expression databases. We present three analytical approaches that take advantage of specific aspects of the time series for transcriptome analysis. We demonstrate the use of CbGRiTS dataset as a community resource to explore patterns of gene expression and develop hypotheses concerning gene regulatory networks in brain development.

The Zebrafish DVD Exchange Project: a bioinformatics initiative.

Scientists who study zebrafish currently have an acute need to increase the rate of visual data exchange within their international community. Although the Internet has provided a revolutionary transformation of information exchange, the Internet is at present unable to serve as a vehicle for the efficient exchange of massive amounts of visual information. Much like an overburdened public water system, the Internet has inherent limits to the services it can provide. It is possible, however, for zebrafishologists to develop and use virtual intranets (such as the approach we outlined in this chapter) to adapt to the growing informatics need of our expanding research community. We need to assess qualitatively the economics of visual bioinformatics in our research community and evaluate the benefit:investment ratio of our collective information-sharing activities. The development of the World Wide Web started in the early 1990s by particle physicists who needed to rapidly exchange visual information within their collaborations. However, because of current limitations in information bandwidth, the World Wide Web cannot be used to easily exchange gigabytes of visual information. The Zebrafish DVD Exchange Project is aimed at by-passing these limitations. Scientists are curiosity-driven tool makers as well as curiosity-driven tool users. We have the capacity to assimilate new tools, as well as to develop new innovations, to serve our collective research needs. As a proactive research community, we need to create new data transfer methodologies (e.g., the Zebrafish DVD Exchange Project) to stay ahead of our bioinformatics needs.