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Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory(More)
We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see(More)
The investigation and modeling of gene regulatory networks requires computational tools specific to the task. We present several locally developed software tools that have been used in support of our ongoing research into the embryogenesis of the sea urchin. These tools are especially well suited to iterative refinement of models through experimental and(More)
We demonstrate that interspecific sequence conservation can provide a systematic guide to the identification of functional cis-regulatory elements within a large expanse of genomic DNA. The test was carried out on the otx gene of Strongylocentrotus purpuratus. This gene plays a major role in the gene regulatory network that underlies endomesoderm(More)
In this paper we present the design and implementation of a Class Ordering System that is driven by a pa-rameterized cost model. The parameters to the model assign weights to the edge types that describe the relationships between the classes in the graphical representation of the program. The nodes in the graph are classes and the edges express(More)
The widespread use of personal digital assistants and smartphones gives securing these devices a high priority. Yet little attention has been placed on protecting handheld devices against viruses. Currently available antivirus software for handhelds is few in number. At this stage, the opportunity exists for the evaluation and improvement of current(More)
Many methodologies have been proposed in the last decade for integration and exchange of medical data. However, little progress has occurred due to the following reasons. First, patients are reluctant to give full access to their historical medical data. Second, institutions are reluctant to open their systems to mediators or any type of external access,(More)
Many systems are constructed without the use of modeling and visualization artifacts, due to constraints imposed by deadlines or a shortage of manpower. Nevertheless, such systems might profit from the visualization provided by diagrams to facilitate maintenance of the constructed system. In this paper , we present a tool, Reveal, to reverse engineer a(More)
As businesses strive to keep pace with the rapid evolution of web technologies, their efforts to maintain automated regression testing strategies are being hindered. Technological migration of a web application can lead to test scripts becoming incapable of validating the migrated application due to differences in the testing platform. Regression tests that(More)