In this paper we have provided an extensive survey of the databases and other resources related to the current research in bioinformatics and the issues that confront the database researcher in helping the biologists. Initially we give an overview of the concepts and principles that are fundamental in understanding the basis of the data that has been captured in these databases. We briefly trace the evolution of biological advances and point out the importance of capturing data about genes, the fundamental building blocks that encode the characteristics of life and proteins that are the essential ingredients for sustaining life. The study of genes and proteins is becoming extremely important and is being known as genomics and proteomics, respectively. Whereas there are numerous databases related to various subfields of biology, we have maintained a focus on genomic and proteomic databases which are the crucial stepping stones for other fields and are expected to play an important role in the future applications of biology and medicine. A detailed listing of these databases with information about their sizes, formats and current status is presented. Related databases like molecular pathways and interconnection network databases are mentioned, but their full coverage would be beyond the scope of a single paper. We comment on the peculiar nature of the data in biology that presents special problems in organizing and accessing these databases. We also discuss the capabilities needed for database development and information management in the bioinformatics arena with particular attention to ontology development. Two research case studies based on our own research are summarized dealing with the development of a new genome database called Mitomap and the creation of a framework for discovery of relationships among genes from the biomedical literature. The paper concludes with an overview of the applications that will be driven from these databases in medicine and healthcare. A glossary of important terms is provided at the end of the paper.

Contemporary end-servers and network-routers rely on traffic shaping to deal with server overload and network congestion. Although such traffic shaping provides a means to mitigate the effects of server overload and network congestion, the lack of cooperation between end-servers and network-routers results in waste of network resources. To remedy this problem, we design, implement, and evaluate NetDraino, a novel mechanism that extends the existing queue-management schemes at routers to exploit the link congestion information at downstream end-servers. Specifically, NetDraino distributes the servers' traffic-shaping rules to the congested routers. The routers can then selectively discard those packets-as early as possible-that overloaded downstream servers will eventually drop, thus saving network resources for forwarding in-transit packets destined for non-overloaded servers. The functionality necessary for servers to distribute these filtering rules to routers is implemented within the Linux iptables and iproute2 architectures. Both of our simulation and experimentation results show that NetDraino significantly improves the overall network throughput with minimal overhead.

Demands have been growing in safety-critical application fields for producing networked real-time embedded computing (NREC) systems together with acceptable assurances of tight service time bounds (STBs). Here a service time can be defined as the amount of time that the NREC system could take in accepting a request, executing an appropriate service method, and returning a valid result. Enabling systematic composition of large-scale NREC systems with STB certifications has been recognized as a highly desirable goal by the research community for many years. An appealing approach for pursuing such a goal is to establish a hard-real-time (HRT) component model that contains its own STB as an integral part. The TMO (Time-Triggered Message-Triggered Object) programming scheme is one HRT distributed computing (DC) component model established by the first co-author and his collaborators over the past 15 years. The TMO programming scheme has been intended to be an advanced high-level RT DC programming scheme that enables development of NREC systems and validation of tight STBs of such systems with efforts far smaller than those required when any existing lower-level RT DC programming scheme is used. An additional goal is to enable maximum exploitation of concurrency without damaging any major structuring and execution approaches adopted for meeting the first two goals. A number of previously untried program structuring approaches and execution rules were adopted from the early development stage of the TMO scheme. This paper presents new concrete justifications for those approaches and rules, and also discusses new extensions of the TMO scheme intended to enable further exploitation of concurrency in NREC system design and programming.

Nowadays, sharing data among organizations is often required during the business collaboration. Data mining technology has enabled efficient extraction of knowledge from large databases. This, however, increases risks of disclosing the sensitive knowledge when the database is released to other parties. To address this privacy issue, one may sanitize the original database so that the sensitive knowledge is hidden. The challenge is to minimize the side effect on the quality of the sanitized database so that non-sensitive knowledge can still be mined. In this paper, we study such a problem in the context of hiding sensitive frequent itemsets by judiciously modifying the transactions in the database. Unlike previous work, we consider the quality of the sanitized database especially on preserving the non-sensitive frequent itemsets. To preserve the non-sensitive frequent itemsets, we propose a border-based approach to efficiently evaluate the impact of any modification to the database during the hiding process. The quality of database can be well maintained by greedily selecting the modifications with minimal side effect. Experiments results are also reported to show the effectiveness of the proposed approach.

Existing systems that support semistructured views do not maintain semantics during the process of designing the views. Thus, these systems do not guarantee the validity and reversibility of the views. In this paper, we propose an approach to address the issue of valid and reversible semistructured views, We design a set of view operators for designing semistructured views. These operators are select, drop, join and swap. For each operator, we develop a complete set of rules to maintain the semantics of the views. In particular, we maintain the evolution and integrity of relationships once an operator is applied. We also examine the reversible view problem under our operators and develop rules to guarantee that the designed views are reversible. Finally, we examine the changes in the participation constraints of relationship types during the view design process, and develop rules to ensure the correctness of the participation constraints.