Artificial ants deposit pheromone to search for regulatory DNA elements

BACKGROUND: Identification of transcription-factor binding motifs (DNA sequences) can be formulated as a combinatorial problem, where an efficient algorithm is indispensable to predict the role of multiple binding motifs. An ant algorithm is a biology-inspired computational technique, through which a combinatorial problem is solved by mimicking the behavior of social insects such as ants. We developed a unique version of ant algorithms to select a set of binding motifs by considering a potential contribution of each of all random DNA sequences of 4- to 7-bp in length. RESULTS: Human chondrogenesis was used as a model system. The results revealed that the ant algorithm was able to identify biologically known binding motifs in chondrogenesis such as AP-1, NFκB, and sox9. Some of the predicted motifs were identical to those previously derived with the genetic algorithm. Unlike the genetic algorithm, however, the ant algorithm was able to evaluate a contribution of individual binding motifs as a spectrum of distributed information and predict core consensus motifs from a wider DNA pool. CONCLUSION: The ant algorithm offers an efficient, reproducible procedure to predict a role of individual transcription-factor binding motifs using a unique definition of artificial ants

A Novel Admission Control Model in Cloud Computing

With the rapid development of Cloud computing technologies and wide adopt of Cloud services and applications, QoS provisioning in Clouds becomes an important research topic. In this paper, we propose an admission control mechanism for Cloud computing. In particular we consider the high volume of simultaneous requests for Cloud services and develop admission control for aggregated traffic flows to address this challenge. By employ network calculus, we determine effective bandwidth for aggregate flow, which is used for making admission control decision. In order to improve network resource allocation while achieving Cloud service QoS, we investigate the relationship between effective bandwidth and equivalent capacity. We have also conducted extensive experiments to evaluate performance of the proposed admission control mechanism

CGPE: A user-friendly gene and pathway explore webserver for public cancer transcriptional data

Digitized for IUPUI ScholarWorks inclusion in 2021.High throughput technology has been widely used by researchers to understand diseases at the molecular level. Database and servers for downloading and analyzing these publicly data is available as well. But there is still lacking tools for facilitating researchers to study the function of genes in pathways views by integrated public omics data