ProKinO: An Ontology for Integrative Analysis of Protein Kinases in Cancer

Protein kinases are a large and diverse family of enzymes that are genomically altered in many human cancers. Targeted cancer genome sequencing efforts have unveiled the mutational profiles of protein kinase genes from many different cancer types. While mutational data on protein kinases is currently catalogued in various databases, integration of mutation data with other forms of data on protein kinases such as sequence, structure, function and pathway is necessary to identify and characterize key cancer causing mutations. Integrative analysis of protein kinase data, however, is a challenge because of the disparate nature of protein kinase data sources and data formats., where the mutations are spread over 82 distinct kinases. We also provide examples of how ontology-based data analysis can be used to generate testable hypotheses regarding cancer mutations.

Snake-in-the-box codes for dimension 7

In the n-dimensional hypercube, an n-snake is a simple path with no chords, while an n-coil is a simple cycle without chords. There has been much interest in determining the length of a maximum n-snake and a maximum n-coil. Only upper and lower bounds for these maximum lengths are known for arbitrary n. Computationally, the problem of nding maximum n-snakes and n-coils su ers from combinatorial explosion, in that the size of the solution space which mustbesearched grows very rapidly as n increases. Previously, the maximum lengths of n-snakes and n-coils have been established only for n 7 and n 6, respectively. In this paper, we report on a coil searching computer program which established that 48 is the maximum length of a coil in the hypercube of dimension 7.

A CP-nets-based design and verification framework for web services composition

Web services aim to support efficient integration of applications over Web. Most Web services are stateful, such as services for business processes, and they converse with each other via properly ordered interactions, instead of individual unrelated invocations. In order to address efficient integration of conversational Web services, we create a unified specification model for both conversation protocol and composition; we propose methods to integrate a partner service with complex conversation protocol into a composition of Web services; assure the correctness of composition by formal verification. The mapping between our model and BPEL4WS is also discussed. 1

JCPNet Tool and Automated Analysis of Distributed Systems ABSTRACT

Model based approach is crucial to the analysis of system design. Colored Petri Nets (CPNet) have been used as software model with good success. It can be used to complement UML diagrams by providing formal modeling and analysis of dynamic behaviors of distributed systems. In order to enable CPNet model to be utilized more flexibly and widely, a new software tool JCPNet has been developed. This paper discusses the background, motivation and development of JCPNet, and its applications to specification and analysis of distributed systems