AD (Attacker Defender) Game

Information Dynamics is a framework for agent-based systems that gives a central position to the role of information, time, and the value of information. We illustrate system design in the Information Dynamics Framework by developing an intelligence game called AD involving attackers, defenders and targets operating in some space of locations. The goal of the attackers is to destroy all targets. Target destruction takes place when the number of attackers in the target's neighborhood exceeds the number of defenders in this neighborhood by a value WINNING_DIFFERENCE. The goal of defenders is to prevent attackers from achieving their goal. (Also UMIACS-TR-2001-45

Context-Free Path Queries on RDF Graphs

Navigational graph queries are an important class of queries that canextract implicit binary relations over the nodes of input graphs. Most of the navigational query languages used in the RDF community, e.g. property paths in W3C SPARQL 1.1 and nested regular expressions in nSPARQL, are based on the regular expressions. It is known that regular expressions have limited expressivity; for instance, some natural queries, like same generation-queries, are not expressible with regular expressions. To overcome this limitation, in this paper, we present cfSPARQL, an extension of SPARQL query language equipped with context-free grammars. The cfSPARQL language is strictly more expressive than property paths and nested expressions. The additional expressivity can be used for modelling graph similarities, graph summarization and ontology alignment. Despite the increasing expressivity, we show that cfSPARQL still enjoys a low computational complexity and can be evaluated efficiently.Comment: 25 page

On the Common Support of Workflow Type and Instance Changes under Correctness Constraints

The capability to rapidly adapt in-progress workflows (WF) is an essential requirement for any workflow system. Adaptations may concern single WF instances or a WF type as a whole. Especially for long-running business processes it is indispensable to propagate WF type changes to in-progress WF instances as well. Very challenging in this context is to correctly adapt a (potentially large) collection of WF instances, which may be in different states and to which various ad-hoc changes may have been previously applied. This paper presents a generic framework for the common support of both WF type and WF instance changes. We establish fundamental correctness principles, position formal theorems, and show how WF instances can be automatically and efficiently migrated to a modified WF schema. The adequate treatment of conflicting WF type and WF instance changes adds to the overall completeness of our approach. By offering more flexibility and adaptability the so promising WF technology will finally deliver

KinView: A visual comparative sequence analysis tool for integrated kinome research

Multiple sequence alignments (MSAs) are a fundamental analysis tool used throughout biology to investigate relationships between protein sequence, structure, function, evolutionary history, and patterns of disease-associated variants. However, their widespread application in systems biology research is currently hindered by the lack of user-friendly tools to simultaneously visualize, manipulate and query the information conceptualized in large sequence alignments, and the challenges in integrating MSAs with multiple orthogonal data such as cancer variants and post-translational modifications, which are often stored in heterogeneous data sources and formats. Here, we present the Multiple Sequence Alignment Ontology (MSAOnt), which represents a profile or consensus alignment in an ontological format. Subsets of the alignment are easily selected through the SPARQL Protocol and RDF Query Language for downstream statistical analysis or visualization. We have also created the Kinome Viewer (KinView), an interactive integrative visualization that places eukaryotic protein kinase cancer variants in the context of natural sequence variation and experimentally determined post-translational modifications, which play central roles in the regulation of cellular signaling pathways. Using KinView, we identified differential phosphorylation patterns between tyrosine and serine/threonine kinases in the activation segment, a major kinase regulatory region that is often mutated in proliferative diseases. We discuss cancer variants that disrupt phosphorylation sites in the activation segment, and show how KinView can be used as a comparative tool to identify differences and similarities in natural variation, cancer variants and post-translational modifications between kinase groups, families and subfamilies. Based on KinView comparisons, we identify and experimentally characterize a regulatory tyrosine (Y177PLK4) in the PLK4 C-terminal activation segment region termed the P+1 loop. To further demonstrate the application of KinView in hypothesis generation and testing, we formulate and validate a hypothesis explaining a novel predicted loss-of-function variant (D523NPKCβ) in the regulatory spine of PKCβ, a recently identified tumor suppressor kinase. KinView provides a novel, extensible interface for performing comparative analyses between subsets of kinases and for integrating multiple types of residue specific annotations in user friendly formats

Four Lessons in Versatility or How Query Languages Adapt to the Web

Exposing not only human-centered information, but machine-processable data on the Web is one of the commonalities of recent Web trends. It has enabled a new kind of applications and businesses where the data is used in ways not foreseen by the data providers. Yet this exposition has fractured the Web into islands of data, each in different Web formats: Some providers choose XML, others RDF, again others JSON or OWL, for their data, even in similar domains. This fracturing stifles innovation as application builders have to cope not only with one Web stack (e.g., XML technology) but with several ones, each of considerable complexity. With Xcerpt we have developed a rule- and pattern based query language that aims to give shield application builders from much of this complexity: In a single query language XML and RDF data can be accessed, processed, combined, and re-published. Though the need for combined access to XML and RDF data has been recognized in previous work (including the W3C’s GRDDL), our approach differs in four main aspects: (1) We provide a single language (rather than two separate or embedded languages), thus minimizing the conceptual overhead of dealing with disparate data formats. (2) Both the declarative (logic-based) and the operational semantics are unified in that they apply for querying XML and RDF in the same way. (3) We show that the resulting query language can be implemented reusing traditional database technology, if desirable. Nevertheless, we also give a unified evaluation approach based on interval labelings of graphs that is at least as fast as existing approaches for tree-shaped XML data, yet provides linear time and space querying also for many RDF graphs. We believe that Web query languages are the right tool for declarative data access in Web applications and that Xcerpt is a significant step towards a more convenient, yet highly efficient data access in a “Web of Data”

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.

Disjoint and Overlapping Process Changes: Challenges, Solutions, Applications

Adaptive process–aware information systems must be able to support ad–hoc changes of single process instances as well as schema modifications at the process type level and their propagation to a collection of related process instances. So far these two kinds of (dynamic) process changes have been mainly considered in an isolated fashion. Especially for long-running processes, however, it must be possible to adequately handle the interplay between type and instance changes as well. One challenge in this context is to determine whether concurrent process type and process instance changes have the same or overlapping effects on the original process schema or not. Information about the degree of overlap is needed, for example, to determine whether and – if yes – how a process type change can be propagated to individually modified process instances as well. This paper provides a formal framework for dealing with overlapping and disjoint process changes and presents adequate migration strategies depending on the particular degree of overlap. In order to obtain a canonical representation of changes an algorithm is introduced which purges change logs from noisy information. Finally, a powerful proof-of-concept prototype exists

Monitoring of Gene Expression in Bacteria during Infections Using an Adaptable Set of Bioluminescent, Fluorescent and Colorigenic Fusion Vectors

A family of versatile promoter-probe plasmids for gene expression analysis was developed based on a modular expression plasmid system (pZ). The vectors contain different replicons with exchangeable antibiotic cassettes to allow compatibility and expression analysis on a low-, midi- and high-copy number basis. Suicide vector variants also permit chromosomal integration of the reporter fusion and stable vector derivatives can be used for in vivo or in situ expression studies under non-selective conditions. Transcriptional and translational fusions to the reporter genes gfpmut3.1, amCyan, dsRed2, luxCDABE, phoA or lacZ can be constructed, and presence of identical multiple cloning sites in the vector system facilitates the interchange of promoters or reporter genes between the plasmids of the series. The promoter of the constitutively expressed gapA gene of Escherichia coli was included to obtain fluorescent and bioluminescent expression constructs. A combination of the plasmids allows simultaneous detection and gene expression analysis in individual bacteria, e.g. in bacterial communities or during mouse infections. To test our vector system, we analyzed and quantified expression of Yersinia pseudotuberculosis virulence genes under laboratory conditions, in association with cells and during the infection process

Semantic Correctness in Adaptive Process Management Systems

Abstract. Adaptivity in Process Management Systems (PMS) is key to their successful applicability in pratice. Approaches have already been de-veloped to ensure the system correctness after arbitrary process changes at the syntactical level. However, still errors may be caused at the se-mantical level. Therefore, the integration of application knowledge will flag a milestone in the development of process management technology. In this paper, we introduce a framework for defining semantic constraints over processes in such a way that they can express real-world applica-tion knowledge. On the other hand, these constraints are still manageable concerning the effort for maintenance and semantic process verification. This can be used, for example, to detect semantic conflicts when ap-plying process changes (e.g., drug incompatibilities). In order to enable the PMS to deal with such semantic conflicts we also introduce a notion of semantic correctness and discuss how to (efficiently) verify semantic correctness in the context of process changes