Towards an aspect weaving BPEL engine

This position paper proposes the use of dynamic aspects and the visitor design pattern to obtain a highly configurable and extensible BPEL engine. Using these two techniques, the core of this infrastructural software can be customised to meet new requirements and add features such as debugging, execution monitoring, or changing to another Web Service selection policy. Additionally, it can easily be extended to cope with customer-specific BPEL extensions. We propose the use of dynamic aspects not only on the engine itself but also on the workflow in order to tackle the problems of Web Service hot deployment and hot fixes to long running processes. In this way, composing aWeb Service "on-the-fly" means weaving its choreography interface into the workflow

Certifying Correctness for Combinatorial Algorithms : by Using Pseudo-Boolean Reasoning

Over the last decades, dramatic improvements in combinatorialoptimisation algorithms have significantly impacted artificialintelligence, operations research, and other areas. These advances,however, are achieved through highly sophisticated algorithms that aredifficult to verify and prone to implementation errors that can causeincorrect results. A promising approach to detect wrong results is touse certifying algorithms that produce not only the desired output butalso a certificate or proof of correctness of the output. An externaltool can then verify the proof to determine that the given answer isvalid. In the Boolean satisfiability (SAT) community, this concept iswell established in the form of proof logging, which has become thestandard solution for generating trustworthy outputs. The problem isthat there are still some SAT solving techniques for which prooflogging is challenging and not yet used in practice. Additionally,there are many formalisms more expressive than SAT, such as constraintprogramming, various graph problems and maximum satisfiability(MaxSAT), for which efficient proof logging is out of reach forstate-of-the-art techniques.This work develops a new proof system building on the cutting planesproof system and operating on pseudo-Boolean constraints (0-1 linearinequalities). We explain how such machine-verifiable proofs can becreated for various problems, including parity reasoning, symmetry anddominance breaking, constraint programming, subgraph isomorphism andmaximum common subgraph problems, and pseudo-Boolean problems. Weimplement and evaluate the resulting algorithms and a verifier for theproof format, demonstrating that the approach is practical for a widerange of problems. We are optimistic that the proposed proof system issuitable for designing certifying variants of algorithms inpseudo-Boolean optimisation, MaxSAT and beyond

Development of a read mapping analysis software and computational pan genome analysis of 20 Pseudomonas aeruginosa strains

Hilker R. Development of a read mapping analysis software and computational pan genome analysis of 20 Pseudomonas aeruginosa strains. Bielefeld: Bielefeld University; 2015.In times of multi-resistant pathogenic bacteria, their detailed study is of utmost importance. Their comparative analysis can even aid the emerging field of personalized medicine by enabling optimized treatment depending on the presence of virulence factors and antibiotic resistances in the infection concerned. The weaknesses and functionality of these pathogenic bacteria can be investigated using modern computer science and novel sequencing technologies. One of these methods is the bioinformatics evaluation of high-throughput sequencing data. A pathogenic bacterium posing severe health care issues is the ubiquitous Pseudomonas aeruginosa. It is involved in a wide range of infections mainly affecting the pulmonary or urinary tract, open wounds and burns. The prevalence of chronic obstructive pulmonary disease cases with P. aeruginosa in Germany alone is ~600,000 per year. Within the framework of this dissertation, computational comparative genomics experiments were conducted with a panel of 20 of the most abundant Pseudomonas aeruginosa strains. 15 of these strains were isolated from clinical cases, while the remaining 5 were strains without a known infection history isolated from the environment. This division was chosen to enable direct comparison of the pathogenic potential of clinical and environmental strains and identification of their possible characteristic differences. When designing the bioinformatics experiments and searching for an efficient visualization and automatic analysis platform for read alignment (mapping) data, it became evident that no adequate solution was available that included all required functionalities. On these grounds, the decision was made to define two main subjects for this dissertation. Besides the P. aeruginosa pan genome analysis, a novel read mapping visualization and analysis software was developed and published in the journal Bioinformatics. This software - ReadXplorer - is partly based upon a prototype, which was developed during a preceding master's thesis at the Center for Biotechnology of the Bielefeld University under the name VAMP. The software was developed into a comprehensive user-friendly platform augmented with several newly developed and implemented automatic bioinformatics read mapping analyses. Two examples of these are the transcription start site detection and the single nucleotide polymorphism detection. Moreover, new intuitive visualizations were added to the existent ones and existing visualizations were greatly enhanced. ReadXplorer is designed to support not only DNA-seq data as accrued in the P. aeruginosa experiments, but also any kind of standard read mapping data as obtained from RNA-seq or ChIP-seq experiments. The data management was designed to comply with the latest performance and efficiency needs emerging from the large next generation sequencing data sets. Finally, ReadXplorer was empowered to deal with eukaryotic read mapping data as well. Amongst other software, ReadXplorer was then used to analyze different comparative genomics aspects of P. aeruginosa and to draw conclusions regarding the development of their pathogenicity. The list of conducted experiments includes phylogeny and gene set determination, analysis of regions of genomic plasticity and identification of single nucleotide polymorphisms. The achieved results were published in the journal Environmental Biology

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Space station automation of common module power management and distribution

The purpose is to automate a breadboard level Power Management and Distribution (PMAD) system which possesses many functional characteristics of a specified Space Station power system. The automation system was built upon 20 kHz ac source with redundancy of the power buses. There are two power distribution control units which furnish power to six load centers which in turn enable load circuits based upon a system generated schedule. The progress in building this specified autonomous system is described. Automation of Space Station Module PMAD was accomplished by segmenting the complete task in the following four independent tasks: (1) develop a detailed approach for PMAD automation; (2) define the software and hardware elements of automation; (3) develop the automation system for the PMAD breadboard; and (4) select an appropriate host processing environment