Robust execution of service workflows using redundancy and advance reservations

In this paper, we develop a novel algorithm that allows service consumers to execute business processes (or workflows) of interdependent services in a dependable manner within tight time-constraints. In particular, we consider large inter-organisational service-oriented systems, where services are offered by external organisations that demand financial remuneration and where their use has to be negotiated in advance using explicit service-level agreements (as is common in Grids and cloud computing). Here, different providers often offer the same type of service at varying levels of quality and price. Furthermore, some providers may be less trustworthy than others, possibly failing to meet their agreements. To control this unreliability and ensure end-to-end dependability while maximising the profit obtained from completing a business process, our algorithm automatically selects the most suitable providers. Moreover, unlike existing work, it reasons about the dependability properties of a workflow, and it controls these by using service redundancy for critical tasks and by planning for contingencies. Finally, our algorithm reserves services for only parts of its workflow at any time, in order to retain flexibility when failures occur. We show empirically that our algorithm consistently outperforms existing approaches, achieving up to a 35-fold increase in profit and successfully completing most workflows, even when the majority of providers fail

ADEPT2 - Next Generation Process Management Technology

If current process management systems shall be applied to a broad spectrum of applications, they will have to be significantly improved with respect to their technological capabilities. In particular, in dynamic environments it must be possible to quickly implement and deploy new processes, to enable ad-hoc modifications of single process instances at runtime (e.g., to add, delete or shift process steps), and to support process schema evolution with instance migration, i.e., to propagate process schema changes to already running instances. These requirements must be met without affecting process consistency and by preserving the robustness of the process management system. In this paper we describe how these challenges have been addressed and solved in the ADEPT2 Process Management System. Our overall vision is to provide a next generation process management technology which can be used in a variety of application domains

Characterization of Epithelial Growth Factor Transcripts Identified in Crotalus Atrox Venom

Epithelial Growth Factor (EGF) is the primary source in regeneration and stimulation of essential fibroblasts cells commonly found in epithelium. Studies have shown that snake venom components are becoming a growing factor in treating illnesses such as cancer, muscular dystrophy, chronic pain, blood pressure, blood clotting, etc. EGF in human cells contains a promising quaternary structure that can bind to snake venom metalloproteinases, proposing a means of activating biochemical responses through protein-protein interactions to regulate unwanted cellular functions. This supports promising research in achieving a greater understanding of regulation along cellular pathways through ligands, increasing the likelihood of targeting unwanted cellular growths (cancer), treating epithelial injuries, enhance pharmaceutical advancements, etc. The purpose of this study was to identify specific transcripts originating from snake venom. We cloned and retrieved the transcripts of EGF from the venom of Western Diamondback Rattlesnake (C. atrox). C. atrox carries a toxin that is known to carry Epidermal Growth Factor (EGF), a protein found in its venom. Messenger RNA from C. atrox crude venom was reverse-transcribed into cDNA and was further subjected to RT-PCR. The amplicons were purified from agarose gel and ligated into a pJET vector to obtain recombinant DNA found in bacterial colonies. At least three unique snake venom EGF transcripts were obtained after screening 23 bacterial clones using gel electrophoresis by molecular size and enzyme digestion patterns. More research would be essential to discovering protein-protein interactions that benefit treatments of illnesses and injuries along epithelium

Prediction of protein interactions on HIV-1-human PPI data using a novel closure-based integrated approach

Discovering Protein-Protein Interactions (PPI) is a new interesting challenge in computational biology. Identifying interactions among proteins was shown to be useful for finding new drugs and preventing several kinds of diseases. The identification of interactions between HIV-1 proteins and Human proteins is a particular PPI problem whose study might lead to the discovery of drugs and important interactions responsible for AIDS. We present the FIST algorithm for extracting hierarchical bi-clusters and minimal covers of association rules in one process. This algorithm is based on the frequent closed itemsets framework to efficiently generate a hierarchy of conceptual clusters and non-redundant sets of association rules with supporting object lists. Experiments conducted on a HIV-1 and Human proteins interaction dataset show that the approach efficiently identifies interactions previously predicted in the literature and can be used to predict new interactions based on previous biological knowledge

Prediction of protein interactions on HIV-1-human PPI data using a novel closure-based integrated approach

Discovering Protein-Protein Interactions (PPI) is a new interesting challenge in computational biology. Identifying interactions among proteins was shown to be useful for finding new drugs and preventing several kinds of diseases. The identification of interactions between HIV-1 proteins and Human proteins is a particular PPI problem whose study might lead to the discovery of drugs and important interactions responsible for AIDS. We present the FIST algorithm for extracting hierarchical bi-clusters and minimal covers of association rules in one process. This algorithm is based on the frequent closed itemsets framework to efficiently generate a hierarchy of conceptual clusters and non-redundant sets of association rules with supporting object lists. Experiments conducted on a HIV-1 and Human proteins interaction dataset show that the approach efficiently identifies interactions previously predicted in the literature and can be used to predict new interactions based on previous biological knowledge

PIE: an online prediction system for protein–protein interactions from text

Protein–protein interaction (PPI) extraction has been an important research topic in bio-text mining area, since the PPI information is critical for understanding biological processes. However, there are very few open systems available on the Web and most of the systems focus on keyword searching based on predefined PPIs. PIE (Protein Interaction information Extraction system) is a configurable Web service to extract PPIs from literature, including user-provided papers as well as PubMed articles. After providing abstracts or papers, the prediction results are displayed in an easily readable form with essential, yet compact features. The PIE interface supports more features such as PDF file extraction, PubMed search tool and network communication, which are useful for biologists and bio-system developers. The PIE system utilizes natural language processing techniques and machine learning methodologies to predict PPI sentences, which results in high precision performance for Web users. PIE is freely available at http://bi.snu.ac.kr/pie/

Towards Truly Flexible and Adaptive Process-Aware Information Systems

If current process management systems shall be applied to a broad spectrum of applications, they will have to be significantly improved with respect to their technological capabilities. Particularly, in dynamic environments it must be possible to quickly implement and deploy new processes, to enable ad-hoc modifications of running process instances on-the-fly (e.g., to dynamically add, delete or move process steps), and to support process schema evolution with instance migration (i.e., to propagate process schema changes to already running instances if desired). These requirements must be met without affecting process consistency and by preserving the robustness of the process management system. In this paper we describe how these challenges have been addressed and solved in the ADEPT2 Process Management System. Our overall vision is to provide a next generation process management technology which can be used in a variety of application domains

Smart Environments for Collaborative Design, Implementation, and Interpretation of Scientific Experiments

Ambient intelligence promises to enable humans to smoothly interact with their environment, mediated by computer technology. In the literature on ambient intelligence, empirical scientists are not often mentioned. Yet they form an interesting target group for this technology. In this position paper, we describe a project aimed at realising an ambient intelligence environment for face-to-face meetings of researchers with different academic backgrounds involved in molecular biology “omics” experiments. In particular, microarray experiments are a focus of attention because these experiments require multidisciplinary collaboration for their design, analysis, and interpretation. Such an environment is characterised by a high degree of complexity that has to be mitigated by ambient intelligence technology. By experimenting in a real-life setting, we will learn more about life scientists as a user group

Flexible provisioning of Web service workflows

Web services promise to revolutionise the way computational resources and business processes are offered and invoked in open, distributed systems, such as the Internet. These services are described using machine-readable meta-data, which enables consumer applications to automatically discover and provision suitable services for their workflows at run-time. However, current approaches have typically assumed service descriptions are accurate and deterministic, and so have neglected to account for the fact that services in these open systems are inherently unreliable and uncertain. Specifically, network failures, software bugs and competition for services may regularly lead to execution delays or even service failures. To address this problem, the process of provisioning services needs to be performed in a more flexible manner than has so far been considered, in order to proactively deal with failures and to recover workflows that have partially failed. To this end, we devise and present a heuristic strategy that varies the provisioning of services according to their predicted performance. Using simulation, we then benchmark our algorithm and show that it leads to a 700% improvement in average utility, while successfully completing up to eight times as many workflows as approaches that do not consider service failures

Mutual Interactions between Aquaporins and Membrane Components

During the last years, a number of studies have been focused on the structural evaluation of protein complexes in order to get mechanistic insights into how proteins communicate at the molecular level within the cell. Specific sites of protein-aquaporin interaction have been evaluated and new regulations of aquaporins described based on these associations. Aquaporin isoforms heterotetramerizations are considered as novel regulatory mechanisms for plasma membrane (PIPs) and tonoplast (TIPs) proteins, influencing their intrinsic permeability and trafficking dynamics in the adaptive response to changing environmental conditions. However, protein-protein interaction is an extensive theme that is difficult to tackle and new methodologies of physical interactions are being used in approaches to its study. Bimolecular fluorescence complementation (BiFC) and the identification of cross-linked peptides based on tandem mass spectra, which resulted complementary to other methodologies such as heterologous expression, co-precipitation assays or confocal fluorescence microscopy, have been discussed in this review. The chemical composition or physical characteristics of the lipid bilayer also influences many aspects of membrane aquaporins, including their functionality. The molecular driving forces stabilizing the observed lipid positions around aquaporins could define their activity, which could alter the conformational properties. Therefore, an integrative approach to the relevance of the membrane-aquaporin interaction to different processes related to plant cell physiology is shown. Finally, the interactions between aquaporins and copolymer matrixes or biological compounds offer an opportunity for the functional incorporation of aquaporins into new biotechnological advances