Speeding up systems biology simulations of biochemical pathways using condor

This is the accepted version of the following article: Speeding up Systems Biology Simulations of Biochemical Pathways using Condor". Concurrency and Computation: Practice and Experience Volume 26, Issue 17, pages 2727–2742, 10 December 2014 which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/cpe.3161/abstractSystems biology is a scientific field that uses computational modelling to study biological and biochemical systems. The simulation and analysis of models of these systems typically explore behaviour over a wide range of parameter values; as such, they are usually characterised by the need for nontrivial amounts of computing power. Grid computing provides access to such computational resources. In previous research, we created the grid-enabled biochemical networks simulation environment to attempt to speed up system biology simulations over a grid (the UK National Grid Service and ScotGrid). Following on from this work, we have created the simulation modelling of the epidermal growth factor receptor microtubule-associated protein kinase pathway utility, a standalone simulation tool dedicated to the modelling and analysis of the epidermal growth factor receptor microtubule-associated protein kinase pathway. This builds on experiences from biochemical networks simulation environment by decoupling the simulation modelling elements from the Grid middleware. This new utility enables us to interface with different grid technologies. This paper therefore describes the new SIMAP utility and an empirical investigation of its performance when deployed over a desktop grid based on the high throughput computing middleware Condor. We present our results based on a case study with a model of the mammalian ErbB signalling pathway, a pathway strongly linked to cance

SWARM: Scheduling Large-Scale Jobs over the Loosely-Coupled HPC Clusters

Abstract — Compute-intensive scientific applications are heavily reliant on the available quantity of computing resources. The Grid paradigm provides a large scale computing environment for scientific users. However, conventional Grid job submission tools do not provide a high-level job scheduling environment for these users across multiple institutions. For extremely large number of jobs, a more scalable job scheduling framework that can leverage highly distributed clusters and supercomputers is required. In this paper, we propose a high-level job scheduling Web service framework, Swarm. Swarm is developed for scientific applications that must submit massive number of high-throughput jobs or workflows to highly distributed computing clusters. The Swarm service itself is designed to b

Context-aware multi-factor authentication

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia InformáticaAuthentication systems, as available today, are inappropriate for the requirements of ubiquitous, heterogeneous and large scale distributed systems. Some important limitations are: (i) the use of weak or rigid authentication factors as principal’s identity proofs, (ii) non flexibility to combine different authentication modes for dynamic and context-aware interaction criteria, (iii) not being extensible models to integrate new or emergent pervasive authentication factors and (iv) difficulty to manage the coexistence of multi-factor authentication proofs in a unified single sign-on solution. The objective of this dissertation is the design, implementation and experimental evaluation of a platform supporting multi-factor authentication services, as a contribution to overcome the above limitations. The devised platform will provide a uniform and flexible authentication base for multi-factor authentication requirements and context-aware authentication modes for ubiquitous applications and services. The main contribution is focused on the design and implementation of an extensible authentication framework model, integrating classic as well as new pervasive authentication factors that can be composed for different context-aware dynamic requirements. Flexibility criteria are addressed by the establishment of a unified authentication back-end, supporting authentication modes as defined processes and rules expressed in a SAML based declarative markup language. The authentication base supports an extended single sign-on system that can be dynamically tailored for multi-factor authentication policies, considering large scale distributed applications and according with ubiquitous interaction needs

Extending an open source enterprise service bus for multi-tenancy support focusing on administration and management

As part of cloud computing, the service model Platform-as-a-Service (PaaS) has emerged, where customers can develop and host internet-scale applications on cloud infrastructure. The Enterprise Service Bus (ESB) is one possible building block of a PaaS offering, providing integration capabilities for service-oriented architectures. Bringing the ESB to the cloud requires scalability and multi-tenancy support. When applied, these characteristics lead to economies of scale, reducing the costs per customer. In this diploma thesis we specify, design, and implement a multi-tenant management application for an existing open source ESB. The management application grants tenant users limited configuration access to the ESB’s connectivity and integration services. A tenant registry and a service registry serve as platform-wide databases. We ensure data isolation between tenants for the management application and ESB message flows. Furthermore, the management application can control clusters of ESB instances, retaining elasticity. These goals also involve extensions to the ESB itself, which implements the Java Business Integration (JBI) specification. As a result, an integration scenario emerged from the EU-funded project 4CaaSt was applied to the system

Generalized techniques for using system execution traces to support software performance analysis

This dissertation proposes generalized techniques to support software performance analysis using system execution traces in the absence of software development artifacts such as source code. The proposed techniques do not require modifications to the source code, or to the software binaries, for the purpose of software analysis (non-intrusive). The proposed techniques are also not tightly coupled to the architecture specific details of the system being analyzed. This dissertation extends the current techniques of using system execution traces to evaluate software performance properties, such as response times, service times. The dissertation also proposes a novel technique to auto-construct a dataflow model from the system execution trace, which will be useful in evaluating software performance properties. Finally, it showcases how we can use execution traces in a novel technique to detect Excessive Dynamic Memory Allocations software performance anti-pattern. This is the first attempt, according to the author\u27s best knowledge, of a technique to detect automatically the excessive dynamic memory allocations anti-pattern. The contributions from this dissertation will ease the laborious process of software performance analysis and provide a foundation for helping software developers quickly locate the causes for negative performance results via execution traces

Distributed Handler Architecture

Thesis (PhD) - Indiana University, Computer Sciences, 2007Over the last couple of decades, distributed systems have been demonstrated an architectural evolvement based on models including client/server, multi-tier, distributed objects, messaging and peer-to-peer. One recent evolutionary step is Service Oriented Architecture (SOA), whose goal is to achieve loose-coupling among the interacting software applications for scalability and interoperability. The SOA model is engendered in Web Services, which provide software platforms to build applications as services and to create seamless and loosely-coupled interactions. Web Services utilize supportive functionalities such as security, reliability, monitoring, logging and so forth. These functionalities are typically provisioned as handlers, which incrementally add new capabilities to the services by building an execution chain. Even though handlers are very important to the service, the way of utilization is very crucial to attain the potential benefits. Every attempt to support a service with an additive functionality increases the chance of having an overwhelmingly crowded chain: this makes Web Service fat. Moreover, a handler may become a bottleneck because of having a comparably higher processing time. In this dissertation, we present Distributed Handler Architecture (DHArch) to provide an efficient, scalable and modular architecture to manage the execution of the handlers. The system distributes the handlers by utilizing a Message Oriented Middleware and orchestrates their execution in an efficient fashion. We also present an empirical evaluation of the system to demonstrate the suitability of this architecture to cope with the issues that exist in the conventional Web Service handler structures

Reputation Description and Interpretation

Reputation is an opinion held by others about a particular person, group, organisation, or resource. As a tool, reputation can be used to forecast the reliability of others based on their previous actions, moreover, in some domains it can even be used to estimate trustworthiness. Due to the large scale of virtual communities it is impossible to maintain a meaningful relationship with every member. Reputation systems are designed explicitly to manufacture trust within a virtual community by recording and sharing information regarding past interactions. Reputation systems are becoming increasingly popular and widespread, with the information generated varying considerably between domains. Currently, no formal method to exchange reputation information exists. However, the OpenRep framework, currently under development, is designed to federate reputation information, enabling the transparent exchange of information between reputation systems. This thesis presents a reputation description and interpretation system, designed as a foundation for the OpenRep framework. The description and interpretation system focuses on enabling the consistent and reliable expression and interpretation of reputation information across heterogeneous reputation systems. The description and interpretation system includes a strongly typed language, a verification system to validate usage of the language, and a XML based exchange protocol. In addition to these contributions, three case studies are presented as a means of generating requirements for the description and interpretation system, and evaluating the use of the proposed system in a federated reputation environment. The case studies include an electronic auction, virtual community and social network based relationship management service

Reputation Description and Interpretation

Reputation is an opinion held by others about a particular person, group, organisation, or resource. As a tool, reputation can be used to forecast the reliability of others based on their previous actions, moreover, in some domains it can even be used to estimate trustworthiness. Due to the large scale of virtual communities it is impossible to maintain a meaningful relationship with every member. Reputation systems are designed explicitly to manufacture trust within a virtual community by recording and sharing information regarding past interactions. Reputation systems are becoming increasingly popular and widespread, with the information generated varying considerably between domains. Currently, no formal method to exchange reputation information exists. However, the OpenRep framework, currently under development, is designed to federate reputation information, enabling the transparent exchange of information between reputation systems. This thesis presents a reputation description and interpretation system, designed as a foundation for the OpenRep framework. The description and interpretation system focuses on enabling the consistent and reliable expression and interpretation of reputation information across heterogeneous reputation systems. The description and interpretation system includes a strongly typed language, a verification system to validate usage of the language, and a XML based exchange protocol. In addition to these contributions, three case studies are presented as a means of generating requirements for the description and interpretation system, and evaluating the use of the proposed system in a federated reputation environment. The case studies include an electronic auction, virtual community and social network based relationship management service