Systems biology driven software design for the research enterprise

<p>Abstract</p> <p>Background</p> <p>In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools.</p> <p>Results</p> <p>We illustrate an approach, through the discussion of a purpose built software architecture, which allows disparate groups to reuse tools and access data sources in a common manner. The architecture allows for: the rapid development of distributed applications; interoperability, so it can be used by a wide variety of developers and computational biologists; development using standard tools, so that it is easy to maintain and does not require a large development effort; extensibility, so that new technologies and data types can be incorporated; and non intrusive development, insofar as researchers need not to adhere to a pre-existing object model.</p> <p>Conclusion</p> <p>By using a relatively simple integration strategy, based upon a common identity system and dynamically discovered interoperable services, a light-weight software architecture can become the focal point through which scientists can both get access to and analyse the plethora of experimentally derived data.</p

Scenarios for the deployment of distributed engineering applications

Although there are some good reasons to design engineering software as a stand-alone application for a single computer, there are also numerous possibilities for creating distributed engineering applications, in particular using the Internet. This paper presents some typical scenarios how engineering applications can benefit from including network capabilities. Also, some examples of Internet-based engineering applications are discussed to show how the concepts presented can be implemented

JAVA Wrappers for Automated Interoperability

Databases in Networked Information Systems International Workshop DNIS 2000This paper concentrates on the issues related to implementation of interoperability between distributed subsystems, particularly in the context of reengineering and integration of several centralized legacy systems. Currently, most interoperability techniques require the data or services to be tightly coupled to a particular server. Furthermore, as most programmers are trained in designing stand- alone application, developing distributed system proves to be time-consuming and difficult. Here, we addressed those concerns by creating an interface wrapper model that allows developers to treat distributed objects as local objects. A tool that automatically generates the features of Java interface wrapper from a specification language called the Prototyping System Description Language has been developed based on the model.U.S. Army Research OfficeARO 40473.30-MA-S

Alternative Java Security Policy Model

Récemment, les systèmes distribués sont devenus une catégorie fondamentale de systèmes informatiques. Par conséquent, leur sécurité est devenue essentielle. La recherche décrite dans ce document vise à apporter un éclaircissement sur leurs vulnérabilités quant à la sécurité. Pour ce faire, on a examiné les propriétés de sécurité qu'un système distribué considéré sécuritaire doit supporter. En cherchant un système avec lequel travailler, on a étudié des failles de sécurité des systèmes distribués existants. On a étudié la sécurité de Java et des outils utilisés pour sécuriser ces systèmes. Suite à ces recherches, un nouveau modèle de sécurité Java imposant de nouvelles propriétés de sécurité a été développé. Ce document commence par les résultats de notre recherche sur les systèmes distribués, les outils de sécurité, et la sécurité de Java. Ensuite, on décrit les détails du nouveau système pour finalement faire la démonstration des améliorations qu'apporte ce système avec un exemple.Recently, distributed systems have become a fundamental type of computer system. Because of this, their security is essential. The research described in this document aimed to find their weaknesses and to find the means to improve them with regards to their security. To do that, we examined the security properties that a system considered secure must support. While looking for a system with which we could work, we studied security problems in existing distributed systems. We studied the security of Java and some tools used to secure these systems. Following our research, we developed a new Java security model, which imposed new security properties. This document begins with the results of our research in distributed systems, security tools, and Java security. Next, we go into detail about our new system to finally demonstrate the security enhancements of our system using an example

Building Enterprise Architecture Agility and Sustenance with SOA

Service-Oriented Architecture(SOA) is primarily regarded as a technical architecture consisting of tools and service specification to build loosely coupled applications. At another level it is also a means to leverage flexibility and agility to system services as it offers a hierarchical framework to coordinate simultaneous business process design and implementations using loosely coupled service infrastructures. SOA has been debated both in the academy and industry and misinterpretations of its nature impede its adoption. We summarize its historical origins and current evolutions. We review technologies that underlie SOA. In particular, we address how to integrate SOA initiatives with current technology platforms, and how to enforce reuse during the design of loosely coupled systems. We also analyze SOA design methodologies and platforms, and what are their roles in the application integration. Finally we outline challenges and future research directions for SOA

A Comparative Evaluation of .net Remoting and JAVA RMI

Distributed application technologies such as Micrososoft.NET Remoting, and Java Remote Method Invocation (RMI) have evolved over many years to keep up with the constantly increasing requirements of the enterprise. In the broadest sense, a distributed application is one in which the application processing is divided among two or more machines. Distributed middleware technologies have made significant progress over the last decade. Although Remoting and RMI are the two of most popular contemporary middleware technologies, little literature exists that compares them. In this paper, we study the issues involved in designing a distributed system using Java RMI and Microsoft.NET Remoting. In order to perform the comparisons, we designed a distributed distance learning application in both technologies. In this paper, we show both similarities and differences between these two competing technologies. Remoting and RMI both have similar serialization process and let objects serialization to be customized according to the needs. They both provide support to be able to connect to interface definition language such as Common Object Request Broker Architecture (CORBA). They both contain distributed garbage collection support. Our research shows that programs coded using Remoting execute faster than programs coded using RMI. They both have strong support for security although implemented in different ways. In addition, RMI also has additional security mechanisms provided via security policy files. RMI requires a naming service to be able to locate the server address and connection port. This is a big advantage since the clients do not need to know the server location or port number, RMI registry locates it automatically. On the other hand, Remoting does not require a naming service; it requires that the port to connect must be pre-specified and all services must be well-known. RMI applications can be run on any operating system whereas Remoting targets Windows as the primary platform. We found it was easier to design the distance learning application in Remoting than in RMI. Remoting also provides greater flexibility in regard to configuration by providing support for external configuration files. In conclusion, we recommend that before deciding which application to choose careful considerations should be given to the type of application, platform, and resources available to program the application

Towards a mobile computing middleware: a synergy of reflection and mobile code techniques

The increasing popularity of wireless devices, such as mobile phones, personal digital assistants, watches and the like. is enabling new classes of applications that present challenging problems to designers. Applications have to be aware of, and adapt to, frequent variations in the context of execution, such as fluctuating network bandwidth, decreasing batten, power, changes in location or device capabilities, and so on. In this paper, we argue that middleware solutions for wired distributed systems cannot be used in a mobile setting, as the principle of transparency that has driven their design runs counter to the new degrees of awareness imposed by mobility: We propose a synergy of reflection and code mobility as a means for middleware to give applications the desired level of flexibility to react to changes happening in the environment, including those that have not necessarily been foreseen by middleware designers. We ruse the sharing and processing of images as an application scenario to highlight the advantages of our approach

Multi-Tier Diversified Service Architecture for Internet 3.0: The Next Generation Internet

The next generation Internet needs to support multiple diverse application contexts. In this paper, we present Internet 3.0, a diversified, multi-tier architecture for the next generation Internet. Unlike the current Internet, Internet 3.0 defines a new set of primitives that allows diverse applications to compose and optimize their specific contexts over resources belonging to multiple ownerships. The key design philosophy is to enable diversity through explicit representation, negotiation and enforcement of policies at the granularity of network infrastructure, compute resources, data and users. The basis of the Internet 3.0 architecture is a generalized three-tier object model. The bottom tier consists of a high-speed network infrastructure. The second tier consists of compute resources or hosts. The third tier consists of data and users. The “tiered” organization of the entities in the object model depicts the natural dependency relationship between these entities in a communication context. All communication contexts, including the current Internet, may be represented as special cases within this generalized three-tier object model. The key contribution of this paper is a formal architectural representation of the Internet 3.0 architecture over the key primitive of the “Object Abstraction” and a detailed discussion of the various design aspects of the architecture, including the design of the “Context Router-” the key architectural element that powers an evolutionary deployment plan for the clean slate design ideas of Internet 3.0

Engineering Automation for Reliable Software Interim Progress Report (10/01/2000 - 09/30/2001)

Prepared for: U.S. Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211The objective of our effort is to develop a scientific basis for producing reliable software that is also flexible and cost effective for the DoD distributed software domain. This objective addresses the long term goals of increasing the quality of service provided by complex systems while reducing development risks, costs, and time. Our work focuses on "wrap and glue" technology based on a domain specific distributed prototype model. The key to making the proposed approach reliable, flexible, and cost-effective is the automatic generation of glue and wrappers based on a designer's specification. The "wrap and glue" approach allows system designers to concentrate on the difficult interoperability problems and defines solutions in terms of deeper and more difficult interoperability issues, while freeing designers from implementation details. Specific research areas for the proposed effort include technology enabling rapid prototyping, inference for design checking, automatic program generation, distributed real-time scheduling, wrapper and glue technology, and reliability assessment and improvement. The proposed technology will be integrated with past research results to enable a quantum leap forward in the state of the art for rapid prototyping.U. S. Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-22110473-MA-SPApproved for public release; distribution is unlimited