Developments in the tools and methodologies of synthetic biology.

Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a body of knowledge from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community

An investigation of web-based hypermedia design support: methods and tools

Since the Internet networking was first established, the World Wide Web (or WWW) provides a new opportunity to deliver information and to communicate with others. Therefore, many organisations and industries have joined this exciting technology to take advantage of the Web. In recent years, the opportunity has arisen for other tasks to be carried out on the Web apart from delivering information. As the Web applications and documents have become larger and more complex, they have experienced many design and development problems which often lead to very high maintenance cost. To improve the quality of Websites and the structure of information, the designers need structured design methods, guidelines, and tools to assist their work. Some researchers have proposed hypermedia design methods and guidelines, which contain development cycle with formal design techniques to assist the construction of Web page designs. To overcome the design and development problems, this research is carried out by surveying currently available design methods. It shows the ways to apply these methods for developing structured Web sites. The results of this research led to identifying the design stages involved in developing Web sites using hypermedia methods. It also presents a CASE tool to provide a development environment for producing Web pages based on hypermedia design stages. This encourages Web designers to apply structured hypermedia design methods to improve the quality of design and to reduce the maintenance cost. The thesis is relevant for end-users, Web designers from organisations, institutes, and institutes for those who want to apply structured hypermedia design methods for producing their Web documents

A component-based product line architecture for workflow management systems

This paper presents a component-based product line for workflow management systems. The process followed to design the product line was based on the Catalysis method. Extensions were made to represent variability across the process. The domain of workflow management systems has been shown to be appropriate to the application of the product line approach as there are a standard architecture and models established by a regulatory board, the Workflow Management Coalition. In addition, there is a demand for similar workflow management systems but with some different features. The product line architecture was evaluated with Rapide simulation tools. The evaluation was based on selected scenarios, thus, avoiding implementation issues. The strategy that has been used to populate the architecture and experiment with the product line is shown. In particular, the design of the workflow execution manager component is described

Organization and management of ATLAS offline software releases

ATLAS is one of the largest collaborations ever undertaken in the physical sciences. This paper explains how the software infrastructure is organized to manage collaborative code development by around 300 developers with varying degrees of expertise, situated in 30 different countries. ATLAS offline software currently consists of about 2 million source lines of code contained in 6800 C++ classes, organized in almost 1000 packages. We will describe how releases of the offline ATLAS software are built, validated and subsequently deployed to remote sites. Several software management tools have been used, the majority of which are not ATLAS specific; we will show how they have been integrated

The characteristics of the CAT to CAD to rapid prototyping system

ThesisComputer Aided Design (CAD), Rapid Prototyping (RP) and Computer Aided Tomography (CAT) technologies were researched. The project entails a unique combination of the abovementioned technologies, which had to be mastered by the author, on local and international terms. Nine software packages were evaluated to determine the modus operandi, required input and final output results. Fifty Rapid Prototyping systems were investigated to determine the strong and weak areas of the various systems, which showed that prototype materials, machine cost and growing time play an essential role. Thirty Reverse Engineering systems were also researched. Six different RE methods were recorded with several commercial systems available. Nineteen case studies were completed by using several different Computer Aided Tomography (CAT) and Magnetic Resonance Imaging (MRI) centers. Each scanning centre has different apparatus and is discussed in detail in the various case studies. The focus of this project is the data transfer of two dimensional CAT scanning data to threedimensional prototypes by using Reverse Engineering (RE) and Rapid Prototyping (RP). It is therefore of cardinal importance that one is familiar and understands the various fields of interest namely Reverse Engineering, Computer Aided Tomography and Rapid Prototyping. Each of these fields will be discussed in detail, with the latest developments in these fields covered as well. Case studies and research performed in the medical field should gain the medical industry's confidence. Constant marketing and publications will ensure that the technology is applied and transferred to the industry. Commercialisation of the technology is of utmost importanc

Quantifying Shannon's Work Function for Cryptanalytic Attacks

Attacks on cryptographic systems are limited by the available computational resources. A theoretical understanding of these resource limitations is needed to evaluate the security of cryptographic primitives and procedures. This study uses an Attacker versus Environment game formalism based on computability logic to quantify Shannon's work function and evaluate resource use in cryptanalysis. A simple cost function is defined which allows to quantify a wide range of theoretical and real computational resources. With this approach the use of custom hardware, e.g., FPGA boards, in cryptanalysis can be analyzed. Applied to real cryptanalytic problems, it raises, for instance, the expectation that the computer time needed to break some simple 90 bit strong cryptographic primitives might theoretically be less than two years.Comment: 19 page