Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

Strong designated verifier signature in a multi-user setting

The security of strong designated verifier (SDV) signature schemes has thus far been analyzed only in a two-user setting. We observe that security in a two-user setting does not necessarily imply the same in a multi-user setting for SDV signatures. Moreover, we show that existing security notions do not adequately model the security of SDV signatures even in a two-user setting. We then propose revised notions of security in a multi-user setting and show that no existing scheme satisfies these notions. A new SDV signature scheme is then presented and proven secure under the revised notions in the standard model. For the purpose of constructing the SDV signature scheme, we propose a one-pass key establishment protocol in the standard model, which is of independent interest in itself.

Protocol engineering for protection against denial-of-service attacks

Denial-of-service attacks (DoS) and distributed denial-of-service attacks (DDoS) attempt to temporarily disrupt users or computer resources to cause service un- availability to legitimate users in the internetworking system. The most common type of DoS attack occurs when adversaries °ood a large amount of bogus data to interfere or disrupt the service on the server. The attack can be either a single-source attack, which originates at only one host, or a multi-source attack, in which multiple hosts coordinate to °ood a large number of packets to the server. Cryptographic mechanisms in authentication schemes are an example ap- proach to help the server to validate malicious tra±c. Since authentication in key establishment protocols requires the veri¯er to spend some resources before successfully detecting the bogus messages, adversaries might be able to exploit this °aw to mount an attack to overwhelm the server resources. The attacker is able to perform this kind of attack because many key establishment protocols incorporate strong authentication at the beginning phase before they can iden- tify the attacks. This is an example of DoS threats in most key establishment protocols because they have been implemented to support con¯dentiality and data integrity, but do not carefully consider other security objectives, such as availability. The main objective of this research is to design denial-of-service resistant mechanisms in key establishment protocols. In particular, we focus on the design of cryptographic protocols related to key establishment protocols that implement client puzzles to protect the server against resource exhaustion attacks. Another objective is to extend formal analysis techniques to include DoS- resistance. Basically, the formal analysis approach is used not only to analyse and verify the security of a cryptographic scheme carefully but also to help in the design stage of new protocols with a high level of security guarantee. In this research, we focus on an analysis technique of Meadows' cost-based framework, and we implement DoS-resistant model using Coloured Petri Nets. Meadows' cost-based framework is directly proposed to assess denial-of-service vulnerabil- ities in the cryptographic protocols using mathematical proof, while Coloured Petri Nets is used to model and verify the communication protocols using inter- active simulations. In addition, Coloured Petri Nets are able to help the protocol designer to clarify and reduce some inconsistency of the protocol speci¯cation. Therefore, the second objective of this research is to explore vulnerabilities in existing DoS-resistant protocols, as well as extend a formal analysis approach to our new framework for improving DoS-resistance and evaluating the performance of the new proposed mechanism. In summary, the speci¯c outcomes of this research include following results; 1. A taxonomy of denial-of-service resistant strategies and techniques used in key establishment protocols; 2. A critical analysis of existing DoS-resistant key exchange and key estab- lishment protocols; 3. An implementation of Meadows's cost-based framework using Coloured Petri Nets for modelling and evaluating DoS-resistant protocols; and 4. A development of new e±cient and practical DoS-resistant mechanisms to improve the resistance to denial-of-service attacks in key establishment protocols.

SELinux policy management framework for HIS

Health Information Systems (HIS) make extensive use of Information and Communication Technologies (ICT). The use of ICT aids in improving the quality and efficiency of healthcare services by making healthcare information available at the point of care (Goldstein, Groen, Ponkshe, and Wine, 2007). The increasing availability of healthcare data presents security and privacy issues which have not yet been fully addressed (Liu, Caelli, May, and Croll, 2008a). Healthcare organisations have to comply with the security and privacy requirements stated in laws, regulations and ethical standards, while managing healthcare information. Protecting the security and privacy of healthcare information is a very complex task (Liu, May, Caelli and Croll, 2008b). In order to simplify the complexity of providing security and privacy in HIS, appropriate information security services and mechanisms have to be implemented. Solutions at the application layer have already been implemented in HIS such as those existing in healthcare web services (Weaver et al., 2003). In addition, Discretionary Access Control (DAC) is the most commonly implemented access control model to restrict access to resources at the OS layer (Liu, Caelli, May, Croll and Henricksen, 2007a). Nevertheless, the combination of application security mechanisms and DAC at the OS layer has been stated to be insufficient in satisfying security requirements in computer systems (Loscocco et al., 1998). This thesis investigates the feasibility of implementing Security Enhanced Linux (SELinux) to enforce a Role-Based Access Control (RBAC) policy to help protect resources at the Operating System (OS) layer. SELinux provides Mandatory Access Control (MAC) mechanisms at the OS layer. These mechanisms can contain the damage from compromised applications and restrict access to resources according to the security policy implemented. The main contribution of this research is to provide a modern framework to implement and manage SELinux in HIS. The proposed framework introduces SELinux Profiles to restrict access permissions over the system resources to authorised users. The feasibility of using SELinux profiles in HIS was demonstrated through the creation of a prototype, which was submitted to various attack scenarios. The prototype was also subjected to testing during emergency scenarios, where changes to the security policies had to be made on the spot. Attack scenarios were based on vulnerabilities common at the application layer. SELinux demonstrated that it could effectively contain attacks at the application layer and provide adequate flexibility during emergency situations. However, even with the use of current tools, the development of SELinux policies can be very complex. Further research has to be made in order to simplify the management of SELinux policies and access permissions. In addition, SELinux related technologies, such as the Policy Management Server by Tresys Technologies, need to be researched in order to provide solutions at different layers of protection.

Effective web service discovery using a combination of a semantic model and a data mining technique

With the advent of Service Oriented Architecture, Web Services have gained tremendous popularity. Due to the availability of a large number of Web services, finding an appropriate Web service according to the requirement of the user is a challenge. This warrants the need to establish an effective and reliable process of Web service discovery. A considerable body of research has emerged to develop methods to improve the accuracy of Web service discovery to match the best service. The process of Web service discovery results in suggesting many individual services that partially fulfil the user’s interest. By considering the semantic relationships of words used in describing the services as well as the use of input and output parameters can lead to accurate Web service discovery. Appropriate linking of individual matched services should fully satisfy the requirements which the user is looking for. This research proposes to integrate a semantic model and a data mining technique to enhance the accuracy of Web service discovery. A novel three-phase Web service discovery methodology has been proposed. The first phase performs match-making to find semantically similar Web services for a user query. In order to perform semantic analysis on the content present in the Web service description language document, the support-based latent semantic kernel is constructed using an innovative concept of binning and merging on the large quantity of text documents covering diverse areas of domain of knowledge. The use of a generic latent semantic kernel constructed with a large number of terms helps to find the hidden meaning of the query terms which otherwise could not be found. Sometimes a single Web service is unable to fully satisfy the requirement of the user. In such cases, a composition of multiple inter-related Web services is presented to the user. The task of checking the possibility of linking multiple Web services is done in the second phase. Once the feasibility of linking Web services is checked, the objective is to provide the user with the best composition of Web services. In the link analysis phase, the Web services are modelled as nodes of a graph and an allpair shortest-path algorithm is applied to find the optimum path at the minimum cost for traversal. The third phase which is the system integration, integrates the results from the preceding two phases by using an original fusion algorithm in the fusion engine. Finally, the recommendation engine which is an integral part of the system integration phase makes the final recommendations including individual and composite Web services to the user. In order to evaluate the performance of the proposed method, extensive experimentation has been performed. Results of the proposed support-based semantic kernel method of Web service discovery are compared with the results of the standard keyword-based information-retrieval method and a clustering-based machine-learning method of Web service discovery. The proposed method outperforms both information-retrieval and machine-learning based methods. Experimental results and statistical analysis also show that the best Web services compositions are obtained by considering 10 to 15 Web services that are found in phase-I for linking. Empirical results also ascertain that the fusion engine boosts the accuracy of Web service discovery by combining the inputs from both the semantic analysis (phase-I) and the link analysis (phase-II) in a systematic fashion. Overall, the accuracy of Web service discovery with the proposed method shows a significant improvement over traditional discovery methods.

Improving the management of building life cycle : a data mining approach

The construction industry has adapted information technology in its processes in terms of computer aided design and drafting, construction documentation and maintenance. The data generated within the construction industry has become increasingly overwhelming. Data mining is a sophisticated data search capability that uses classification algorithms to discover patterns and correlations within a large volume of data. This paper presents the selection and application of data mining techniques on maintenance data of buildings. The results of applying such techniques and potential benefits of utilising their results to identify useful patterns of knowledge and correlations to support decision making of improving the management of building life cycle are presented and discussed.

Using Agents for Mining Maintenance Data while interacting in 3D Objectoriented Virtual Environments

This report demonstrates the development of: (a) object-oriented representation to provide 3D interactive environment using data provided by Woods Bagot; (b) establishing basis of agent technology for mining building maintenance data, and (C) 3D interaction in virtual environments using object-oriented representation. Applying data mining over industry maintenance database has been demonstrated in the previous report.

Developing Software Agents for Data Mining : [AIMM] Agents for Improving Maintenance Management

This report demonstrates the development of: • Development of software agents for data mining • Link data mining to building model in virtual environments • Link knowledge development with building model in virtual environments • Demonstration of software agents for data mining • Populate with maintenance data

Using data mining to improve building life cycle

The building life cycle process is complex and prone to fragmentation as it moves through its various stages. The number of participants, and the diversity, specialisation and isolation both in space and time of their activities, have dramatically increased over time. The data generated within the construction industry has become increasingly overwhelming. Most currently available computer tools for the building industry have offered productivity improvement in the transmission of graphical drawings and textual specifications, without addressing more fundamental changes in building life cycle management. Facility managers and building owners are primarily concerned with highlighting areas of existing or potential maintenance problems in order to be able to improve the building performance, satisfying occupants and minimising turnover especially the operational cost of maintenance. In doing so, they collect large amounts of data that is stored in the building’s maintenance database. The work described in this paper is targeted at adding value to the design and maintenance of buildings by turning maintenance data into information and knowledge. Data mining technology presents an opportunity to increase significantly the rate at which the volumes of data generated through the maintenance process can be turned into useful information. This can be done using classification algorithms to discover patterns and correlations within a large volume of data. This paper presents how and what data mining techniques can be applied on maintenance data of buildings to identify the impediments to better performance of building assets. It demonstrates what sorts of knowledge can be found in maintenance records. The benefits to the construction industry lie in turning passive data in databases into knowledge that can improve the efficiency of the maintenance process and of future designs that incorporate that maintenance knowledge.

Making visible the coding process : Using qualitative data software in a post-structural study

Qualitative research methods require transparency to ensure the ‘trustworthiness’ of the data analysis. The intricate processes of organizing, coding and analyzing the data are often rendered invisible in the presentation of the research findings, which requires a ‘leap of faith’ for the reader. Computer assisted data analysis software can be used to make the research process more transparent, without sacrificing rich, interpretive analysis by the researcher. This article describes in detail how one software package was used in a poststructural study to link and code multiple forms of data to four research questions for fine-grained analysis. This description will be useful for researchers seeking to use qualitative data analysis software as an analytic tool.

Open Specification for BIM : Sydney Opera House Case Study

Executive Summary The objective of this report was to use the Sydney Opera House as a case study of the application of Building Information Modelling (BIM). The Sydney opera House is a complex, large building with very irregular building configuration, that makes it a challenging test. A number of key concerns are evident at SOH: • the building structure is complex, and building service systems - already the major cost of ongoing maintenance - are undergoing technology change, with new computer based services becoming increasingly important. • the current “documentation” of the facility is comprised of several independent systems, some overlapping and is inadequate to service current and future services required • the building has reached a milestone age in terms of the condition and maintainability of key public areas and service systems, functionality of spaces and longer term strategic management. • many business functions such as space or event management require up-to-date information of the facility that are currently inadequately delivered, expensive and time consuming to update and deliver to customers. • major building upgrades are being planned that will put considerable strain on existing Facilities Portfolio services, and their capacity to manage them effectively While some of these concerns are unique to the House, many will be common to larger commercial and institutional portfolios. The work described here supported a complementary task which sought to identify if a building information model – an integrated building database – could be created, that would support asset & facility management functions (see Sydney Opera House – FM Exemplar Project, Report Number: 2005-001-C-4 Building Information Modelling for FM at Sydney Opera House), a business strategy that has been well demonstrated. The development of the BIMSS - Open Specification for BIM has been surprisingly straightforward. The lack of technical difficulties in converting the House’s existing conventions and standards to the new model based environment can be related to three key factors: • SOH Facilities Portfolio – the internal group responsible for asset and facility management - have already well established building and documentation policies in place. The setting and adherence to well thought out operational standards has been based on the need to create an environment that is understood by all users and that addresses the major business needs of the House. • The second factor is the nature of the IFC Model Specification used to define the BIM protocol. The IFC standard is based on building practice and nomenclature, widely used in the construction industries across the globe. For example the nomenclature of building parts – eg ifcWall, corresponds to our normal terminology, but extends the traditional drawing environment currently used for design and documentation. This demonstrates that the international IFC model accurately represents local practice for building data representation and management. • a BIM environment sets up opportunities for innovative processes that can exploit the rich data in the model and improve services and functions for the House: for example several high-level processes have been identified that could benefit from standardized Building Information Models such as maintenance processes using engineering data, business processes using scheduling, venue access, security data and benchmarking processes using building performance data. The new technology matches business needs for current and new services. The adoption of IFC compliant applications opens the way forward for shared building model collaboration and new processes, a significant new focus of the BIM standards. In summary, SOH current building standards have been successfully drafted for a BIM environment and are confidently expected to be fully developed when BIM is adopted operationally by SOH. These BIM standards and their application to the Opera House are intended as a template for other organisations to adopt for the own procurement and facility management activities. Appendices provide an overview of the IFC Integrated Object Model and an understanding IFC Model Data.

Electronic tendering: an industry perspective

The construction industry is categorised as being an information-intensive industry and described as one of the most important industries in any developed country, facing a period of rapid and unparalleled change (Industry Science Resources 1999) (Love P.E.D., Tucker S.N. et al. 1996). Project communications are becoming increasingly complex, with a growing need and fundamental drive to collaborate electronically at project level and beyond (Olesen K. and Myers M.D. 1999; Thorpe T. and Mead S. 2001; CITE 2003). Yet, the industry is also identified as having a considerable lack of knowledge and awareness about innovative information and communication technology (ICT) and web-based communication processes, systems and solutions which may prove beneficial in the procurement, delivery and life cycle of projects (NSW Government 1998; Kajewski S. and Weippert A. 2000). The Internet has debatably revolutionised the way in which information is stored, exchanged and viewed, opening new avenues for business, which only a decade ago were deemed almost inconceivable (DCITA 1998; IIB 2002). In an attempt to put these ‘new avenues of business’ into perspective, this report provides an overall ‘snapshot’ of current public and private construction industry sector opportunities and practices in the implementation and application of web-based ICT tools, systems and processes (e-Uptake). Research found that even with a reserved uptake, the construction industry and its participating organisations are making concerted efforts (fortunately with positive results) in taking up innovative forms of doing business via the internet, including e-Tendering (making it possible to manage the entire tender letting process electronically and online) (Anumba C.J. and Ruikar K. 2002; ITCBP 2003). Furthermore, Government (often a key client within the construction industry),and with its increased tendency to transact its business electronically, undoubtedly has an effect on how various private industry consultants, contractors, suppliers, etc. do business (Murray M. 2003) – by offering a wide range of (current and anticipated) e-facilities / services, including e-Tendering (Ecommerce 2002). Overall, doing business electronically is found to have a profound impact on the way today’s construction businesses operate - streamlining existing processes, with the growth in innovative tools, such as e-Tender, offering the construction industry new responsibilities and opportunities for all parties involved (ITCBP 2003). It is therefore important that these opportunities should be accessible to as many construction industry businesses as possible (The Construction Confederation 2001). Historically, there is a considerable exchange of information between various parties during a tendering process, where accuracy and efficiency of documentation is critical. Traditionally this process is either paper-based (involving large volumes of supporting tender documentation), or via a number of stand-alone, non-compatible computer systems, usually costly to both the client and contractor. As such, having a standard electronic exchange format that allows all parties involved in an electronic tender process to access one system only via the Internet, saves both time and money, eliminates transcription errors and increases speed of bid analysis (The Construction Confederation 2001). Supporting this research project’s aims and objectives, researchers set to determine today’s construction industry ‘current state-of-play’ in relation to e-Tendering opportunities. The report also provides brief introductions to several Australian and International e-Tender systems identified during this investigation. e-Tendering, in its simplest form, is described as the electronic publishing, communicating, accessing, receiving and submitting of all tender related information and documentation via the internet, thereby replacing the traditional paper-based tender processes, and achieving a more efficient and effective business process for all parties involved (NT Governement 2000; NT Government 2000; NSW Department of Commerce 2003; NSW Government 2003). Although most of the e-Tender websites investigated at the time, maintain their tendering processes and capabilities are ‘electronic’, research shows these ‘eTendering’ systems vary from being reasonably advanced to more ‘basic’ electronic tender notification and archiving services for various industry sectors. Research also indicates an e-Tender system should have a number of basic features and capabilities, including: • All tender documentation to be distributed via a secure web-based tender system – thereby avoiding the need for collating paperwork and couriers. • The client/purchaser should be able to upload a notice and/or invitation to tender onto the system. • Notification is sent out electronically (usually via email) for suppliers to download the information and return their responses electronically (online). • During the tender period, updates and queries are exchanged through the same e-Tender system. • The client/purchaser should only be able to access the tenders after the deadline has passed. • All tender related information is held in a central database, which should be easily searchable and fully audited, with all activities recorded. • It is essential that tender documents are not read or submitted by unauthorised parties. • Users of the e-Tender system are to be properly identified and registered via controlled access. In simple terms, security has to be as good as if not better than a manual tender process. Data is to be encrypted and users authenticated by means such as digital signatures, electronic certificates or smartcards. • All parties must be assured that no 'undetected' alterations can be made to any tender. • The tenderer should be able to amend the bid right up to the deadline – whilst the client/purchaser cannot obtain access until the submission deadline has passed. • The e-Tender system may also include features such as a database of service providers with spreadsheet-based pricing schedules, which can make it easier for a potential tenderer to electronically prepare and analyse a tender. Research indicates the efficiency of an e-Tender process is well supported internationally, with a significant number, yet similar, e-Tender benefits identified during this investigation. Both construction industry and Government participants generally agree that the implementation of an automated e-Tendering process or system enhances the overall quality, timeliness and cost-effectiveness of a tender process, and provides a more streamlined method of receiving, managing, and submitting tender documents than the traditional paper-based process. On the other hand, whilst there are undoubtedly many more barriers challenging the successful implementation and adoption of an e-Tendering system or process, researchers have also identified a range of challenges and perceptions that seem to hinder the uptake of this innovative approach to tendering electronically. A central concern seems to be that of security - when industry organisations have to use the Internet for electronic information transfer. As a result, when it comes to e-Tendering, industry participants insist these innovative tendering systems are developed to ensure the utmost security and integrity. Finally, if Australian organisations continue to explore the competitive ‘dynamics’ of the construction industry, without realising the current and future, trends and benefits of adopting innovative processes, such as e-Tendering, it will limit their globalising opportunities to expand into overseas markets and allow the continuation of international firms successfully entering local markets. As such, researchers believe increased knowledge, awareness and successful implementation of innovative systems and processes raises great expectations regarding their contribution towards ‘stimulating’ the globalisation of electronic procurement activities, and improving overall business and project performances throughout the construction industry sectors and overall marketplace (NSW Government 2002; Harty C. 2003; Murray M. 2003; Pietroforte R. 2003). Achieving the successful integration of an innovative e-Tender solution with an existing / traditional process can be a complex, and if not done correctly, could lead to failure (Bourn J. 2002).

Security and legal issues in E-tendering

The Queensland Department of Public Works (QDPW) and the Queensland Department of Main Roads (QDMR) have identified a need for industry e-contracting guidelines in the short to medium term. Each of these organisations conducts tenders and contracts for over $600 million annually. This report considers the security and legal issues relating to the shift from a paper-based tendering system to an electronic tendering system. The research objectives derived from the industry partners include: • a review of current standards and e-tendering systems; • a summary of legal requirements impacting upon e-tendering; • an analysis of the threats and requirements for any e-tendering system; • the identification of outstanding issues; • an evaluation of possible e-tendering architectures; • recommendations for e-tendering systems.

Sustainable subdivisions – ventilation data analysis

This project, as part of a broader Sustainable Sub-divisions research agenda, addresses the role of natural ventilation in reducing the use of energy required to cool dwellings