Evaluating and Improving the Efficiency of Software and Algorithms for Sequence Data Analysis

With the ever-growing size of sequence data sets, data processing and analysis are an increasingly large portion of the time and money spent on nucleic acid sequencing projects. Correspondingly, the performance of the software and algorithms used to perform that analysis has a direct effect on the time and expense involved. Although the analytical methods are widely varied, certain types of software and algorithms are applicable to a number of areas. Targeting improvements to these common elements has the potential for wide reaching rewards. This dissertation research consisted of several projects to characterize and improve upon the efficiency of several common elements of sequence data analysis software and algorithms. The first project sought to improve the efficiency of the short read mapping process, as mapping is the most time consuming step in many data analysis pipelines. The result was a new short read mapping algorithm and software, demonstrated to be more computationally efficient than existing software and enabling more of the raw data to be utilized. While developing this software, it was discovered that a widely used bioinformatics software library introduced a great deal of inefficiency into the application. Given the potential impact of similar libraries to other applications, and because little research had been done to evaluate library efficiency, the second project evaluated the efficiency of seven of the most popular bioinformatics software libraries, written in C++, Java, Python, and Perl. This evaluation showed that two of libraries written in the most popular language, Java, were an order of magnitude slower and used more memory than expected based on the language in which they were implemented. The third and final project, therefore, was the development of a new general-purpose bioinformatics software library for Java. This library, known as BioMojo, incorporated a new design approach resulting in vastly improved efficiency. Assessing the performance of this new library using the benchmark methods developed for the second project showed that BioMojo outperformed all of the other libraries across all benchmark tasks, being up to 30 times more CPU efficient than existing Java libraries

Assessing the Performance of OpenTitan as Cryptographic Accelerator in Secure Open-Hardware System-on-Chips

RISC-V open-source systems are emerging in deployment scenarios where safety and security are critical. OpenTitan is an open-source silicon root-of-trust designed to be deployed in a wide range of systems, from high-end to deeply embedded secure environments. Despite the availability of various cryptographic hardware accelerators that make OpenTitan suitable for offloading cryptographic workloads from the main processor, there has been no accurate and quantitative establishment of the benefits derived from using OpenTitan as a secure accelerator. This paper addresses this gap by thoroughly analysing strengths and inefficiencies when offloading cryptographic workloads to OpenTitan. The focus is on three key IPs - HMAC, AES, and OpenTitan Big Number accelerator (OTBN) - which can accelerate four security workloads: Secure Hash Functions, Message Authentication Codes, Symmetric cryptography, and Asymmetric cryptography. For every workload, we develop a bare-metal driver for the OpenTitan accelerator and analyze its efficiency when computation is offloaded from a RISC-V application core within a System-on-Chip designed for secure Cyber-Physical Systems applications. Finally, we assess it against a software implementation on the application core. The characterization was conducted on a cycle-accurate RTL simulator of the System-on-Chip (SoC). Our study demonstrates that OpenTitan significantly outperforms software implementations, with speedups ranging from 4.3x to 12.5x. However, there is potential for even greater gains as the current OpenTitan utilizes a fraction of the accelerator bandwidths, which ranges from 16% to 61%, depending on the memory being accessed and the accelerator used. Our results open the way to the optimization of OpenTitan-based secure platforms, providing design guidelines to unlock the full potential of its accelerators in secure applications.Comment: 8 pages, 2 figures, accepted at CF'24 conference, pre camera-ready versio

A framework for cost-sensitive automated selection of intrusion response

In recent years, cost-sensitive intrusion response has gained significant interest due to its emphasis on the balance between potential damage incurred by the intrusion and cost of the response. However, one of the challenges in applying this approach is defining a consistent and adaptable measurement framework to evaluate the expected benefit of a response. In this thesis we present a model and framework for the cost-sensitive assessment and selection of intrusion response. Specifically, we introduce a set of measurements that characterize the potential costs associated with the intrusion handling process, and propose an intrusion response evaluation method with respect to the risk of potential intrusion damage, the effectiveness of the response action and the response cost for a system. The proposed framework has the important quality of abstracting the system security policy from the response selection mechanism, permitting policy adjustments to be made without changes to the model. We provide an implementation of the proposed solution as an IDS-independent plugin tool, and demonstrate its advantages over traditional static response systems and an existing dynamic response system

Transfer Control for Resilient End-to-End Transport

Residing between the network layer and the application layer, the transport layer exchanges application data using the services provided by the network. Given the unreliable nature of the underlying network, reliable data transfer has become one of the key requirements for those transport-layer protocols such as TCP. Studying the various mechanisms developed for TCP to increase the correctness of data transmission while fully utilizing the network's bandwidth provides us a strong background for our study and development of our own resilient end-to-end transport protocol. Given this motivation, in this thesis, we study the different TCP's error control and congestion control techniques by simulating them under different network scenarios using ns-3. For error control, we narrow our research to acknowledgement methods such as cumulative ACK - the traditional TCP's way of ACKing, SACK, NAK, and SNACK. The congestion control analysis covers some TCP variants including Tahoe, Reno, NewReno, Vegas, Westwood, Westwood+, and TCP SACK

Infrastructure, transport and productivity

This information sheet reviews trends in Australian productivity with a focus on the transport sector. Well targeted investments in transport infrastructure result in productivity increases that benefit many other industries. The paper provides for specific examples that cover trucks, freight, waterfront and rail productivity enhancements

Group Authentication Scheme for Neighbourhood Area Networks(NANs) In Smart Grids

A Neighbourhood Area Network is a functional component of the Smart Grid that interconnects the end user domain with the Energy Services Provider (ESP) domain. It forms the “edge” of the provider network, interconnecting homes instrumented with Smart Meters (SM) with the ESP. The SM is a dual interface, wireless communication device through which information is transacted across the user (a home) and ESP domains. The security risk to the ESP increases since the components within the home, interconnected to the ESP via the SM, are not managed by the ESP. Secure operation of the SM is a necessary requirement. The SM should be resilient to attacks, which might be targeted either directly or via the network in the home. This paper presents and discusses a security scheme for groups of SMs in a Neighbourhood Area Network that enable entire groups to authenticate themselves, rather than one at a time. The results show that a significant improvement in terms of resilience against node capture attacks, replay attacks, confidentiality, authentication for groups of SMs in a NAN that enable entire groups to authenticate themselves, rather than one at a time