T. D. Sutherland, T. D. Rapson, M. G. Huson, J. S. Church

Recombinant proteins are polymers that offer the materials engineer absolute control over chain length and composition: key attributes required for design of advanced polymeric materials. Through this control, these polymers can be encoded to contain information that enables them to respond as the environment changes. However, despite their promise, protein-based materials are under represented in materials science. In this chapter we investigate why this is and describe recent efforts to address this. We discuss constraints limiting rational design of structural proteins for advanced materials; advantages and disadvantages of different recombinant expression platforms; and, methods to fabricate proteins into solid-state materials. Finally, we describe the silk proteins used in our laboratory as templates for information-containing polymers.

J. S. Church, A. L. Woodhead

Cotton fibre wax is a complex lipid material that forms the major component of an outer hydrophobic barrier on the cotton fibre surface. Other non-cellulosic constituents present on the cotton fibre surface are sugars, pectin and surface electrolytes. The presence of these components on the cotton fibre surface have both significant positive and negative effects on the processing of cotton fibres into textiles. While traditional alkali scouring is highly effective there has been a move to more environmentally friendly and possibly more controlled methods to remove cotton wax and other surface active species. Significant advancements have recently been made in the ability to obtain chemical information directly from the cotton fibre surface. The two recently developed techniques of IGC-SEA at infinite dilution and infrared ATR mapping using focal plane array detectors have potential to provide new and useful information about the cotton fibre surface.

P. Church, H. Mueller, C. Ryan, S. Gogouvitis, A. Goscinski, H. Haitof, Z. Tari

SCADA (Supervisory Control And Data Acquisition) systems allow users to monitor (using sensors) and control (using actuators) an industrial system remotely. Larger SCADA systems can support several 100,000 sensors, sending and storing hundreds of thousands of messages per second, generating large amounts of data. As these systems are critical to industrial processes, they are often run on highly reliable and dedicated hardware. This is in contrast to the current state of computing, which is moving from running applications on internally hosted servers to cheaper, internal or external cloud environments. Clouds can benefit SCADA users by providing the storage and processing power to analyse the collected data. The goal of this chapter is twofold; provide an introduction to techniques for migrating SCADA to clouds, and devise a conceptual system which supports the process of migrating a SCADA application to a cloud resource while fulfilling key SCADA requirements (such as; support for big data storage).

A. Goscinski, P. Church

Since the development of the computer, user orientated innovations such as graphical operating systems, mice, and mobile devices have made computing ubiquitous in modern society. The cloud is the next step in this process. Through the cloud, computing has undergone co modification and has been made available as a utility. However, in comparison to other commodities such as water and electricity, clouds (in particular IaaS and PaaS) have not reached the same penetration into the global market. We propose that through further abstraction, future clouds will be ubiquitous and transparent, made accessible to ordinary users and integrated into all aspects of society. This paper presents a concept and path to this ubiquitous and transparent cloud, accessible by the masses.

P. Church, H. Mueller, C. Ryan, S. Gogouvitis, A. Goscinski, H. Haitof, Z. Tari

SCADA systems allow users to monitor and/or control physical devices, processes and events remotely. As these systems are critical to industrial processes, they are often run on highly reliable and dedicated hardware. Moving these SCADA systems to an Infrastructure as a Service (IaaS) cloud, allows for: cheaper deployments, system redundancy support, and increased uptime, however it is not clear to what degree clouds can support the real-time requirements. Experiments were carried out to examine the effects of using cloud resources and public networks have on SCADA systems. Using the "Life-and-Shift" approach, eclipseSCADA was deployed to the NeCTAR research cloud. Performance metrics were collected from the deployed eclipseSCADA system under different loads. From these collected metrics, a series of recommendations are provided for deploying and modifying a SCADA system on IaaS cloud resources.

P. Church, A. Goscinski, A. Wong, Z. Tari

Cloud-based technologies—in all of their many varieties—have completely transformed enterprise I.T. These technologies have revolutionized how users access computational resources, empowering users with on-demand access to computational resources exposed as services, their high scalability and availability, and providing services through easy to use web-forms. With the world moving to web-based tools to support business activities such as share trading and e-commerce, as well as daily life activities such as online shopping and banking, it is no wonder computational biologists and pharmaceutical companies are also moving toward cloud-based eScience (web-based online science) to conduct their research. This chapter presents a SaaS cloud framework to support genomic and medical research. By first investigating how HPC is delivered on clouds, the problems encountered by researchers utilizing the cloud to run HPC applications are identified. To solve these issues, a research cloud framework is proposed which incorporates aspects of currently used eScience and cloud solutions which support research (in biology and medicine). This framework simplifies cloud access and cloud resource management while allowing researchers to take the role of a cloud service developer. A prototype of our proposed cloud framework, called Uncinus, is then implemented and validated through a case study which demonstrates how research clouds can simplify personalized medicine via access to cheap, on-demand HPC facilities.

P. Church, A. Goscinski, Z. Tari

By processing big data using clouds, scientific researchers can achieve remarkable outcomes. However, these non-computing specialists do not have the computing knowledge and skills to deal with big data, build HPC applications, and execute them on clouds. Non-computing specialists also face a major problem with accessing HPC and cloud resources through a command driven interfaces, preferring to use menu-driven interfaces. In response we propose that that the future of big data processing lies in SaaS clouds and exposing applications as services. In this way, researchers are relieved from computing activities and concentrate on their research goals. This paper presents a SaaS cloud framework to support eScience, starting with software tools and other SaaS clouds, a description of an implementation of the proposed framework, and study of its features.

P. Church, A. Goscinski

High Performance Computing (HPC) clouds have started to change the way how research in science, in particular medicine and genomics (bioinformatics) is being carried out. Researchers who have taken advantage of this technology can process larger amounts of data and speed up scientific discovery. However, most HPC clouds are provided at an Infrastructure as a Service (IaaS) level, users are presented with a set of virtual servers which need to be put together to form HPC environments via time consuming resource management and software configuration tasks, which make them practically unusable by discipline, non-computing specialists. In response, there is a new trend to expose cloud applications as services to simplify access and execution on clouds. This paper firstly examines commonly used cloud-based genomic analysis services (Tuxedo Suite, Galaxy and Cloud Bio Linux). As a follow up, we propose two new solutions (HPCaaS and Uncinus), which aim to automate aspects of the service development and deployment process. By comparing and contrasting these five solutions, we identify key mechanisms of service creation, execution and access that are required to support genomic research on the SaaS cloud, in particular by discipline specialists.