RestrictionDigest: A powerful Perl module for simulating genomic restriction digests

Background: Reduced-representation sequencing technology iswidely used in genotyping for its economical and efficient features. A popular way to construct the reduced-representation sequencing libraries is to digest the genomic DNA with restriction enzymes. A key factor of this method is to determine the restriction enzyme(s). But there are few computer programs which can evaluate the usability of restriction enzymes in reduced-representation sequencing. SimRAD is an R package which can simulate the digestion of DNA sequence by restriction enzymes and return enzyme loci number as well as fragment number. But for linkage mapping analysis, enzyme loci distribution is also an important factor to evaluate the enzyme. For phylogenetic studies, comparison of the enzyme performance across multiple genomes is important. It is strongly needed to develop a simulation tool to implement these functions. Results: Here, we introduce a Perl module named RestrictionDigest with more functions and improved performance. It can analyze multiple genomes at one run and generate concise comparison of enzyme performance across the genomes. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process and generate comprehensive information of the simulation including enzyme loci number, fragment number, sequences of the fragments, positions of restriction sites on the genome, the coverage of digested fragments on different genome regions and detailed fragment length distribution. Conclusions: RestrictionDigest is an easy-to-use Perl module with flexible parameter settings.With the help of the information produced by the module, researchers can easily determine the most appropriate enzymes to construct the reduced-representation libraries to meet their experimental requirements.

Genetic Structure of the Florida Key Tree Cactus, Pilosocereus robinii, using Restriction Site associated DNA (RAD) markers

Rare plant conservation efforts must utilize current genetic methods to ensure the evolutionary potential of populations is preserved. One such effort involves the Key Tree Cactus, Pilosocereus robinii, which is an endangered columnar cactus native to the Florida Keys. The populations have precipitously declined over the past decade because of habitat loss and increasing soil salinity from rising sea levels and storm surge. Next-generation DNA sequencing was used to assess the genetic structure of the populations. Twenty individuals representative of both wild and extirpated cacti were chosen for Restriction Site Associated DNA (RAD) analysis. Samples processed using the HindIII and NotIII restriction enzymes produced 82,382,440 high quality reads used for genetic mapping, from which 5,265 Single Nucleotide Polymorphisms (SNPs) were discovered. The analysis revealed that the Keys’ populations are closely related with little population differentiation. In addition, the populations display evidence of inbreeding and low genetic diversity.

Mapping of indoor environments by robots using low-cost vision sensors

For robots to operate in human environments they must be able to make their own maps because it is unrealistic to expect a user to enter a map into the robot’s memory; existing floorplans are often incorrect; and human environments tend to change. Traditionally robots have used sonar, infra-red or laser range finders to perform the mapping task. Digital cameras have become very cheap in recent years and they have opened up new possibilities as a sensor for robot perception. Any robot that must interact with humans can reasonably be expected to have a camera for tasks such as face recognition, so it makes sense to also use the camera for navigation. Cameras have advantages over other sensors such as colour information (not available with any other sensor), better immunity to noise (compared to sonar), and not being restricted to operating in a plane (like laser range finders). However, there are disadvantages too, with the principal one being the effect of perspective. This research investigated ways to use a single colour camera as a range sensor to guide an autonomous robot and allow it to build a map of its environment, a process referred to as Simultaneous Localization and Mapping (SLAM). An experimental system was built using a robot controlled via a wireless network connection. Using the on-board camera as the only sensor, the robot successfully explored and mapped indoor office environments. The quality of the resulting maps is comparable to those that have been reported in the literature for sonar or infra-red sensors. Although the maps are not as accurate as ones created with a laser range finder, the solution using a camera is significantly cheaper and is more appropriate for toys and early domestic robots.

A new educational technology for media and communication studies : mapping media in Australia and Sweden

This chapter reports on Australian and Swedish experiences in the iterative design, development, and ongoing use of interactive educational systems we call ‘Media Maps.’ Like maps in general, Media Maps are usefully understood as complex cultural technologies; that is, they are not only physical objects, tools and artefacts, but also information creation and distribution technologies, the use and development of which are embedded in systems of knowledge and social meaning. Drawing upon Australian and Swedish experiences with one Media Map technology, this paper illustrates this three-layered approach to the development of media mapping. It shows how media mapping is being used to create authentic learning experiences for students preparing for work in the rapidly evolving media and communication industries. We also contextualise media mapping as a response to various challenges for curriculum and learning design in Media and Communication Studies that arise from shifts in tertiary education policy in a global knowledge economy.

Mapping the regulatory environment : implications for construction firms

As regulators, governments are often criticised for over‐regulating industries. This research project seeks to examine the regulation affecting the construction industry in a federal system of government. It uses a case study of the Australian system of government to focus on the question of the implications of regulation in the construction industry. Having established the extent of the regulatory environment, the research project considers the costs associated with this environment. Consequently, ways in which the regulatory burden on industry can be reduced are evaluated. The Construction Industry Business Environment project is working with industry and government agencies to improve regulatory harmonisation in Australia, and thereby reduce the regulatory burden on industry. It is found that while taxation and compliance costs are not likely to be reduced in the short term, costs arising from having to adapt to variation between regulatory regimes in a federal system of government, seem the most promising way of reducing regulatory costs. Identifying and reducing adaptive costs across jurisdictional are argued to present a novel approach to regulatory reform.

Curriculum mapping of the Spatial Science Program, QUT : what was the cartography journey?

There are currently a number of issues of great importance affecting universities and the way in which their programs are now offered. Many issues are largely being driven top-down and impact both at a university-wide and at an individual discipline level. This paper provides a brief history of cartography and digital mapping education at the Queensland University of Technology (QUT). It also provides an overview of what is curriculum mapping and presents some interesting findings from the program review process. Further, this review process has triggered discussion and action for the review, mapping and embedding of graduate attributes within the spatial science major program. Some form of practical based learning is expected in vocationally oriented degrees that lead to professional accreditation and are generally regarded as a good learning exposure. With the restructure of academic programs across the Faculty of Built Environment and Engineering in 2006, spatial science and surveying students now undertake a formal work integrated learning unit. There is little doubt that students acquire the skills of their discipline (mapping science, spatial) by being immersed in the industry culture- learning how to process information and solve real-world problems within context. The broad theme of where geo-spatial mapping skills are embedded in this broad-based tertiary education course are examined with some focused discussion on the learning objectives, outcomes and examples of some student learning experiences

Mapping the Australian political blogosphere

Network crawling and visualisation tools and other datamining systems are now advanced enough to provide significant new impulses to the study of cultural activity on the Web. A growing range of studies focus on communicative processes in the blogosphere – including for example Adamic & Glance’s 2005 map of political allegiances during the 2004 U.S. presidential election and Kelly & Etling’s 2008 study of blogging practices in Iran. There remain a number of significant shortcomings in the application of such tools and methodologies to the study of blogging; these relate both to how the content of blogs is analysed, and to how the network maps resulting from such studies are understood. Our project highlights and addresses such shortcomings.

Green Marketing Communities and blogs : mapping consumer’s attitudes for future sustainable marketing

The last three decades have seen consumers’ environmental consciousness grow as the environment has moved to a mainstream issue. Results from our study of green marketing blog site comments in the first half of 2009 finds thirteen prominent concepts: carbon, consumers, global and energy were the largest themes, while crisis, power, people, water, fuel, product, work, time, water, organic, content and interest were the others. However sub issues were also identified, as the driving factor of this information is coming from consumer led social networks. While marketers hold some power, consumers are the real key factor to possess influence for change. They want to drive change and importantly, they have the power. Power to the people.

Mapping personal trip OD from probe data

The paper analyses the expected value of OD volumes from probe with fixed error, error that is proportional to zone size and inversely proportional to zone size. To add realism to the analysis, real trip ODs in the Tokyo Metropolitan Region are synthesised. The results show that for small zone coding with average radius of 1.1km, and fixed measurement error of 100m, an accuracy of 70% can be expected. The equivalent accuracy for medium zone coding with average radius of 5km would translate into a fixed error of approximately 300m. As expected small zone coding is more sensitive than medium zone coding as the chances of the probe error envelope falling into adjacent zones are higher. For the same error radii, error proportional to zone size would deliver higher level of accuracy. As over half (54.8%) of the trip ends start or end at zone with equivalent radius of ≤ 1.2 km and only 13% of trips ends occurred at zones with equivalent radius ≥2.5km, measurement error that is proportional to zone size such as mobile phone would deliver higher level of accuracy. The synthesis of real OD with different probe error characteristics have shown that expected value of >85% is difficult to achieve for small zone coding with average radius of 1.1km. For most transport applications, OD matrix at medium zone coding is sufficient for transport management. From this study it can be drawn that GPS with error range between 2 and 5m, and at medium zone coding (average radius of 5km) would provide OD estimates greater than 90% of the expected value. However, for a typical mobile phone operating error range at medium zone coding the expected value would be lower than 85%. This paper assumes transmission of one origin and one destination positions from the probe. However, if multiple positions within the origin and destination zones are transmitted, map matching to transport network could be performed and it would greatly improve the accuracy of the probe data.

Graduate Attribute Mapping With the Extended CDIO Framework

The CDIO (Conceive-Design-Implement-Operate) Initiative has been globally recognised as an enabler for engineering education reform. With the CDIO process, the CDIO Standards and the CDIO Syllabus, many scholarly contributions have been made around cultural change, curriculum reform and learning environments. In the Australasian region, reform is gaining significant momentum within the engineering education community, the profession, and higher education institutions. This paper presents the CDIO Syllabus cast into the Australian context by mapping it to the Engineers Australia Graduate Attributes, the Washington Accord Graduate Attributes and the Queensland University of Technology Graduate Capabilities. Furthermore, in recognition that many secondary schools and technical training institutions offer introductory engineering technology subjects, this paper presents an extended self-rating framework suited for recognising developing levels of proficiency at a preparatory level. A demonstrator mapping tool has been created to demonstrate the application of this extended graduate attribute mapping framework as a precursor to an integrated curriculum information model.

A conceptual framework for a systematic mapping of layout design principles by using Yin and Yang theory

There are various principles for layout design such as balance, rhythm, unity and harmony, but each principle has often been introduced as a separate concept rather than within an integrated and systematic structure, so that designers and design students have to keep practices for the acquisition of skills. The paper seeks to develop a conceptual framework for a systematic mapping of layout design principles by using Yin and Yang and the Five Elements. Yin and Yang theory explains all natural phenomena with its own conceptual model and facilitates finding harmony and balance between the visual elements in terms of systematic and organic relations. Most common and well-known layout design principles are defined with 10 different resources such as design books and articles, and have been remapped following with the structure of Yin and Yang and the Five Elements. A systematic framework explaining the relationships of design principles was created and 32 design students participated in its efficiency test. The outcome suggests there is a high possibility that the framework can be used in professional fields and design education.

Value-mapping for major economic infrastructure projects

The establishment of corporate objectives regarding economic, environmental, social, and ethical responsibilities, to inform business practice, has been gaining credibility in the business sector since the early 1990’s. This is witnessed through (i) the formation of international forums for sustainable and accountable development, (ii) the emergence of standards, systems, and frameworks to provide common ground for regulatory and corporate dialogue, and (iii) the significant quantum of relevant popular and academic literature in a diverse range of disciplines. How then has this move towards greater corporate responsibility become evident in the provision of major urban infrastructure projects? The gap identified, in both academic literature and industry practice, is a structured and auditable link between corporate intent and project outcomes. Limited literature has been discovered which makes a link between corporate responsibility; project performance indicators (or critical success factors) and major infrastructure provision. This search revealed that a comprehensive mapping framework, from an organisation’s corporate objectives through to intended, anticipated and actual outcomes and impacts has not yet been developed for the delivery of such projects. The research problem thus explored is ‘the need to better identify, map and account for the outcomes, impacts and risks associated with economic, environmental, social and ethical outcomes and impacts which arise from major economic infrastructure projects, both now, and into the future’. The methodology being used to undertake this research is based on Checkland’s soft system methodology, engaging in action research on three collaborative case studies. A key outcome of this research is a value-mapping framework applicable to Australian public sector agencies. This is a decision-making methodology which will enable project teams responsible for delivering major projects, to better identify and align project objectives and impacts with stated corporate objectives.