GEDI: a user-friendly toolbox for analysis of large-scale gene expression data

Abstract Background Several mathematical and statistical methods have been proposed in the last few years to analyze microarray data. Most of those methods involve complicated formulas, and software implementations that require advanced computer programming skills. Researchers from other areas may experience difficulties when they attempting to use those methods in their research. Here we present an user-friendly toolbox which allows large-scale gene expression analysis to be carried out by biomedical researchers with limited programming skills. Results Here, we introduce an user-friendly toolbox called GEDI (Gene Expression Data Interpreter), an extensible, open-source, and freely-available tool that we believe will be useful to a wide range of laboratories, and to researchers with no background in Mathematics and Computer Science, allowing them to analyze their own data by applying both classical and advanced approaches developed and recently published by Fujita et al. Conclusion GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us. It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations. Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology.

User friendly guide for rehabilitation or strengthening of bridge structures using fiber reinforced polymer composites

A worldwide interest is being generated in the use of fibre reinforced polymer composites (FRP) in rehabilitation of reinforced concrete structures. As a replacement for the traditional steel plates or external post-tensioning in strengthening applications, various types of FRP plates, with their high strength to weight ratio and good resistance to corrosion, represent a class of ideal material in external retrofitting. Within the last ten years, many design guidelines have been published to provide guidance for the selection, design and installation of FRP systems for external strengthening of concrete structures. Use of these guidelines requires understanding of a number of issues pertaining to different properties and structural failure modes specific to these materials. A research initiative funded by the CRC for Construction Innovation was undertaken (primarily at RMIT) to develop a decision support tool and a user friendly guide for use of fibre reinforced polymer composites in rehabilitation of concrete structures. The user guidelines presented in this report were developed after industry consultation and a comprehensive review of the state of the art technology. The scope of the guide was mainly developed based on outcomes of two workshops with Queensland Department of Main Roads (QDMR). The document covers material properties, recommended construction requirements, design philosophy, flexural, shear and torsional strengthening of beams and strengthening of columns. In developing this document, the guidelines published on FIB Bulletin 14 (2002), Task group 9.3, International Federation of Structural Concrete (FIB) and American Concrete Institute Committee 440 report (2002) were consulted in conjunction with provisions of the Austroads Bridge design code (1992) and Australian Concrete Structures code AS3600 (2002). In conclusion, the user guide presents design examples covering typical strengthening scenarios.

Using user-friendly telecommunications to improve cardiac and diabetes self-management programme : a pilot study

Previous studies exploring the incidence and readmission rates of cardiac patients admitted to a coronary care unit (CCU) with type 2 diabetes [1] have been undertaken by the first author. Interviews of these patients regarding their experiences in managing their everyday conditions [2] provided the basis for developing the initial cardiac–diabetes self-management programme (CDSMP) [3]. Findings from each of these previous studies highlighted the complexity of self-management for patients with both conditions and contributed to the creation of a new self-management programme, the CDSMP, based on Bandura’s (2004) self-efficacy theory [4]. From patient and staff feedback received for the CDSMP [3], it became evident that further revision of the programme was needed to improve self-management levels of patients and possibility of incorporating methods of information technology (IT). Little is known about the applicability of different methods of technology for delivering self-management programmes for patients with chronic diseases such as those with type 2 diabetes and cardiac conditions. Although there is some evidence supporting the benefits and the great potential of using IT in supporting self-management programmes, it is not strong, and further research on the use of IT in such programmes is recommended [5–7]. Therefore, this study was designed to pilot test feasibility of the CDSMP incorporating telephone and text-messaging as follow-up approaches.

Elicitator : a user-friendly, interactive tool to support scenario-based elicitation of expert knowledge

Expert elicitation is the process of determining what expert knowledge is relevant to support a quantitative analysis and then eliciting this information in a form that supports analysis or decision-making. The credibility of the overall analysis, therefore, relies on the credibility of the elicited knowledge. This, in turn, is determined by the rigor of the design and execution of the elicitation methodology, as well as by its clear communication to ensure transparency and repeatability. It is difficult to establish rigor when the elicitation methods are not documented, as often occurs in ecological research. In this chapter, we describe software that can be combined with a well-structured elicitation process to improve the rigor of expert elicitation and documentation of the results

From impact assessment to user-friendly risk management decision-making

In earlier cultures and societies, hazards and risks to human health were dealt with by methods derived from myth, metaphor and ritual. In modem society however, notions of hazard and risk have been transformed from the level of a folk discourse to that of an expert centred concept (Plough & Krimsky, 1987). With the professionalization of risk and hazard analysis came a preferred framework for decision making based on a range of 'technical' methodologies (Giere, 1991 ). This is especially true for decision processes relating to risk assessment and management, and impact assessment. Such approaches however, often entail narrow technical-based theoretical assumptions about human behaviour and the natural world, and the· methods used. They therefore carry 'in-built' error factors that contribute considerable uncertainty to the results.

An economical, adaptable and user-friendly drip-perfusion bioreactor system designed for in vitro three dimensional cell culturing

This research project investigated a bioreactor system capable of high density cell growth intended for use in regenerative medicine and protein production. The bioreactor was based on a drip-perfusion concept and constructed with minimal costs, readily available components, and straightforward processes for usage. This study involved the design, construction, and testing of the bioreactor where the results showed promising three dimensional cell growth within a polymer structure. The accessibility of this equipment and the capability of high density, three dimensional cell growth would be suitable for future research in pharmaceutical drug manufacturing, and human organ and tissue regeneration.

Using resource discovery techniques to create a user friendly web presence

Implementing resource discovery techniques at the Museum of English Rural Life and Special Collections, University of Reading Using resource discovery techniques to create a user friendly web presence

Development of user-friendly, high throughput screening for ligands and inhibitors of carbohydrate modifying enzymes

This paper describes the impact of cloud computing and the use of GPUs on the performance of Autodock and Gromacs respectively. Cloud computing was applicable to reducing the ‘‘tail’’ seen in running Autodock on desktop grids and the GPU version of Gromacs showed significant improvement over the CPU version. A large (200,000 compounds) library of small molecules, seven sialic acid analogues of the putative substrate and 8000 sugar molecules were converted into pdbqt format and used to interrogate the Trichomonas vaginalis neuraminidase using Autodock Vina. Good binding energy was noted for some of the small molecules (~-9 kcal/mol), but the sugars bound with affinity of less than -7.6 kcal/mol. The screening of the sugar library resulted in a ‘‘top hit’’ with a-2,3-sialyllacto-N-fucopentaose III, a derivative of the sialyl Lewisx structure and a known substrate of the enzyme. Indeed in the top 100 hits 8 were related to this structure. A comparison of Autodock Vina and Autodock 4.2 was made for the high affinity small molecules and in some cases the results were superimposable whereas in others, the match was less good. The validation of this work will require extensive ‘‘wet lab’’ work to determine the utility of the workflow in the prediction of potential enzyme inhibitors.

Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract part of this information but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIY ABC) for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIY ABC can be used to compare competing scenarios, estimate parameters for one or more scenarios and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real dataset, both with complex evolutionary scenarios, illustrates the main possibilities of DIY ABC.

User-friendly free-text keystroke dynamics authentication for practical applications

This paper introduces a novel approach for free-text keystroke dynamics authentication which incorporates the use of the keyboard’s key-layout. The method extracts timing features from specific key-pairs. The Euclidean distance is then utilized to find the level of similarity between a user’s profile data and his/her test data. The results obtained from this method are reasonable for free-text authentication while maintaining the maximum level of user relaxation. Moreover, it has been proven in this study that flight time yields better authentication results when compared with dwell time. In particular, the results were obtained with only one training sample for the purpose of practicality and ease of real life application.

Toward highly available, self-healing, adaptable, grid-like and user friendly nondedicated clusters

The human body was used to illustrate an Autonomic Computing system that possesses self-knowledge, self-configuration, self-optimization, self-healing, and self-protection, knowledge of its environment and user friendliness properties. Autonomic Computing was identified by IBM as one of the Grand Challenges. Many researchers and research groups have responded positively to the challenge by initiating research around one or two of the characteristics
identified by IBM as the requirements for Autonomic Computing. One of the areas that could benefit from the comprehensive approach created by the Autonomic Computing vision is parallel processing on nondedicated clusters. This paper shows a general design of services and initial implementation of a system that moves parallel processing on clusters to the computing mainstream using the Autonomic Computing vision.

Knowledge change regarding osteoporosis prevention: translating recommended guidelines into user-friendly messages within a community forum.

Osteoporosis is a skeletal disorder characterised by low bone mineral density and increased fracture risk. Nationally the total costs of this chronic disease are currently estimated at $2.754 billion annually. Effective public health messages providing clear recommendations are vital in supporting prevention efforts. This research aimed to investigate knowledge change associated with the translation of preventive guidelines into accessible messages for the community.