BACKGROUND: Detection and preventing entry of exotic viruses and viroids at the border is critical for protecting plant industries trade worldwide. Existing post entry quarantine screening protocols rely on time-consuming biological indicators and/or molecular assays that require knowledge of infecting viral pathogens. Plants have developed the ability to recognise and respond to viral infections through Dicer-like enzymes that cleave viral sequences into specific small RNA products. Many studies reported the use of a broad range of small RNAs encompassing the product sizes of several Dicer enzymes involved in distinct biological pathways. Here we optimise the assembly of viral sequences by using specific small RNA subsets. RESULTS: We sequenced the small RNA fractions of 21 plants held at quarantine glasshouse facilities in Australia and New Zealand. Benchmarking of several de novo assembler tools yielded SPAdes using a kmer of 19 to produce the best assembly outcomes. We also found that de novo assembly using 21-25 nt small RNAs can result in chimeric assemblies of viral sequences and plant host sequences. Such non-specific assemblies can be resolved by using 21-22 nt or 24 nt small RNAs subsets. Among the 21 selected samples, we identified contigs with sequence similarity to 18 viruses and 3 viroids in 13 samples. Most of the viruses were assembled using only 21-22 nt long virus-derived siRNAs (viRNAs), except for one Citrus endogenous pararetrovirus that was more efficiently assembled using 24 nt long viRNAs. All three viroids found in this study were fully assembled using either 21-22 nt or 24 nt viRNAs. Optimised analysis workflows were customised within the Yabi web-based analytical environment. We present a fully automated viral surveillance and diagnosis web-based bioinformatics toolkit that provides a flexible, user-friendly, robust and scalable interface for the discovery and diagnosis of viral pathogens. CONCLUSIONS: We have implemented an automated viral surveillance and diagnosis (VSD) bioinformatics toolkit that produces improved viruses and viroid sequence assemblies. The VSD toolkit provides several optimised and reusable workflows applicable to distinct viral pathogens. We envisage that this resource will facilitate the surveillance and diagnosis viral pathogens in plants, insects and invertebrates.

Summary form only given. Bioinformatics is an important application area for grid computing. The grid computing issues required to tackle current bioinformatics challenges include processing power, large-scale data access and management, security, application integration, data integrity and curation, control/automation/tracking of workflows, data format consistency and resource discovery. In this poster, we describe preliminary steps taken to develop a grid environment to advance bioinformatics research. We developed a system called Grendel, with the aims of providing bioinformatics researchers transparent access to basic computational resources used in their research. Grendel is a platform and language independent Web-services based system for distributed resource management utilising Sun Grid Engine that provides a single entry point for computational tasks while keeping the actual resources transparent to the user. Grendel is developed in Java and deployed using the Tomcat. Client libraries have been developed in Perl and Java to provide access to computation resource exported via Grendel.

Discusses the concept of uniform frequency images, which exhibit uniform local frequency properties. Such images make optimal use of space when sampled close to their Nyquist limit. A warping function may be applied to an arbitrary image to redistribute its local frequency content, reducing its highest frequencies and increasing its lowest frequencies in order to approach this uniform frequency ideal. The warped image may then be downsampled according to its new, reduced Nyquist limit, thereby reducing its storage requirements. To reconstruct the original image, the inverse warp is applied. We present a general, top-down algorithm to automatically generate a piecewise-linear warping function with this frequency balancing property for a given input image. The image size is reduced by applying the warp and then downsampling. We store this warped, downsampled image plus a small number of polygons with texture coordinates to describe the inverse warp. The original image is later reconstructed by rendering the associated polygons with the warped image applied as a texture map, a process which is easily accelerated by current graphics hardware. As compared to previous image compression techniques, we generate a similar graceful space-quality tradeoff with the advantage of being able to "uncompress" images during rendering. We report results for several images with sizes ranging from 15,000 to 300,000 pixels, achieving reduction rates of 70-90% with improved quality over downsampling alone.

MOTIVATION: There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. RESULTS: We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.