The DISOPRED server for the prediction of protein disorder

Dynamically disordered regions appear to be relatively abundant in eukaryotic proteomes. The DISOPRED server allows users to submit a protein sequence, and returns a probability estimate of each residue in the sequence being disordered. The results are sent in both plain text and graphical formats, and the server can also supply predictions of secondary structure to provide further structural information.

The PSIPRED protein structure prediction server

The PSIPRED protein structure prediction server allows users to submit a protein sequence, perform a prediction of their choice and receive the results of the prediction both textually via e-mail and graphically via the web. The user may select one of three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version of a widely used transmembrane topology prediction method; or GenTHREADER, a sequence profile based fold recognition method.

The ModFOLD4 server for the quality assessment of 3D protein models

Once you have generated a 3D model of a protein, how do you know whether it bears any resemblance to the actual structure? To determine the usefulness of 3D models of proteins, they must be assessed in terms of their quality by methods that predict their similarity to the native structure. The ModFOLD4 server is the latest version of our leading independent server for the estimation of both the global and local (per-residue) quality of 3D protein models. The server produces both machine readable and graphical output, providing users with intuitive visual reports on the quality of predicted protein tertiary structures. The ModFOLD4 server is freely available to all at: http://www.reading.ac.uk/bioinf/ModFOLD/.

The FunFOLD2 server for the prediction of protein-ligand interactions

The FunFOLD2 server is a new independent server that integrates our novel protein–ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our function prediction software easily accessible to all via a simple web interface and, second, to produce integrated output for predictions that can be easily interpreted. The server provides a clean web interface so that results can be viewed on a single page and interpreted by non-experts at a glance. The output for the prediction is an image of the top predicted tertiary structure annotated to indicate putative ligand-binding site residues. The results page also includes a list of the most likely binding site residues and the types of predicted ligands and their frequencies in similar structures. The protein–ligand interactions can also be interactively visualized in 3D using the Jmol plug-in. The raw machine readable data are provided for developers, which comply with the Critical Assessment of Techniques for Protein Structure Prediction data standards for FN predictions. The FunFOLD2 webserver is freely available to all at the following web site: http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html.

Assessing the quality of modelled 3D protein structures using the ModFOLD server

Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies.Here, we briefly discuss protein tertiary structure prediction, along with the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition and their key role in driving the field of protein model quality assessment methods (MQAPs). We also briefly discuss the top MQAPs from the previous CASP competitions. Additionally, we describe our downloadable and webserver-based model quality assessment methods: ModFOLD3, ModFOLDclust, ModFOLDclustQ, ModFOLDclust2, and IntFOLD-QA. We provide a practical step-by-step guide on using our downloadable and webserver-based tools and include examples of their application for improving tertiary structure prediction, ligand binding site residue prediction, and oligomer predictions.

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/

Upgrading a TCABR data analysis and acquisition system for remote participation using Java, XML, RCP and modern client/server communication/authentication

The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The architecture of the new system uses Java language as programming environment. Since application parameters and hardware in a joint experiment are complex with a large variability of components, requirements and specification solutions need to be flexible and modular, independent from operating system and computer architecture. To describe and organize the information on all the components and the connections among them, systems are developed using the extensible Markup Language (XML) technology. The communication between clients and servers uses remote procedure call (RPC) based on the XML (RPC-XML technology). The integration among Java language, XML and RPC-XML technologies allows to develop easily a standard data and communication access layer between users and laboratories using common software libraries and Web application. The libraries allow data retrieval using the same methods for all user laboratories in the joint collaboration, and the Web application allows a simple graphical user interface (GUI) access. The TCABR tokamak team in collaboration with the IPFN (Instituto de Plasmas e Fusao Nuclear, Instituto Superior Tecnico, Universidade Tecnica de Lisboa) is implementing this remote participation technologies. The first version was tested at the Joint Experiment on TCABR (TCABRJE), a Host Laboratory Experiment, organized in cooperation with the IAEA (International Atomic Energy Agency) in the framework of the IAEA Coordinated Research Project (CRP) on ""Joint Research Using Small Tokamaks"". (C) 2010 Elsevier B.V. All rights reserved.

A load balancing algorithm for web based server grids

Load balance is a critical issue in distributed systems, such as server grids. In this paper, we propose a Balanced Load Queue (BLQ) model, which combines the queuing theory and hydro-dynamic theory, to model load balance in server grids. Base on the BLQ model, we claim that if the system is in the state of global fairness, then the performance of the whole system is the best. We propose a load balanced algorithm based on the model: the algorithm tries its best to keep the system in the global fairness status using job deviation. We present three strategies: best node, best neighbour, and random selection, for job deviation. A number of experiments are conducted for the comparison of the three strategies, and the results show that the best neighbour strategy is the best among the proposed strategies. Furthermore, the proposed algorithm with best neighbour strategy is better than the traditional round robin algorithm in term of processing delay, and the proposed algorithm needs very limited system information and is robust.

High reliability replication technique for Web-server cluster systems

Providing reliable and efficient services are primary goals in designing a web server system. Data replication can be used to improve the reliability of the system. However, mapping mechanism is one of the primary concerns to data replication. In this paper, we propose a mapping mechanism model called enhanced domain name server (E-DNS) that dispatches the user requests through the URL-name to IP-address under Neighbor Replica Distribution Technique (NRDT) to improve the reliability of the system.

Towards the development of a project decision support framework for adoption of an integrated building information model using a model server

This chapter discusses an action research study towards the development of a decision framework to support a fully integrated multi disciplinary Building Information Model (BIM) using a Model Server. The framework was proposed to facilitate multi disciplinary collaborative BIM adoption through, informed selection of a project specific BIM approach and tools contingent upon project collaborators’ readiness, tool capabilities and workflow dependencies. The aim of the research was to explore the technical concerns in relation to Model Servers to support multi disciplinary model integration and collaboration; however it became clear that there were both technical and non technical issues that needed consideration. The evidence also suggests that there are varying levels of adoption which impacts upon further diffusion of the technologies. Therefore the need for a decision framework was identified based on the findings from an exploratory study conducted to investigate industry expectations. The study revealed that even the market leaders who are early technology adopters in the Australian industry in many cases have varying degrees of practical experiential knowledge of BIM and hence at times low levels of confidence of the future diffusion of BIM technology throughout the industry. The study did not focus on the benefits of BIM implementation as this was not the intention, as the industry partners involved are market leaders and early adopters of the technology and did not need convincing of the benefits. Coupled with this there are various other past studies that have contributed to the ‘benefits’ debate. There were numerous factors affecting BIM adoption which were grouped in to two main areas; technical tool functional requirements and needs, and non technical strategic issues. The need for guidance on where to start, what tools were available and how to work through the legal, procurement and cultural challenges was evidenced in the exploratory study. Therefore a BIM decision framework was initiated, based upon these industry concerns. Eight case studies informed the development of the framework and a summary of the key findings is presented. Primary and secondary case studies from firms that have adopted a structured approach to technology adoption are presented. The Framework consists of four interrelated key elements including a strategic purpose and scoping matrix, work process mapping, technical requirements for BIM tools and Model Servers, and framework implementation guide. The BIM framework was presented in draft format again to key industry stakeholders and considered in comparison with current best practice BIM adoption to further validate the framework. There was no request to change any part of the Framework. However, it is an ongoing process and it will be presented again to industry through the various project partners. The Framework may be refined within the boundaries of the action research process as an ongoing activity as more experiential knowledge can be incorporated.