Design of a grid service-based platform for in silico protein-ligand screenings

Grid computing offers the powerful alternative of sharing resources on a worldwide scale, across different institutions to run computationally intensive, scientific applications without the need for a centralized supercomputer. Much effort has been put into development of software that deploys legacy applications on a grid-based infrastructure and efficiently uses available resources. One field that can benefit greatly from the use of grid resources is that of drug discovery since molecular docking simulations are an integral part of the discovery process. In this paper, we present a scalable, reusable platform to choreograph large virtual screening experiments over a computational grid using the molecular docking simulation software DOCK. Software components are applied on multiple levels to create automated workflows consisting of input data delivery, job scheduling, status query, and collection of output to be displayed in a manageable fashion for further analysis. This was achieved using Opal OP to wrap the DOCK application as a grid service and PERL for data manipulation purposes, alleviating the requirement for extensive knowledge of grid infrastructure. With the platform in place, a screening of the ZINC 2,066,906 compound "drug-like" subset database against an enzyme's catalytic site was successfully performed using the MPI version of DOCK 5.4 on the PRAGMA grid testbed. The screening required 11.56 days laboratory time and utilized 200 processors over 7 clusters.     

Indoor robot gardening: design and implementation

This paper describes the architecture and implementation of a distributed autonomous gardening system with applications in urban/indoor precision agriculture. The garden is a mesh network of robots and plants. The gardening robots are mobile manipulators with an eye-in-hand camera. They are capable of locating plants in the garden, watering them, and locating and grasping fruit. The plants are potted cherry tomatoes enhanced with sensors and computation to monitor their well-being (e.g. soil humidity, state of fruits) and with networking to communicate servicing requests to the robots. By embedding sensing, computation, and communication into the pots, task allocation in the system is de-centrally coordinated, which makes the system scalable and robust against the failure of a centralized agent. We describe the architecture of this system and present experimental results for navigation, object recognition, and manipulation as well as challenges that lie ahead toward autonomous precision agriculture with multi-robot teams.     

A new framework for understanding educational digital library use: re-examining digital divides in U.S. schools

Despite their decade of deployment, educational digital libraries have not achieved sustained use in elementary and secondary schools in the United States. Barriers to accessing the Internet and computers have been widely targeted by myriad initiatives, but efforts aimed at bridging this first-level “digital divide” have not led to increased use of the Internet and digital library resources in U.S. classrooms. In fact, such programs have revealed additional divides that affect educators’ use. This paper examines the additional digital divide levels and proposes a new framework for understanding technology innovation in schools that can improve development and outreach approaches by digital library developers.     

Graph visualization and navigation in information visualization: Asurvey

This is a survey on graph visualization and navigation techniques, as used in information visualization. Graphs appear in numerous applications such as Web browsing, state-transition diagrams, and data structures. The ability to visualize and to navigate in these potentially large, abstract graphs is often a crucial part of an application. Information visualization has specific requirements, which means that this survey approaches the results of traditional graph drawing from a different perspective     

Configuration Maintenance for Distributed Applications Management

The MANDAS project has defined a layered architecture for the management of distributed applications. In this paper we examine a vertical slice of this architecture, namely the management applications and services related to configuration management. We introduce an information model which captures the configuration information for distributed applications and discuss a repository service based on the model. We define a set of services and management applications to support maintenance of configuration information, and describe how the different types of configuration information are collected. Finally, we present two management applications that use configuration information.     

An Exploratory Study: Supporting Collaborative Multimedia Systems Design

Multimedia systems design generally requires a collaborative effort from a group of designers with a variety of backgrounds and tasks, such as content experts, instructional designers, media specialists, users, and so forth. However, currently available design tools on the market are mainly designed for a single user. Tools intended to support a collaborative design process should coordinate independent activities of individual designers.This research investigated support for work groups engaged in designing multimedia systems. Specifically, it discussed a new collaborative design environment, called the KMS (Knowledge Management System)-based design environment, in which multimedia designers could share their design knowledge freely. Through two experimental groups, the research investigated impacts of the KMS-based design environment on their collaborative design activities (knowledge creating, knowledge securing, knowledge distributing, and knowledge retrieving activities). The research findings showed that the KMS-based design environment was a promising environment for collaborative multimedia systems design. More specifically, the research findings indicated that the KMS-based design environment supported creating, securing, and retrieving knowledge, but it did not support distributing knowledge. In addition, the research found that the social interactions between group members played important roles in the success of the collaborative multimedia systems design and that the KMS-based design environment did not support the socialization of group members. Furthermore, the research found that the inability of the KMS-based design environment to support the socialization was linked to its low performance level in supporting the knowledge distributing activity. The research explored the desired features of a collaborative support tool for multimedia systems design.     

Gaussian beam ray-equivalent modeling and optical design

It is shown that the propagation and transformation of a simply astigmatic Gaussian beam by an optical system with a characteristic ABCD matrix can be modeled by relatively simple equations whose terms consist solely of the heights and slopes of two paraxial rays. These equations are derived from the ABCD law of Gaussian beam transformation. They can be used in conjunction with a conventional automatic optical design program to design and optimize Gaussian beam optical systems. Several design examples are given using the CODE-V optical design package.     

SPAWNING OF THE ENDANGERED AUSTRALIAN LUNGFISH (NEOCERATODUS FORSTERI) IN A HEAVILY REGULATED RIVER: A PULSE FOR LIFE

The Australian lungfish is an endangered native species currently protected under various state, federal and international agreements. Scarce information on their early life history is available due to the absence of juveniles collected in the wild. This has led to concerns about the sustainability of the species and become a driver for the conservation effort for Australian lungfish. This study aimed to consolidate knowledge on the critical hydraulic habitat requirements of this species within a water resource management context. In this study, spawning of Australian lungfish was found to be a seasonal strategy that is highly reliant on a variable low‐flow regime within riverine habitat. Suitable conditions for spawning were characterized by small flow events in early‐to‐mid spring when water temperatures are between 18 and 28 °C, leading to oviposition on short dense macrophytes in shallow water. Importantly, many of the key environmental factors driving the ecological response are manageable through existing water resource infrastructure. Specifically, releases from water storages within the current distribution of Australian lungfish should mimic the natural inflow and temperature regime within the spawning period, and also provide suitable riverine habitat within projected full supply limits. Copyright © 2012 John Wiley & Sons, Ltd.     

Negative cognitive styles, dysfunctional attitudes, and the remitted depression paradigm: A search for the elusive cognitive vulnerability to depression factor among remitted depressives.

Results from studies using a behavioral high-risk design and approximations to it generally have corroborated the cognitive vulnerability hypothesis of depression, whereas results from remitted depression studies typically have not. Suspecting that design features of previously conducted remitted designs likely precluded them from detecting maladaptive cognitive patterns, the authors conducted a study featuring the remitted design that has been successful in studies of a biological vulnerability for depression. Participants' current depressive symptoms, negative cognitive styles (hopelessness theory), dysfunctional attitudes (Beck's theory), and lifetime prevalence of clinically significant depression were assessed. Participants who had remitted from an episode of clinically significant depression had more negative cognitive styles, but not greater levels of dysfunctional attitudes, than did never depressed individuals. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Conditional phase-type distributions for modelling patient length of stay in hospital

The proportion of elderly in the population is continuing to increase, placing additional demands on highly competitive medical budgets. The management of the care of the elderly within hospitals can be assisted by the accurate modelling of the length of stay of patients in hospital. This paper uses conditional phase‐type distributions for modelling the length of stay of a group of elderly patients in hospital. The model incorporates the use of Bayesian belief networks with Coxian phase‐type distributions, a special type of Markov model that describes the duration of stay in hospital as a process consisting of a sequence of latent phases. The incorporation of the Bayesian belief network in the model permits the inclusion of additional patient information which may provide a better understanding of the system, in particular the incorporation of any potential causal information that may exist in the data.