BackgroundThe Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types.ResultsThe work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here.ConclusionsAvogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.

We present a comprehensive approach to using electronic medical records (EMR) for constructing contact networks of healthcare workers in a hospital. This approach is applied at the University of Iowa Hospitals and Clinics (UIHC) – a 3.2 million square foot facility with 700 beds and about 8,000 healthcare workers – by obtaining 19.8 million EMR data points, spread over more than 21 months. We use these data to construct 9,000 different healthcare worker contact networks, which serve as proxies for patterns of actual healthcare worker contacts. Unlike earlier approaches, our methods are based on large-scale data and do not make any a priori assumptions about edges (contacts) between healthcare workers, degree distributions of healthcare workers, their assignment to wards, etc. Preliminary validation using data gathered from a 10-day long deployment of a wireless sensor network in the Medical Intensive Care Unit suggests that EMR logins can serve as realistic proxies for hospital-wide healthcare worker movement and contact patterns. Despite spatial and job-related constraints on healthcare worker movement and interactions, analysis reveals a strong structural similarity between the healthcare worker contact networks we generate and social networks that arise in other (e.g., online) settings. Furthermore, our analysis shows that disease can spread much more rapidly within the constructed contact networks as compared to random networks of similar size and density. Using the generated contact networks, we evaluate several alternate vaccination policies and conclude that a simple policy that vaccinates the most mobile healthcare workers first, is robust and quite effective relative to a random vaccination policy.

Aid administration is characterised by high moral objectives and often frustratingly low achievements. This article explores the idea that the problem lies not in inadequate policy or instruments as such but in the thinking processes that emerge within policy circles, at delivery levels within aid administration and at the interface between donor and recipient, to which the trade likes to apply the notion of ‘partnership’. Cultural Theory identifies three distinct and often contradictory ways of thinking that reflect individualist, group and hierarchical value premises. It is adopted here to explore how these types of thinking apply within aid administration, finding that the policy process is a surprisingly ‘groupie’ kind of activity, emphasising the sharing of values and understandings within donor circles. Delivery agents (donor field offices) by contrast are under hierarchical pressure to turn the outcomes into packaged deliverables, whether the ‘good’ is packageable or not. Supported by NPM orthodoxies, these agents seek control through linear programming and performance monitoring. A third contradiction is revealed when the donor attempts to bring such packages into a partnership relationship with recipient governments. Partnership is about sharing and dealing. But what the recipient is offered is a package with Henry Ford type characteristics: ‘any colour you like (social aspiration), as long as it is black (PRSP formula)’. The article is biased; from the perspective of a consultant caught in the middle; but if there is truth in the findings it might just open the door to new styles of aid relationship and novel delivery vehicles. Copyright © 2004 John Wiley & Sons, Ltd.

Government-donor relations in Bangladesh are shaped by a history of donor dependence and reaction against it. Sustained growth, substantial social sector achievements and a growing proportion of the investment budget serviced from national resources now gives the government confidence and increasing room for manoeuvre. But many in Bangladesh see donor pressure for public sector reform as a sign of low government ownership and a loss of sovereignty in economic management. Donor policies can be seen as a result of 'group think' at the top level of agencies, leading to the perception that donors are 'ganging up' on the government. Each donor, at implementation level, tends to demand compliance, leaving little room for local interpretation of needs. On the government side the centre-perceiving itself to be weak and subject to sustained criticism-tries to keep a hold on funds and programmes, leaving little room for manoeuvre or discretion on the part of programme-level officers. The resultant tension between the government and the donor community underlies aid management relationships and stands in contrast to the language of partnership that donors these days propose. This article reviews the concerns of Bangladesh government officials managing aid in regard to donor practices, particularly the difficulties that they perceive in donor conditionality; and donors' seemingly poor appreciation of the government's systems, priorities and limited capacity. Donor perspectives on the other hand are conditioned by the ever-changing value imperatives of aid as well as the ever-present need to disburse. Experience with the Local Consultative Group, a donor side initiative to build partnership, illustrates the theme.

This paper describes a spatial model for healthcare workers' location in a large hospital facility. Such models have many applications in healthcare, such as supporting timeand-motion efficiency studies to improve healthcare delivery, or modeling the spread of hospital-acquired infections. We use our model to estimate spatial distributions for healthcare workers in The University of Iowa Hospitals and Clinics (UIHC), a 700-bed comprehensive academic medical center spanning a total of 3.2 million square feet and employing about 8,000 healthcare workers. We model the UIHC as a metric space induced by walking distance between pairs of rooms, and with each room having a level of attractiveness representing the activity level in that room. We combine this with a model in which each healthcare worker has a center of activity and a probability density function that decays polynomially as we move away from the center. Using 12 million Electronic Medical Record (EMR) logins collected over 22 months, we solve for the model parameters for each room and each healthcare worker using heuristic techniques to make the problem computationally tractable. We then validate the model parameters obtained by comparing realworld expectations of healthcare worker behavior for several job categories to our model predictions (e.g., we verify that Unit Clerks are much more stationary than Respiratory Therapists). Finally we present solutions to two important applications. First, we use healthcare worker spatial distributions to generate random walks representing their movement through the hospital. We use these random walks to construct healthcare worker contact networks in order to study the spread of hospital-acquired infections. Second, using the healthcare worker spatial distributions, we find a near-optimal placement of hospital resources which minimizes the average distance a healthcare worker has to travel to access that resource.