Understanding the role of scale is critical to ecologists' ability to make appropriate measurements, to ''scale up'' from local, short-term experiments to larger areas and longer times, to formulate models of community structure, and to address important conservation problems. Although these issues have received increased attention in recent years, empirical measurements of the scales of ecologically important variables are still rare. Here, we measure the spatial and temporal scales of variability of 15 ecologically relevant physical and biological processes in the wave-swept intertidal zone at Mussel Point, near Hopkins Marine Station in California. We analyze temporal variability in wave height, ocean temperature, upwelling intensity, solar irradiance, and body temperature for periods ranging from ten minutes to fifty years. In addition, we measure spatial variation in shoreline topography, wave force, wave-induced disturbance, body temperature, species diversity, recruitment, primary productivity, and the abundances of grazers, predators, and the competitive dominant occupier of space. Each of these spatial variables is measured along three horizontal transects in the upper intertidal zone: a short transect (44 m long with sampling locations spaced at ϳ0.5-m intervals), a medium transect (175 m long with sampling locations spaced at ϳ1.7-m intervals), and a long transect (334 m long with sampling locations spaced at ϳ3.4-m intervals). Six different methods are used to quantify the scale of each variable.Distinct scales are evident in all but one of our temporal variables, demonstrating that our methods for quantifying scale can work effectively with relatively simple, periodic phenomena. However, our spatial results reveal basic problems that arise when attempting to measure the scale of variability for more complex phenomena. For a given variable and length of transect, different methods of calculating scale seldom agree, and in some cases estimates differ by more than an order of magnitude. For a given variable and method of calculating spatial scale, measurements are sensitive to the length of a transect; the longer the transect, the larger the estimate of scale. We propose that the ''1/f noise'' nature of the data can explain both the variability among methods for calculating scale and the length dependence of spatial scales of variation, and that the 1/f noise character of the data may be driven by the fractal geometry of shoreline topography. We conclude that it may not be possible to define a meaningful spatial scale of variation in this system. As an alternative to the boiled-down concept of ''scale,'' we suggest that it is more appropriate to examine explicitly the pattern in which variability changes with the extent of measurement (e.g., the spectrum). Knowledge of this pattern can provide useful ecological scaling ''rules'' even when a well-defined scale (or hierarchy of scales) cannot be discerned.

BackgroundBroad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely.ResultsTo meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment.Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350 organizations. It tracks roughly 27,000 assay runs, 860,000 specimen vials and 1,300,000 vial transfers.ConclusionsSharing data, analysis tools and infrastructure can speed the efforts of large research consortia by enhancing efficiency and enabling new insights. The Atlas installation of LabKey Server demonstrates the utility of the LabKey platform for collaborative research. Stable, supported builds of LabKey Server are freely available for download at http://www.labkey.org. Documentation and source code are available under the Apache License 2.0.

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BackgroundMultiple types of assays allow sensitive detection of virus-specific neutralizing antibodies. For example, the extent of antibody neutralization of HIV-1, SIV and SHIV can be measured in the TZM-bl cell line through the degree of luciferase reporter gene expression after infection. In the past, neutralization curves and titers for this standard assay have been calculated using an Excel macro. Updating all instances of such a macro with new techniques can be unwieldy and introduce non-uniformity across multi-lab teams. Using Excel also poses challenges in centrally storing, sharing and associating raw data files and results.ResultsWe present LabKey Server's NAb tool for organizing, analyzing and securely sharing data, files and results for neutralizing antibody (NAb) assays, including the luciferase-based TZM-bl NAb assay. The customizable tool supports high-throughput experiments and includes a graphical plate template designer, allowing researchers to quickly adapt calculations to new plate layouts. The tool calculates the percent neutralization for each serum dilution based on luminescence measurements, fits a range of neutralization curves to titration results and uses these curves to estimate the neutralizing antibody titers for benchmark dilutions. Results, curve visualizations and raw data files are stored in a database and shared through a secure, web-based interface. NAb results can be integrated with other data sources based on sample identifiers. It is simple to make results public after publication by updating folder security settings.ConclusionsStandardized tools for analyzing, archiving and sharing assay results can improve the reproducibility, comparability and reliability of results obtained across many labs. LabKey Server and its NAb tool are freely available as open source software at http://www.labkey.com under the Apache 2.0 license. Many members of the HIV research community can also access the LabKey Server NAb tool without installing the software by using the Atlas Science Portal (https://atlas.scharp.org). Atlas is an installation of LabKey Server.