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" Mendeley/PLoS API Binary Battle Build an application with our data, make science more open, win $10,001 and more! What's it all about? PLoS and Mendeley, the popular reference manager and academic social network, teamed up to create a Binary Battle contest to build the best apps that make science more open using PLoS and/or Mendeley's APIs (Application Programming Interface)."

PyBossa is a free, open-source, platform for creating and running crowd-sourcing applications that utilise online assistance in performing tasks that require human cognition, knowledge or intelligence such as image classification, transcription, geocoding and more! Start contributing now "

PyBossa is a free, open-source, platform for creating and running crowd-sourcing applications that utilise online assistance in performing tasks that require human cognition, knowledge or intelligence such as image classification, transcription, geocoding and more!

Results: Participatory health is a growing area with individuals using health social networks, crowdsourced studies, smartphone health applications, and personal health records to achieve positive outcomes for a variety of health conditions. PatientsLikeMe and 23andMe are the leading operators of researcher-organized, crowdsourced health research studies. These operators have published findings in the areas of disease research, drug response, user experience in crowdsourced studies, and genetic association. Quantified Self, Genomera, and DIYgenomics are communities of participant-organized health research studies where individuals conduct self-experimentation and group studies. Crowdsourced health research studies have a diversity of intended outcomes and levels of scientific rigor.s

Complex coupled multi-physics simulations are playing increasingly important roles in scientific and engineering applications such as fusion plasma and climate modeling. At the same time, extreme scales, high levels of concurrency and the advent of multicore and many core technologies are making the high-end parallel computing systems on which these simulations run, hard to program. While the Partitioned Global Address Space (PGAS) languages is attempting to address the problem, the PGAS model does not easily support the coupling of multiple application codes, which is necessary for the coupled multi-physics simulations. Furthermore, existing frameworks that support coupled simulations have been developed for fragmented programming models such as message passing, and are conceptually mismatched with the shared memory address space abstraction in the PGAS programming model. This paper explores how multi-physics coupled simulations can be supported within the PGAS programming framework. Specifically, in this paper, we present the design and implementation of the XpressSpace programming system, which enables efficient and productive development of coupled simulations across multiple independent PGAS Unified Parallel C (UPC) executables. XpressSpace provides the global-view style programming interface that is consistent with the memory model in UPC, and provides an efficient runtime system that can dynamically capture the data decomposition of global-view arrays and enable fast exchange of parallel data structures between coupled codes. In addition, XpressSpace provides the flexibility to define the coupling process in specification file that is independent of the program source codes. We evaluate the performance and scalability of Xpress Space prototype implementation using different coupling patterns extracted from real world multi-physics simulation scenarios, on the Jaguar Cray XT5 system of Oak Ridge National Laboratory.

CyberTracker is the most efficient method of gps field data collection. You can use CyberTracker on a Smartphone or handheld computer to record any type of observation. CyberTracker, which requires no programming skills, allows you to customize an Application for your own data collection needs.

VORPAL enables researchers to simulate complex physical phenomena in less time and at a much lower cost than empirically testing process changes for plasma and vapor deposition processes. VORPAL offers a unique combination of physical models to cover the entire range of plasma simulation problems. Ionization and neutral gas models enable VORPAL to bridge the gap between plasma and neutral flow physics. VORPAL software runs on a wide range of computing platforms, from desktop machines to massively parallel supercomputers with thousands of processors. The use of standard data formats allows data analysis at various levels of sophistication, including your own preferred data analysis tool. VORPAL is used by scientists and engineers to simulate the physical behavior of devices and processes for many industrial and research applications, including laser wakefield accelerators, plasma thrusters, high-power microwave guides, and plasma processing chambers.

This paper describes the design of OpenFOAM, an object- oriented library for Computational Fluid Dynamics (CFD) and struc- tural analysis. Efficient and flexible implementation of complex physi- cal models in Continuum Mechanics is achieved by mimicking the form of partial differential equation in software. The library provides Fi- nite Volume and Finite Element discretisation in operator form and with polyhedral mesh support, with relevant auxiliary tools and sup- port for massively parallel computing. Functionality of OpenFOAM is illustrated on three levels: improvements in linear solver technology with CG-AMG solvers, LES data analysis using Proper Orthogonal Decom- position (POD) and a self-contained fluid-structure interaction solver.

A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes. Since the program utilizes the X-window system and the Motif widget set, it is portable on a wide range of UNIX workstations. The design objective was to provide maximal computer support for the analysis of spectra, while providing the user with complete control over the final resonance assignments. Technically important features of XEASY are the use and flexible visual display of lsquostripsrsquo, i.e., two-dimensional spectral regions that contain the relevant parts of 3D or 4D NMR spectra, automated sorting routines to narrow down the selection of strips that need to be interactively considered in a particular assignment step, a protocol of resonance assignments that can be used for reliable bookkeeping, independent of the assignment strategy used, and capabilities for proper treatment of spectral folding and efficient transfer of resonance assignments between spectra of different types and different dimensionality, including projected, reduced-dimensionality triple-resonance experiments.

Comprehensive protein-protein interaction maps promise to reveal many aspects of the complex regulatory network underlying cellular function. Recently, large-scale approaches have predicted many new protein interactions in yeast. To measure their accuracy and potential as well as to identify biases, strengths and weaknesses, we compare the methods with each other and with a reference set of previously reported protein interactions.

GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web.

The Remote Sensing Information Gateway (RSIG) offers a new way for users to get the multi-terabyte, environmental datasets they want via an interactive, Web browser-based application. A file download and parsing process that now takes months will be reduced via RSIG to minutes.

Widespread use of a comprehensive CI framework has the potential to revolutionize every science and engineering discipline as well as education. Computing power, data volumes, software, and network capacities are all on exponential growth paths. Highly diverse, multidisciplinary collaborations and partnerships are growing dramatically, greatly enabled by new and emerging technologies, spanning multiple agencies and international domains to address complex grand challenge problems. Scientific discovery is being advanced by linking computational facilities and instruments to build highly-capable simulation models, sophisticated algorithms, software, and other tools and services. CIF21 will enable new approaches to research and education - supporting new modalities such as distributed collaborative networks, allowing researchers to more easily adapt to changes in the research and education process, and providing an integrated framework for people, instruments, and tools to address complex problems and conduct multidisciplinary research. CIF21 will consist of secure, geographically distributed, and connected CI: advanced computing facilities, scientific instruments, software environments, advanced networks, data storage capabilities, and the critically important human capital and expertise.

The FES SciDAC portfolio focuses on the development and application of high physics fidelity simulation codes that can advance the fundamental science of magnetically confined plasmas by fully exploiting leadership class computing resources and contribute to the FES goal of developing the predictive capability needed for a sustainable fusion energy source. The specific areas of interest of the Partnerships are: Edge Physics Multiscale Integrated Modeling Materials Science

ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.

The Kepler Project is dedicated to furthering and supporting the capabilities, use, and awareness of the free and open source, scientific workflow application, Kepler. Kepler is designed to help scien­tists, analysts, and computer programmers create, execute, and share models and analyses across a broad range of scientific and engineering disciplines. Kepler can operate on data stored in a variety of formats, locally and over the internet, and is an effective environment for integrating disparate software components, such as merging "R" scripts with compiled "C" code, or facilitating remote, distributed execution of models. Using Kepler's graphical user interface, users simply select and then connect pertinent analytical components and data sources to create a "scientific workflow"-an executable representation of the steps required to generate results. The Kepler software helps users share and reuse data, workflows, and compo­nents developed by the scientific community to address common needs.

New requirements for future users and uses (by Serena Cangiano)