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"EMAPS (Electronic Maps to Assist Public Science) is a collaborative research project aiming at answering in the most innovative way the topic SiS.2011.3.0.6-1 which calls for an assessment of "the opportunities and risks in the use of the web and the social media as a meaningful information tool and for developing a participatory communication between scientists and the different publics". To do that, our proposal focuses first on the emerging uses of the web as a tool of collective endeavor and public debate, then on engaging actors involved in two particular technoscientific issues (aging/life expectancy and climate change adaptation) in an 'open-air' experiment using online interactive platforms that will be designed and developed within the project."

"Unlike many journals which attempt to use the peer review process to determine whether or not an article reaches the level of 'importance' required by a given journal, PLoS ONE uses peer review to determine whether a paper is technically sound and worthy of inclusion in the published scientific record. Once the work is published in PLoS ONE, the broader community is then able to discuss and evaluate the significance of the article (through the number of citations it attracts; the downloads it achieves; the media and blog coverage it receives; and the post-publication Notes, Comments and Ratings that it receives on PLoS ONE etc)."

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.

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.

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.

Since Google Earth hit the Web in 2005, besides instantly turning all office desk globes into decorative accessories, it has opened the world up to global exploration at the click of a mouse. But it's not just a neat toy; some extraordinary things have been discovered with its one-click access to satellite imagery.

Milkyway@Home uses the BOINC platform to harness volunteered computing resources, creating a highly accurate three dimensional model of the Milky Way galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science. In computer science, the project is investigating different optimization methods which are resilient to the fault-prone, heterogeneous and asynchronous nature of Internet computing; such as evolutionary and genetic algorithms, as well as asynchronous newton methods. While in astroinformatics, Milkyway@Home is generating highly accurate three dimensional models of the Sagittarius stream, which provides knowledge about how the Milky Way galaxy was formed and how tidal tails are created when galaxies merge.

DREAM (Dialogue for Reverse Engineering Assessments and Methods) poses fundamental questions about systems biology, and invites participants to propose solutions. The main objective is to catalyze the interaction between theory and experiment, specifically in the area of cellular network inference and quantitative model building. DREAM challenges address how we can assess the quality of our descriptions of networks that underlie biological systems, and of our predictions of the outcomes of novel experiments. These are not simple questions. Researchers have used a variety of algorithms to deduce the structure of biological networks and/or to predict the outcome of perturbations to their systems. They have also evaluated the success of their methodologies using a diverse set of non-standardised metrics. What is still needed, and what DREAM aims to achieve, is a fair comparison of the strengths and weaknesses of these methods and a clear sense of the reliability of the models that researchers create.

Bossa is an open-source software framework for distributed thinking - the use of volunteers on the Internet to perform tasks that use human cognition, knowledge, or intelligence. Bossa minimizes the effort of creating and operating a distributed thinking project.

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

" 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)."

The Ion Proton™ Sequencer, priced at $149,000, is based on the next generation of semiconductor sequencing technology that has made its predecessor, the Ion Personal Genome Machine™ (PGM™), the fastest-selling sequencer in the world. Up to now, it has taken weeks or months to sequence a human genome at a cost of $5,000 to $10,000 using optical-based sequencing technologies. The slow pace and the high instrument cost of $500,000 to $750,000 have limited human genome sequencing to relatively few research labs. Baylor College of Medicine, Yale School of Medicine, and The Broad Institute, have each signed up for multiple Ion Proton™ Sequencers and will be the first customers to adopt this transformative technology.

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.

For the average biologist, hands-on literature mining currently means a keyword search in PubMed. However, methods for extracting biomedical facts from the scientific literature have improved considerably, and the associated tools will probably soon be used in many laboratories to automatically annotate and analyse the growing number of system-wide experimental data sets. Owing to the increasing body of text and the open-access policies of many journals, literature mining is also becoming useful for both hypothesis generation and biological discovery. However, the latter will require the integration of literature and high-throughput data, which should encourage close collaborations between biologists and computational linguists.

In the past decade, there have been remarkable advances in proteomic technologies. Mass spectrometry has emerged as the preferred method for in-depth characterization of the protein components of biological systems. Using mass spectrometry, key insights into the composition, regulation and function of molecular complexes and pathways have been gained. From these studies, it is clear that mass-spectrometry-based proteomics is now a powerful 'hypothesis-generating engine' that, when combined with complementary molecular, cellular and pharmacological techniques, provides a framework for translating large data sets into an understanding of complex biological processes.

"So I thought it might be useful to post a summary of the current state of open access. There's a lot going on, so even though this essay appears lengthy, it's actually a very brief and incomplete summary of what's happening. I have links to further reading at the end."

Explorable Explanations is my umbrella project for ideas that enable and encourage truly active reading. The goal is to change people's relationship with text. People currently think of text as information to be consumed. I want text to be used as an environment to think in.

VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured meshes. VisIt was designed to handle very large data set sizes in the terascale range and yet can also handle small data sets in the kilobyte range. See the table below for more details about the tool's features.

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.