Group items tagged

Our community guide allows you to set up your own MPI (Message Passing Interface) based supercomputer cluster with the Playstation 3. This guide was co-written by Gaurav Khanna, based on his previous work on the Gravity Grid and is a current run-time environment for the research of co-author (Chris Poulin), based on his current work in distributed pattern recognition. As such, we currently utilize the Fedora Core for this infrastructure and illustrate a "how-to" below. NOTE: We focus on the Fedora 8 distribution, due to prevalence of Fedora and its Cell SDK (3.0) compatibility. Finally, this content should be considered open source, and here is the license.

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc.

The advent of the World Wide Web has led to an explosion in the number of diverse resources available to neuroscientists. Despite the availability of powerful search engines, locating these diverse resources has become increasingly difficult and time consuming. The NIF project utilizes both advanced machine-based search technologies and old-fashioned human legwork to provide access to neuroscience-relevant resources on the Web. Resources include research materials, Web pages, software tools, data sets, literature and general information. The NIF has developed technologies that allow a user to search across these different types of resources, all from a single interface. A unique feature of the NIF is the ability to issue direct queries against multiple databases simultaneously, retrieving content that is largely hidden from traditional search engines. A second unique feature is an extensive vocabulary covering major neuroscience domains for describing and searching these resources. The NIF takes advantage of advances in knowledge engineering to broaden and refine searches based on related concepts. The NIF beta test site was developed to gain feedback on the NIF search interface and content. Users will be asked to search the NIF, explore the vocabularies, and answer a questionnaire about their experience.

We are focused on providing tools to our users to ensure that they can add information of interest to structure-based records in ChemSpider. We have introduced DOI-based associations recently allowing users to connect publications of interest to chemical compounds on our database. The process is simple. Find the structure record of interest, use the Add DOI function and Publish. The process is outlined graphically below.

Existing studies on BitTorrent systems are single-torrent based, while more than 85% of all peers participate in multiple torrents according to our trace analysis. In addition, these studies are not sufficiently insightful and accurate even for single-torrent models, due to some unrealistic assumptions. Our analysis of representative BitTorrent traffic provides several new findings regarding the limitations of BitTorrent systems: (1) Due to the exponentially decreasing peer arrival rate in reality, service availability in such systems becomes poor quickly, after which it is difficult for the file to be located and downloaded. (2) Client performance in the BitTorrent-like systems is unstable, and fluctuates widely with the peer population. (3) Existing systems could provide unfair services to peers, where peers with high downloading speed tend to download more and upload less. In this paper, we study these limitations on torrent evolution in realistic environments. Motivated by the analysis and modeling results, we further build a graph based multi-torrent model to study inter-torrent collaboration. Our model quantitatively provides strong motivation for inter-torrent collaboration instead of directly stimulating seeds to stay longer. We also discuss a system design to show the feasibility of multi-torrent collaboration.

SWAN (Semantic Web Applications in Neuromedicine) is a Web-based collaborative program that aims to organize and annotate scientific knowledge about Alzheimer disease (AD) and other neurodegenerative disorders. Its goal is to facilitate the formation, development and testing of hypotheses about the disease. The ultimate goal of this project is to create tools and resources to manage the evolving universe of data and information about AD in such a way that researchers can easily comprehend their larger context ("what hypothesis does this support or contradict?"), compare and contrast hypotheses ("where do these two hypotheses agree and disagree?"), identify unanswered questions and synthesize concepts and data into ever more comprehensive and useful hypotheses and treatment targets for this disease. The SWAN project is designed to allow the community of AD researchers to author, curate and connect a diversity of data and ideas about AD via secure personal and public SWAN workspaces, using the emerging Semantic Web paradigm for deep interconnection of data, information and knowledge. We are initially focusing on developing a fully public Web resource deployed as part of the Alzheimer Research Forum web site (www.alzforum.org). After the public resource has been launched, we will also develop secure personal workspaces (MySWAN) and semi-private lab workspaces (LabSWAN). An essential component of this project is development of an initial, core knowledge base within SWAN, which will provide immediate value to researchers at the time of deployment. This is a critically important part of our strategy to ensure that the SWAN system gains wide adoption and active participation by the AD research community. As part of our development strategy, we are also recruiting a "beta test" community of AD researchers to enter their own hypotheses, add commentaries and citations, and provide feedback on the technology and content. SWAN is being developed by a collaborative team from

Generates an HTML page including a Processing.js visualization based on entered or remote source code.

mobibot is the #mobitopia IRC channel bot. It is built on Paul Mutton's PircBot Java-based Framework. mobibot is making extensive use of various open source libraries, including: * Commons CLI * Commons HTTPClient * Commons Logging * Commons Net * delicious-java * Google Tag Library * JWeather * MathEvaluator * Rome * Apache XML-RPC * Twitter4J mobibot was written by Erik C. Thauvin as a replacement for the channel's original ChumpBot. Features mobibot's main functionality is to capture URLs posted on the channel. The URLs are automatically gathered into a publishable RSS feed. Other features include: * Performing calculations * Converting between currencies * Rolling dice * Performing Google searches * Displaying the latest entries on Mobitopia * Performing DNS lookups * Recapping public channel messages * Performing Google spelling queries * Retrieving stock quotes * Displaying the time in various time zones * Listing the users on the channel * Displaying weather information * Posting to Jaiku's #mobitopia channel * Posting to Twitter Some of the internal features include RSS feed backlogs, rolling logs, debugging toggle and much more. If you have any feature suggestions, please post them to the mobibot wiki.

What is WebcamStudio? Your own TV studio in your computer for broadcasting thru a virtual webcam. Mix multiple video source as webcams, movies, images, your desktop and log in your prefered video streaming site like Stikam or BlogTV and start your own show or video blog with: - Cool Special Effects - Text overlay - Video Source transition/rotation/movement... - Animations and Faces! - A webcam at your own image See the features! Why for GNU/Linux? Because there are no solution for Linux and Windows users already have acces to this kind of software. And mostly because I use a lot of Linux technologies that are not available under Microsoft Windows. (Sorry guys!) Based on... * Gstreamer libraries and plugins * gstreamer-java libraries * Java 6 (from Sun)

The Neuroscience Information Framework (NIF) is a dynamic inventory of web-based neurosciences data, resources, and tools that scientists and students can access via any computer connected to the Internet. An initiative of the NIH Blueprint for Neuroscience Research, the NIF will advance neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment.

Through its resource registry and concept based query system, NIF enhances neuroscience research by enabling discovery and access to research data and tools worldwide.

If required, entire databases can be downloaded from our FTP site in a variety of formats, from flat files to MySQL dumps. Please be aware that these files can run to many gigabytes of data. To facilitate storage and download all databases are GNU Zip (gzip, *.gz) compressed. Please note: Ensembl supports downloading of many correlation tables via the highly customisable BioMart data mining tool. You may find exploring this web-based data mining tool easier than extracting information from our database dumps.

his meeting was about "Making the Web Work for Science and the Impact of e-Science and the Cyberinfrastructure." I provided an overview of how access to information has changed over the past 20 years for me. I talked about the challenges for publishers serving the chemistry community and how their business models are being challenged and how I empathize with the struggle to figure out how to deal with it. I talked about quality and how care must be taken when using information online. We are ALL challenged with errors - whether you consider PubChem, ChemSpider, Wikipedia or any of the other online databases they all have errors - how do you find them? Some of them are obvious and I pointed to obvious examples in the talk. I hoped to educate the attendees in regards to the value of InChI which, while not a perfect fit yet, is a great start to structure-based communication of chemistry. I publicly blessed the efforts of publishers such as the RSC and Nature Publishing group for the efforts they are making to support InChI and improve the quality of document presentation online. I blessed CAS as a treasure trove of information and the gold standard of curated chemistry. We need them all to be successful for the sake of our science. The challenge is how to fit into the ongoing proliferation of free access to information without modifying the business models.

This semantic wiki at OpenResearch.org aims at making the world of science more visible and accessible. Everybody can add his favorite events (e.g. conferences and workshops), co-workers, tools / datasets, community fora or journals. Pooled together these pieces of information constitute a vast knowledge base about who and what moves science forward.

WikiGenes is the first wiki system to combine the collaborative and largely altruistic possibilities of wikis with explicit authorship. In view of the extraordinary success of Wikipedia there remains no doubt about the potential of collaborative publishing, yet its adoption in science has been limited. Here I discuss a dynamic collaborative knowledge base for the life sciences that provides authors with due credit and that can evolve via continual revision and traditional peer review into a rigorous scientific

This FUSE-base VFS (Virtual FileSystem) enables all programs to look inside archived or compressed files, or access remote files without recompiling the programs or changing the kernel. At the moment it supports floppies, tar and gzip files, zip, bzip2, ar and rar files, ftp sessions, http, webdav, rsh/rcp, ssh/scp. Quite a few other handlers are implemented with the Midnight Commander's external FS.

BioMart is a query-oriented data management system developed jointly by the Ontario Institute for Cancer Research (OiCR) and the European Bioinformatics Institute (EBI). The system can be used with any type of data and is particularly suited for providing 'data mining' like searches of complex descriptive data. BioMart comes with an 'out of the box' website that can be installed, configured and customised according to user requirements. Further access is provided by graphical and text based applications or programmatically using web services or API written in Perl and Java. BioMart has built-in support for query optimisation and data federation and in addition can be configured to work as a DAS 1.5 Annotation server. The process of converting a data source into BioMart format is fully automated by the tools included in the package. Currently supported RDBMS platforms are MySQL, Oracle and Postgres. BioMart is completely Open Source, licensed under the LGPL, and freely available to anyone without restrictions.

ChemSpider is a free access service providing a structure centric community for chemists. Providing access to millions of chemical structures and integration to a multitude of other online services ChemSpider is the richest single source of structure-based chemistry information.