OpenSciInfo

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of 25 million reads per hour on a typical workstation with 2 gigabytes of memory. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: 1.3 GB for the human genome. It supports alignment policies equivalent to Maq and SOAP but is much faster: about 35x faster than Maq and over 350x faster than SOAP when aligning to the human genome.

The establishment of open access literature makes it possible for knowledge to be extracted from scholarly articles and included in other resources. BioLit aims to extract database identifiers and rich meta-data from open access articles in the life sciences and integrate that information with existing biological databases. We have begun prototyping this effort using a clone of the RCSB Protein Data Bank, a database of macromolecular structures.

The world's largest and best Life Science Forum and Scientist's Discusion group

OpenCV is an open source computer vision library originally developed by Intel. It is free for commercial and research use under a BSD license. The library is cross-platform, and runs on Mac OS X, Windows and Linux. It focuses mainly towards real-time image processing, as such, if it finds Intel's Integrated Performance Primitives on the system, it will use these commercial optimized routines to accelerate itself. This implementation is not a complete port of OpenCV. Currently, this library supports : * real-time capture * video file import * basic image treatment (brightness, contrast, threshold, …) * object detection (face, body, …) * blob detection Future versions will include more advanced functions such as motion analysis, object and color tracking, multiple OpenCV object instances … For more information about OpenCV visit the Open Source Computer Vision Library Intel webpage, the OpenCV Library Wiki, and the OpenCV Reference Manual (pdf).

The following are confirmed poster presentations. Note that there is no dedicated poster session for the workshop - there is just one general poster session for the conference. The information below should help you to find the posters relevant to our workshop.

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.

Well, not entirely limited to libraries. Useful stuff for visualization practitioners sounded a little non-specific, though. These are all freely available.

Zotz is a Firefox add-on giving you the ability to publish citations from Zotero to an Exhibit in one step.

We build here a repository of assembled transcript sequences from the contigation (Expressed Sequence Tag (known as EST) & mRNA) in order to discover new genes from already existing data. Publicly available EST & mRNA sequences are clusterised and then contigated with specific bioinformatic tools (see technology).

The Bioinformatics Toolkit is a platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality. The toolkit includes, among others: NucleotideBLAST, ProteinBLAST, PSI-BLAST, fastHMMER, HHsenser; ClustalW, MUSCLE, Mafft, ProbCons; HHrep, PCOILS, REPPER; Quick2D; HHpred, Modeller; CLANS, ANCESCON, PHYLIP; Reformat, RetrieveSeq, gi2promoter. For a short description of the tools, click the section tabs.

Eggdrop is the world's most popular Open Source IRC bot, designed for flexibility and ease of use, and is freely distributable under the GNU General Public License (GPL). Eggdrop was originally developed by Robey Pointer; however, he no longer works on Eggdrop so please do not contact him for help solving a problem or bug. Some features of Eggdrop: * Designed to run on Linux, *BSD, SunOs, Windows, Mac OS X, etc ... * Extendable with Tcl scripts and/or C modules * Support for the big five IRC networks (Undernet, DALnet, EFnet, IRCnet, and QuakeNet) * The ability to form botnets and share partylines and userfiles between bots Some benefits of Eggdrop: * The oldest IRC bot still in active development (Eggdrop was created in 1993) * Established IRC help channels and web sites dedicated to Eggdrop * Thousands of premade Tcl scripts and C modules * Best of all ... It's FREE!

PircBot is a Java framework for writing IRC bots quickly and easily. Its features include an event-driven architecture to handle common IRC events, flood protection, DCC resuming support, ident support, and more. Its comprehensive logfile format is suitable for use with pisg to generate channel statistics. Full documentation is included, and this page contains a 5-minute step-by-step guide to making your first IRC bot. PircBot allows you to perform a variety of fun tasks on IRC, but it is also used for more serious applications by the US Navy, the US Air Force, the CIA (unconfirmed), several national defence agencies, and inside the Azureus bittorrent client. But don't let that put you off - it's still easy to use!

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.

CloudBurst: Highly Sensitive Short Read Mapping with MapReduce Michael Schatz Center for Bioinformatics and Computational Biology, University of Maryland Next-generation DNA sequencing machines are generating an enormous amount of sequence data, placing unprecedented demands on traditional single-processor read mapping algorithms. CloudBurst is a new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics. It is modeled after the short read mapping program RMAP, and reports either all alignments or the unambiguous best alignment for each read with any number of mismatches or differences. This level of sensitivity could be prohibitively time consuming, but CloudBurst uses the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes. CloudBurst's running time scales linearly with the number of reads mapped, and with near linear speedup as the number of processors increases. In a 24-processor core configuration, CloudBurst is up to 30 times faster than RMAP executing on a single core, while computing an identical set of alignments. In a large remote compute clouds with 96 cores, CloudBurst reduces the running time from hours to mere minutes for typical jobs involving mapping of millions of short reads to the human genome. CloudBurst is available open-source as a model for parallelizing other bioinformatics algorithms with MapReduce.

Hadoop comes bundled with launch scripts to simplify initializing an Amazon Elastic Compute Cloud (EC2) cloud for Hadoop. Once initialized, running CloudBurst is identical to running on a local cluster. If you use EC2 regularly with the same datasets (i.e. the human genome as a reference), you will probably want to copy the data once to Amazon Simple Storage Service (S3) so you can quickly copy the data from S3 to your cloud at low cost.

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.

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.

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