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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.

The AAAS Science and Human Rights Coalition is a network of scientific organizations that recognizes a role for science and scientists in efforts to realize human rights. Composed of scientific associations, societies and academies, as well as individual scientists, the Coalition aims to facilitate communication and partnerships on human rights within and across scientific communities, and between these and human rights communities. The Coalition's programs are being carried out by the following five working groups: 1. Welfare of Scientists 2. Science Ethics and Human Rights 3. Service to the Scientific Community 4. Service to the Human Rights Community 5. Education and Information Resources The Coalition is also pursuing a joint initiative to realize the human right to "the benefits of scientific progress" (Article 15, International Covenant on Economic, Social and Cultural Rights).

The National Center for Biomedical Ontology is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods allowing scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our visionis that all biomedical knowledge and data are disseminated on the Internet using principled ontologies, such that they are semantically interoperable and useful for improving biomedical science and clinical care. Our resources include the Open Biomedical Ontologies (OBO) library, the Open Biomedical Data (OBD) repositories, and tools for accessing and using this information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects to enable outside research and stimulate technology development in the Center. The Center undertakes outreach and educational activities (Biomedical Informatics Program) to train future researchers to use biomedical ontologies and related tools with the goal of enhancing scientific discovery.

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.

GenBioWiki is the student home page for the Genetics, Bioinformatics, and Computational Biology (GBCB) program at Virginia Tech. Bioinformatics and computational biology provide a research platform to acquire, manage, analyze, and display large amounts of data, which in turn catalyze a systems approach to understanding biological organisms, as well as making useful predictions about their behavior in response to environmental and other perturbations. Moreover, bioinformatics is the study of biological systems and large biological data sets using analytical methods borrowed from computer science, mathematics, statistics, and the physical sciences. This transdisciplinary approach to research requires graduates with extensive cross-cultural professional and technical training and provides ample employment opportunities for Ph.D. graduates. [1]

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics and funded by the NIH National Center for Research Resources (grant P41-RR01081).

The Open Bioinformatics Foundation or O|B|F is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics. The foundation grew out of the volunteer projects BioPerl, BioJava and BioPython and was formally incorporated in order to handle our modest requirements of hardware ownership, domain name management and funding for conferences and workshops.The Foundation does not participate directly in the development or structure of the open source work, but as the members of the foundation are drawn from the member projects, there is clear commonality of direction and purpose. Occasionally the O|B|F directors may make announcements about our direction or purpose (a recent one was on the licensing of academic software) when the board feels there is a need to clarify matters, but in general we prefer to remain simply the administrative support organization for our member projects. Our main activities are: * Underwriting and supporting the BOSC conferences * Organizing and supporting developer-centric "hackathon" events * Managing our servers, colocation facilities, bank account & other assets We are incorporated in the state of Delaware, USA as a not-for-profit company.

SciPy (pronounced "Sigh Pie") is open-source software for mathematics, science, and engineering. It is also the name of a very popular conference on scientific programming with Python. The SciPy library depends on NumPy, which provides convenient and fast N-dimensional array manipulation. The SciPy library is built to work with NumPy arrays, and provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization. Together, they run on all popular operating systems, are quick to install, and are free of charge. NumPy and SciPy are easy to use, but powerful enough to be depended upon by some of the world's leading scientists and engineers. If you need to manipulate numbers on a computer and display or publish the results, give SciPy a try!

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

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.

The Open Computer Vision Library has > 500 algorithms, documentation and sample code for real time computer vision. Tutorial documentation is in O'Reilly Book: Learning OpenCV http://www.amazon.com/Learning-OpenCV-Computer-Vision-Library/dp/0596516134