Volume 11 Supplement 12

Proceedings of the 11th Annual Bioinformatics Open Source Conference (BOSC) 2010

Proceedings

Edited by Kam D Dahlquist

The 11th Annual Bioinformatics Open Source Conference (BOSC) 2010. Go to conference site.

Boston, MA, USA

9-10 July 2010

  1. Proceedings

    SeqWare Query Engine: storing and searching sequence data in the cloud

    Since the introduction of next-generation DNA sequencers the rapid increase in sequencer throughput, and associated drop in costs, has resulted in more than a dozen human genomes being resequenced over the las...

    Brian D O’Connor, Barry Merriman and Stanley F Nelson

    BMC Bioinformatics 2010 11(Suppl 12):S2

    Published on: 21 December 2010

  2. Proceedings

    Hybrid cloud and cluster computing paradigms for life science applications

    Clouds and MapReduce have shown themselves to be a broadly useful approach to scientific computing especially for parallel data intensive applications. However they have limited applicability to some areas suc...

    Judy Qiu, Jaliya Ekanayake, Thilina Gunarathne, Jong Youl Choi, Seung-Hee Bae, Hui Li, Bingjing Zhang, Tak-Lon Wu, Yang Ruan, Saliya Ekanayake, Adam Hughes and Geoffrey Fox

    BMC Bioinformatics 2010 11(Suppl 12):S3

    Published on: 21 December 2010

  3. Proceedings

    Galaxy CloudMan: delivering cloud compute clusters

    Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research. An alternative to building and maintaini...

    Enis Afgan, Dannon Baker, Nate Coraor, Brad Chapman, Anton Nekrutenko and James Taylor

    BMC Bioinformatics 2010 11(Suppl 12):S4

    Published on: 21 December 2010

  4. Proceedings

    Community-driven computational biology with Debian Linux

    The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates ...

    Steffen Möller, Hajo Nils Krabbenhöft, Andreas Tille, David Paleino, Alan Williams, Katy Wolstencroft, Carole Goble, Richard Holland, Dominique Belhachemi and Charles Plessy

    BMC Bioinformatics 2010 11(Suppl 12):S5

    Published on: 21 December 2010

  5. Proceedings

    WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures

    An important focus of genomic science is the discovery and characterization of all functional elements within genomes. In silico methods are used in genome studies to discover putative regulatory genomic elements...

    Jens Lichtenberg, Kyle Kurz, Xiaoyu Liang, Rami Al-ouran, Lev Neiman, Lee J Nau, Joshua D Welch, Edwin Jacox, Thomas Bitterman, Klaus Ecker, Laura Elnitski, Frank Drews, Stephen Sauchi Lee and Lonnie R Welch

    BMC Bioinformatics 2010 11(Suppl 12):S6

    Published on: 21 December 2010

  6. Proceedings

    SADI, SHARE, and the in silico scientific method

    The emergence and uptake of Semantic Web technologies by the Life Sciences provides exciting opportunities for exploring novel ways to conduct in silico science. Web Service Workflows are already becoming first-c...

    Mark D Wilkinson, Luke McCarthy, Benjamin Vandervalk, David Withers, Edward Kawas and Soroush Samadian

    BMC Bioinformatics 2010 11(Suppl 12):S7

    Published on: 21 December 2010

  7. Proceedings

    ONTO-ToolKit: enabling bio-ontology engineering via Galaxy

    The biosciences increasingly face the challenge of integrating a wide variety of available data, information and knowledge in order to gain an understanding of biological systems. Data integration is supported...

    Erick Antezana, Aravind Venkatesan, Chris Mungall, Vladimir Mironov and Martin Kuiper

    BMC Bioinformatics 2010 11(Suppl 12):S8

    Published on: 21 December 2010

  8. Proceedings

    The Musite open-source framework for phosphorylation-site prediction

    With the rapid accumulation of phosphoproteomics data, phosphorylation-site prediction is becoming an increasingly active research area. More than a dozen phosphorylation-site prediction tools have been releas...

    Jianjiong Gao and Dong Xu

    BMC Bioinformatics 2010 11(Suppl 12):S9

    Published on: 21 December 2010

  9. Proceedings

    interPopula: a Python API to access the HapMap Project dataset

    The HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This im...

    Tiago Antao

    BMC Bioinformatics 2010 11(Suppl 12):S10

    Published on: 21 December 2010

  10. Proceedings

    The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

    There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. ...

    Morris A Swertz, Martijn Dijkstra, Tomasz Adamusiak, Joeri K van der Velde, Alexandros Kanterakis, Erik T Roos, Joris Lops, Gudmundur A Thorisson, Danny Arends, George Byelas, Juha Muilu, Anthony J Brookes, Engbert O de Brock, Ritsert C Jansen and Helen Parkinson

    BMC Bioinformatics 2010 11(Suppl 12):S12

    Published on: 21 December 2010

  11. Proceedings

    IPRStats: visualization of the functional potential of an InterProScan run

    InterPro is a collection of protein signatures for the classification and automated annotation of proteins. Interproscan is a software tool that scans protein sequences against Interpro member databases using ...

    Ryan J Kelly, David E Vincent and Iddo Friedberg

    BMC Bioinformatics 2010 11(Suppl 12):S13

    Published on: 21 December 2010