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Difference between revisions of "BOSC 2012 Schedule"
From Open Bioinformatics Foundation
(→Day 1: Friday, July 13 (Preliminary Schedule)) |
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| Sophia Cheng | | Sophia Cheng | ||
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| − | | 5:20 | + | | 5:20 |
| Introduction to the [http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation] | | Introduction to the [http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation] | ||
| Hilmar Lapp (President, Open Bioinformatics Foundation) | | Hilmar Lapp (President, Open Bioinformatics Foundation) | ||
| + | |- | ||
| + | | 5:30 | ||
| + | | Announcements | ||
| + | | Nomi Harris (Chair, BOSC 2012) | ||
|- | |- | ||
| 5:30-6:30 | | 5:30-6:30 | ||
Revision as of 23:30, 13 July 2012
BOSC Attendees: Pay-your-own-way BOSC dinner ($25/person) tonight at 7pm: George’s Greek Café, 135 Pine Avenue, Long Beach. (Registration for the dinner is now closed.)
Click here to download this schedule as PDF
Please note: hardcopies of this schedule will be distributed at BOSC, but hardcopies of the complete program will not, so attendees should print the program before leaving for BOSC, if they want it on paper. There will not be access to printers at the meeting.
Day 1: Friday, July 13 (Preliminary Schedule)
| Time | Topic | Speaker or Moderator |
|---|---|---|
| 7:30-9:00 | Registration (Early arrival is recommended as there are usually long lines) | Registration |
| 9:00-9:15 | Introduction and welcome | Nomi Harris (Chair, BOSC 2012) |
| 9:15-10:15 | [Keynote] Science Wants to Be Open - If Only We Could Get Out of Its Way | Jonathan Eisen (University of California, Davis) |
| 10:15-10:45 | Coffee Break | |
| 10:45-12:30 | Session: Cloud and Parallel Computing | Chair: Richard Holland |
| 10:45 | [Cloud] Cloudgene - an execution platform for MapReduce programs in public and private clouds | Sebastian Schönherr |
| 11:10 | [Cloud] Data reduction and division approaches for assembling short-read data in the cloud | C. Titus Brown |
| 11:35 | [Cloud] MGTAXA - a toolkit and a Web server for predicting taxonomy of the metagenomic sequences with Galaxy front-end and parallel computational back-end | Andrey Tovchigrechko |
| 12:00 | [Cloud] Workflows on the Cloud - Scaling for National Service | Katy Wolstencroft |
| 12:15 | [Cloud] How to use BioJava to calculate one billion protein structure alignments at the RCSB PDB website | Andreas Prlic |
| 12:30-1:30 | Lunch | |
| 12:30-2:00 | Poster Session I (Instructions for submitting last-minute poster abstract) | |
| 2:00-3:30 | Session: Genome-scale Data Management | Chair: Ronald Taylor |
| 2:00 | [Genome-scale] Using HDF5 to Work With Large Quantities of Biological Data | Dana Robinson |
| 2:15 | [Genome-scale] Large scale data management in Chipster 2 workflow environment | Aleksi Kallio |
| 2:30 | [Genome-scale] JBrowse 2012 | (Ian Holmes is sick--instead we will see a short talk on JBrowse by Robert Buels) |
| 2:38 | Report on Codefest 2012 | Brad Chapman |
| 2:45 | [Genome-scale] Khmer: A probabilistic approach for efficient counting of k-mers | Qingpeng Zhang |
| 3:00 | [Genome-scale] AmiGO 2: a document-oriented approach to ontology software and escaping the heartache of an SQL backend | Seth Carbon |
| 3:15 | [Genome-scale] Discovery of motif-based regulatory signatures in whole genome methylation experiments | Jens Lichtenberg |
| 3:30-4:00 | Coffee Break | |
| 4:00-5:20 | Session: Linked Data and Translational Knowledge Discovery | Chair: Jan Aerts |
| 4:00 | [Linked / Translational] The open source ISA metadata tracking framework: from data curation and management at the source, to the linked data universe | Philippe Rocca-Serra |
| 4:25 | [Linked / Translational] Automated infrastructure for custom variant comparison and analysis | Brad Chapman |
| 4:50 | [Linked / Translational] KUPKB: Sharing, Connecting and Exposing Kidney and Urinary Knowledge using RDF and OWL | Julie Klein |
| 5:05 | [Linked / Translational] eagle-i: development and expansion of a scientific resource discovery network | Sophia Cheng |
| 5:20 | Introduction to the Open Bioinformatics Foundation | Hilmar Lapp (President, Open Bioinformatics Foundation) |
| 5:30 | Announcements | Nomi Harris (Chair, BOSC 2012) |
| 5:30-6:30 | Poster Session II (Room TBA) | |
| 5:30-6:30 | BOFs | |
| 7:00 | Pay-your-own-way BOSC dinner ($25/person): George’s Greek Café, 135 Pine Avenue, Long Beach. (Registration for dinner is now closed.) |
Day 2: Saturday, July 14 (Preliminary Schedule)
| Time | Topic | Speaker or Moderator |
|---|---|---|
| 8:45-8:50 | Announcements | Nomi Harris |
| 8:50-9:50 | [Keynote] If I Build It Will They Come? | Carole Goble (University of Manchester) |
| 9:50-10:15 | [Misc.] Pistoia Alliance Sequence Squeeze: Using a competition model to spur development of novel open-source algorithms | Richard Holland |
| 10:15-10:45 | Coffee Break | |
| 10:45-12:30 | Session: Software Interoperability | Chair: Hilmar Lapp |
| 10:45-11:00 | [Interoperability] GenomeSpace: An open source environment for frictionless bioinformatics | Michael Reich |
| 11:00-11:15 | [Interoperability] Galaxy Project Update | Dannon Baker |
| 11:15-11:30 | [Interoperability] Zero to a Bioinformatics Analysis Platform in 4 Minutes | Enis Afgan |
| 11:30-11:55 | [Interoperability] PyPedia: A python crowdsourcing development environment for bioinformatics and computational biology | Alexandros Kanterakis |
| 11:55-12:10 | [Interoperability] InterMine - Embeddable Data-Mining Components | Alexis Kalderimis |
| 12:10-12:25 | [Interoperability] Creating biology pipelines with BioUno | Bruno Kinoshi ta |
| 12:30-1:30 | Lunch | |
| 12:30-1:45 | Poster Session III (Room TBA) | |
| 1:45-3:30 | Session: Bioinformatics Open Source Project Updates | Chair: Jeremy Goecks |
| 1:45-2:00 | [Project Updates] Mobyle Web Framework: New Features | Hervé Ménager |
| 2:00-2:15 | [Project Updates] Biopython Project Update | Eric Talevich |
| 2:15-2:40 | [Project Updates] Biogem,Ruby UCSC API, and BioRuby | Hiroyuki Mishima |
| 2:40-2:55 | [Project Updates] A Framework for Interactive Visual Analysis of NGS Data using Galaxy | Jeremy Goecks |
| 2:55-3:10 | [Project Updates] Why Scientists Should Contribute to Wikipedia | Spencer Bliven |
| 3:10-3:25 | [Project Updates] scabio - a framework for bioinformatics algorithms in Scala | Markus Gumbel |
| 3:30-4:00 | Coffee Break | |
| 4:00-4:30 | Session: Lightning Talks (Send last-minute lightning talk abstracts to bosc @ open-bio.org!) | Chair: Kam Dahlquist |
| 4:00-4:07 | [Lightning] bioKepler: A Comprehensive Bioinformatics Scientific Workflow Module for Distributed Analysis of Large-Scale Biological Data | Jianwu Wang |
| 4:07-4:14 | [Lightning] Dao: a novel programming language for bioinformatics | Limin Fu |
| 4:14-4:21 | [Lightning] GMOD in the Cloud | Scott Cain |
| 4:21-4:28 | [Lightning] Bioinformatics Testing Consortium: Codebase peer-review to improve robustness of bioinformatic pipelines | Ben Temperton |
| 4:30-5:30 | Panel: Bioinformatics Paper Reviews: Openness of Standards and Standards of Openness | Moderator: Brad Chapman
Panelists: C. Titus Brown, Iain Hrynaszkiewicz, Hilmar Lapp, Scott Markel, Ben Temperton |
| 5:30-5:40 | Presentation of awards | Nomi Harris |
| 5:40-6:40 | BOFs |
Click here to download this schedule as PDF
Click here to download the complete BOSC program as PDF
