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Difference between revisions of "BOSC 2011 Schedule"
From Open Bioinformatics Foundation
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| 10:45-11:05 | | 10:45-11:05 | ||
| − | |[Genome Content Management] Unipro UGENE: an open source toolkit for complex genome analysis | + | |[Genome Content Management] Unipro UGENE: an open source toolkit for complex genome analysis [http://www.slideshare.net/bosc2011/unipro-ugene-bosc-2011-update ***SLIDES***] |
| Konstantin Okonechnikov | | Konstantin Okonechnikov | ||
|- | |- | ||
| 11:05-11:25 | | 11:05-11:25 | ||
| − | |[Genome Content Management] Exploring the genome with Dalliance | + | |[Genome Content Management] Exploring the genome with Dalliance [http://www.biodalliance.org/people/thomas/dalliance-talk-201107/dalliance.html ***SLIDES webpage***] |
| Thomas Down | | Thomas Down | ||
|- | |- | ||
| 11:25-11:45 | | 11:25-11:45 | ||
| − | |[Genome Content Management] InterMine - Using RESTful Webservices for Interoperability | + | |[Genome Content Management] InterMine - Using RESTful Webservices for Interoperability [http://www.slideshare.net/bosc2011/alex-interminebosc-presentation ***SLIDES***] |
| Alex Kalderimis | | Alex Kalderimis | ||
|- | |- | ||
| Line 48: | Line 48: | ||
|- | |- | ||
| 12:05-12:15 | | 12:05-12:15 | ||
| − | |[Genome Content Management] Mobyle 1.0: new features, new types of services | + | |[Genome Content Management] Mobyle 1.0: new features, new types of services [http://www.slideshare.net/bosc2011/mobyle-1-0newfeaturesnewtypesofservice ***SLIDES***] |
| Hervé Ménager | | Hervé Ménager | ||
|- | |- | ||
| 12:15-12:25 | | 12:15-12:25 | ||
| − | |[Genome Content Management] BioMart 0.8 offers new tools, more interfaces, and increased flexibility through plug-ins | + | |[Genome Content Management] BioMart 0.8 offers new tools, more interfaces, and increased flexibility through plug-ins [http://www.slideshare.net/bosc2011/b07genomecontentbiomart ***SLIDES***] |
| Junjun Zhang | | Junjun Zhang | ||
|- | |- | ||
| 12:25-12:32 | | 12:25-12:32 | ||
| − | |[Genome Content Management] Running Workflows Through Taverna Server [lightning] | + | |[Genome Content Management] Running Workflows Through Taverna Server [lightning] [http://www.slideshare.net/bosc2011/running-workflows-through-galaxy-bosc-presentation ***SLIDES***] |
| Donal Fellows | | Donal Fellows | ||
|- | |- | ||
| Line 72: | Line 72: | ||
|- | |- | ||
| 2:30-2:50 | | 2:30-2:50 | ||
| − | |[Visualization] Cytoscape 3.0: Architecture for Extension | + | |[Visualization] Cytoscape 3.0: Architecture for Extension [http://www.slideshare.net/bosc2011/bosc-talk-7152011x ***SLIDES***] |
| Michael Smoot | | Michael Smoot | ||
|- | |- | ||
| Line 85: | Line 85: | ||
|- | |- | ||
| 3:20-3:30 | | 3:20-3:30 | ||
| − | | [Visualization] The isobar R package: Analysis of quantitative proteomics data | + | | [Visualization] The isobar R package: Analysis of quantitative proteomics data [http://www.slideshare.net/bosc2011/bosc2011-isobarfbp ***SLIDES***] |
| Florian Breitwieser | | Florian Breitwieser | ||
|- | |- | ||
| Line 109: | Line 109: | ||
|- | |- | ||
| 4:50-5:00 | | 4:50-5:00 | ||
| − | | [Next-Generation Sequencing] Goby framework: native support in GSNAP, BWA and IGV 2.0 | + | | [Next-Generation Sequencing] Goby framework: native support in GSNAP, BWA and IGV 2.0 [http://campagnelab.org/files/campagne-lab-bosc-presentation-2011-final.zip ***SLIDES as PREZI***] |
| Kevin C. Dorff | | Kevin C. Dorff | ||
|- | |- | ||
| Line 170: | Line 170: | ||
|- | |- | ||
| 11:05-11:25 | | 11:05-11:25 | ||
| − | |[Cloud Computing] Cloud BioLinux: open source, fully-customizable bioinformatics computing on the cloud for the genomics | + | |[Cloud Computing] Cloud BioLinux: open source, fully-customizable bioinformatics computing on the cloud for the genomics community and beyond [http://www.slideshare.net/bosc2011/bosc2011-ntinokrampisfull ***SLIDES***] |
| − | community and beyond | ||
| Konstantinos Krampis | | Konstantinos Krampis | ||
|- | |- | ||
| Line 207: | Line 206: | ||
|- | |- | ||
| 2:00-2:10 | | 2:00-2:10 | ||
| − | |[Semantic Web] SADI for GMOD: Bringing Model Organism Data onto the Semantic Web | + | |[Semantic Web] SADI for GMOD: Bringing Model Organism Data onto the Semantic Web [http://www.slideshare.net/bosc2011/talk1-ben-sadi-forgmodbosc2011 ***SLIDES***] |
| Ben Vandervalk | | Ben Vandervalk | ||
|- | |- | ||
| 2:10-2:20 | | 2:10-2:20 | ||
| − | |[Semantic Web] Scufl2: because a workflow is more than its definition | + | |[Semantic Web] Scufl2: because a workflow is more than its definition [http://www.slideshare.net/soilandreyes/2011-0716-scufl2-because-a-workflow-is-more-than-its-definition-bosc-2011 ***SLIDES***] |
| Stian Soiland-Reyes | | Stian Soiland-Reyes | ||
|- | |- | ||
| 2:20-2:30 | | 2:20-2:30 | ||
| − | |[Semantic Web] OntoCAT - an integrated programming toolkit for common ontology application tasks | + | |[Semantic Web] OntoCAT - an integrated programming toolkit for common ontology application tasks [http://www.slideshare.net/bosc2011/np-adamusiak-bosc2011ontocat ***SLIDES***] |
| Tomasz Adamusiak | | Tomasz Adamusiak | ||
|- | |- | ||
| Line 227: | Line 226: | ||
|- | |- | ||
| 3:10-3:20 | | 3:10-3:20 | ||
| − | |[Misc.] Biopython Project Update | + | |[Misc.] Biopython Project Update 2011 [http://www.slideshare.net/bosc2011/talk6-biopython-bosc2011 *** SLIDES***] |
| Peter Cock | | Peter Cock | ||
|- | |- | ||
| Line 251: | Line 250: | ||
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| 4:10-4:20 | | 4:10-4:20 | ||
| − | |[Misc.] G-language Project: the last 10 years and beyond | + | |[Misc.] G-language Project: the last 10 years and beyond [http://www.slideshare.net/bosc2011/bosc2011-arakawa ***SLIDES***] |
| Kazuharu Arakawa | | Kazuharu Arakawa | ||
|- | |- | ||
| 4:20-4:30 | | 4:20-4:30 | ||
| − | |[Misc.] A Framework for Bioinformatics on the Microsoft Platform | + | |[Misc.] A Framework for Bioinformatics on the Microsoft Platform [http://www.slideshare.net/bosc2011/bosc-mercer ***SLIDES***] |
| Simon Mercer | | Simon Mercer | ||
|- | |- | ||
Latest revision as of 20:18, 10 September 2013
Day 1: Friday, July 15 (Austria Center Vienna, Room F2)
| Time | Topic | Speaker or Moderator |
|---|---|---|
| 7:30-9:00 | Pick up badges for BOSC 2011, Austria Center Vienna
(Early arrival is recommended as there are usually long lines) |
Registration |
| 9:00-9:15 | Introduction and welcome | Nomi Harris (Co-Chair, BOSC) |
| 9:15-10:15 | [Keynote] The role of openness in knowledge-based systems for biomedicine ***SLIDES*** | Lawrence Hunter (University of Colorado) |
| 10:15-10:45 | Coffee Break | |
| 10:45-12:30 | Session: Genome Content Management | Chair: Peter Rice |
| 10:45-11:05 | [Genome Content Management] Unipro UGENE: an open source toolkit for complex genome analysis ***SLIDES*** | Konstantin Okonechnikov |
| 11:05-11:25 | [Genome Content Management] Exploring the genome with Dalliance ***SLIDES webpage*** | Thomas Down |
| 11:25-11:45 | [Genome Content Management] InterMine - Using RESTful Webservices for Interoperability ***SLIDES*** | Alex Kalderimis |
| 11:45-11:55 | [Genome Content Management] easyDAS: Automatic creation of DAS servers ***SLIDES*** | Bernat Gel |
| 11:55-12:05 | [Genome Content Management] Enacting Taverna Workflows through Galaxy | Kostas Karasavvas |
| 12:05-12:15 | [Genome Content Management] Mobyle 1.0: new features, new types of services ***SLIDES*** | Hervé Ménager |
| 12:15-12:25 | [Genome Content Management] BioMart 0.8 offers new tools, more interfaces, and increased flexibility through plug-ins ***SLIDES*** | Junjun Zhang |
| 12:25-12:32 | [Genome Content Management] Running Workflows Through Taverna Server [lightning] ***SLIDES*** | Donal Fellows |
| 12:30-2:00 | Lunch | |
| 1:30-2:30 | Poster Session I (Foyer A) | |
| 2:30-3:30 | Session: Visualization | Chair: Jan Aerts |
| 2:30-2:50 | [Visualization] Cytoscape 3.0: Architecture for Extension ***SLIDES*** | Michael Smoot |
| 2:50-3:10 | [Visualization] Applying Visual Analytics to Extend the Genome Browser from Visualization Tool to Analysis Tool ***SLIDES*** | Jeremy Goecks |
| 3:10-3:20 | [Visualization] WebApollo: A web-based sequence annotation editor for community annotation ***SLIDES*** | Nomi Harris |
| 3:20-3:30 | [Visualization] The isobar R package: Analysis of quantitative proteomics data ***SLIDES*** | Florian Breitwieser |
| 3:30-4:00 | Coffee Break | |
| 4:00-5:30 | Session: Next-Generation Sequencing and Parallel Processing | Chair: Thomas Down |
| 4:00-4:20 | [Next-Generation Sequencing] Stacks: building and genotyping loci de novo from short-read sequences | Julian Catchen |
| 4:20-4:40 | [Next-Generation Sequencing] Large scale NGS pipelines using the MOLGENIS platform: processing the Genome of the Netherlands ***SLIDES*** | Morris Swertz |
| 4:40-4:50 | [Next-Generation Sequencing] Bio-NGS: BioRuby plugin to conduct programmable workflows for Next Generation Sequencing data ***SLIDES*** | Raoul Bonnal |
| 4:50-5:00 | [Next-Generation Sequencing] Goby framework: native support in GSNAP, BWA and IGV 2.0 ***SLIDES as PREZI*** | Kevin C. Dorff |
| 5:00-5:10 | [Parallel Processing] A Scalable Multicore Implementation of the TEIRESIAS Algorithm | Frank Drews |
| 5:10-5:20 | [Parallel Processing] Biomanycores, open-source parallel code for many-core bioinformatics | Jean-Frédéric Berthelot |
| 5:20-5:30 | [Next-Generation Sequencing] GemSIM: General, Error-Model Based Simulator of next-generation sequencing | Kerensa McElroy |
| 5:30-6:30 | Poster Session II (Foyer A) | |
| 5:30-6:30 | BOFs | |
| 7:00 | Pay-your-own-way optional dinner |
Day 2: Saturday, July 16 (Austria Center Vienna, Room F2)
| Time | Topic | Speaker or Moderator |
|---|---|---|
| 8:45-8:50 | Announcements | |
| 8:50-9:50 | [Keynote] Into the Wonderful | Matt Wood (Amazon) |
| 9:50-10:15 | [Cloud computing] Securing and sharing bioinformatics in the cloud | Richard Holland (Eagle Genomics) |
| 10:15-10:45 | Coffee Break | |
| 10:45-12:30 | Session: Cloud Computing | Chair: Brad Chapman |
| 10:45-11:05 | [Cloud Computing] Mygene.info: Gene Annotation as a Service - GAaaS ***SLIDES*** | Chunlei Wu |
| 11:05-11:25 | [Cloud Computing] Cloud BioLinux: open source, fully-customizable bioinformatics computing on the cloud for the genomics community and beyond ***SLIDES*** | Konstantinos Krampis |
| 11:25-11:35 | [Cloud Computing] OBIWEE : an open source bioinformatics cloud environment ***SLIDES*** | Olivier Sallou |
| 11:35-11:45 | [Cloud Computing] SeqWare: Analyzing Whole Human Genome Sequence Data on Amazon's Cloud | Brian O'Connor |
| 11:45-12:05 | [Cloud Computing] Sequencescape - a cloud enabled Laboratory Information Management Systems (LIMS) for second and third generation sequencing ***SLIDES*** | Lars Jorgensen |
| 12:05-12:15 | [Cloud Computing] Enabling NGS Analysis with(out) the Infrastructure ***SLIDES*** | Enis Afgan |
| 12:15-12:25 | [Cloud Computing] Hadoop-BAM: A Library for Genomic Data Processing ***SLIDES*** | Aleksi Kallio |
| 12:30-2:00 | Lunch | |
| 1:00-2:00 | Poster Session III (Foyer A) | |
| 2:00-3:30 | Session: Semantic Web and Misc. Open Source Projects | Chair: Peter Cock |
| 2:00-2:10 | [Semantic Web] SADI for GMOD: Bringing Model Organism Data onto the Semantic Web ***SLIDES*** | Ben Vandervalk |
| 2:10-2:20 | [Semantic Web] Scufl2: because a workflow is more than its definition ***SLIDES*** | Stian Soiland-Reyes |
| 2:20-2:30 | [Semantic Web] OntoCAT - an integrated programming toolkit for common ontology application tasks ***SLIDES*** | Tomasz Adamusiak |
| 2:30-2:50 | [Misc.] Debian Med: individuals' expertize and their sharing of package build instructions ***SLIDES*** | Steffen Möller |
| 2:50-3:10 | [Misc.] The BALL project: The Biochemical Algorithms Library (BALL) for Rapid Application Development in Structural Bioinformatics and its graphical user interface BALLView | Andreas Hildebrandt |
| 3:10-3:20 | [Misc.] Biopython Project Update 2011 *** SLIDES*** | Peter Cock |
| 3:20-3:27 | [Misc.] What's new with GMOD [lightning] ***SLIDES*** | Scott Cain |
| 3:27-3:34 | [Misc.] Exploring human variation data with Clojure [lightning] | Brad Chapman |
| 3:30-4:00 | Coffee Break | |
| 4:00-4:30 | Session: Misc. Open Source Projects | Chair: Jim Procter |
| 4:00-4:10 | [Misc.] EMBOSS: New developments and extended data access ***SLIDES*** | Peter Rice |
| 4:10-4:20 | [Misc.] G-language Project: the last 10 years and beyond ***SLIDES*** | Kazuharu Arakawa |
| 4:20-4:30 | [Misc.] A Framework for Bioinformatics on the Microsoft Platform ***SLIDES*** | Simon Mercer |
| 4:30-5:20 | Panel: Meeting the challenges of inter-institutional collaboration | Moderator: Brad Chapman
Panelists: Richard Holland (Eagle Genomics), Hilmar Lapp (National Evolutionary Synthesis Center), Jean Peccoud (Virginia Bioinformatics Institute), Peter Rice (European Bioinformatics Institute) |
| 5:20-5:30 | Presentation of awards | Nomi Harris |
| 5:30-6:30 | BOFs |
