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Difference between revisions of "BOSC 2010 Schedule"

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* Return to '''[[BOSC_2010 | BOSC 2010]]''' main page.
 
* Return to '''[[BOSC_2010 | BOSC 2010]]''' main page.
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<!--* Click '''[[Media:BOSC2009_program_20090601.pdf | here]]''' to download full program in PDF format (2 MB).
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* '''BOSC 2010 Proceedings: The [http://www.biomedcentral.com/1471-2105/11?issue=S12 Proceedings] have been published as of 21 December 2010 in ''BMC Bioinformatics''.'''
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* Important '''[[BOSC_2009#Information_for_Speakers | Information for Speakers]]'''-->
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* Click '''[[Media:BOSC2010_program_20100615_frontmatter.pdf | here]]''' to download the BOSC 2010 program and schedule as a PDF file (5 pages, 300k)
 +
* Click '''[[Media:BOSC2010_program_20100615_compiledabstracts.pdf | here]]''' to download all abstracts compiled into one PDF file (2 MB).
 +
* Important '''[[BOSC_2010#Information_for_Speakers | Information for Speakers]]'''
 +
* '''''Slides''''' for both days' talks are up on [http://www.slideshare.net/bosc2010/presentations SlideShare] under the username "bosc2010".  Individual links to each talk are posted on the schedule below.
  
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== Keynote Speakers ==
+
== Schedule ==
  
−
=== Guy Coates ===
+
Click on the talk title to view the individual abstract as a PDF file.
  
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[http://uk.linkedin.com/pub/guy-coates/3/b5b/9b0 Guy Coates], Group leader of the Informatics Systems Group at the [http://www.sanger.ac.uk/ Wellome Trust Sanger Institute], will be one of our keynote speakers at BOSC 2010. Guy Coates is an expert in large Linux/Unix systems architecture, management and application optimization, next-gen DNA sequencing pipelines, very large database systems (>50TB), and high performance compute clusters (1500+ CPUs). He will lead off the conference, with a talk entitled:
+
{| border="1" cellspacing="0" cellpadding="10" align="left"
 +
! Day 1
 +
! Friday
 +
! July 9: Hynes Convention Center room 207
 +
|-
 +
| 7:30-9:00AM
 +
| Registration
 +
| Pick up badges for BOSC 2010, Hynes Convention Center (early arrival is recommended as there are usually long lines)
 +
|-
 +
| 9:00-9:15AM
 +
| Kam Dahlquist
 +
| [Welcome] Introduction to the <nowiki>OBF</nowiki> and Welcome to BOSC 2010
 +
|-
 +
| 9:15-10:15
 +
| Guy Coates
 +
| [Keynote] [[BOSC_2010#Guy_Coates | Clouds: all fluff and no substance?]] [http://www.slideshare.net/bosc2010/coates-bosc2010-cloudsfluffandnosubstance ***SLIDES***]
 +
|-
 +
| '''10:15-10:45'''
 +
|
 +
| '''Coffee Break'''
 +
|-
 +
| 10:45-11:05
 +
| Ronald Taylor
 +
| [Cloud Computing/HT 'omics Data] [[Media:29_BOSC2010.pdf | An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics]] [http://www.slideshare.net/bosc2010/taylor-bosc2010 ***SLIDES***]
 +
|-
 +
| 11:05-11:25
 +
| M. Hanna
 +
| [Cloud Computing/HT 'omics Data] [[Media:18_BOSC2010.pdf | The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data]] [http://www.slideshare.net/bosc2010/hanna-bosc2010 ***SLIDES***]
 +
|-
 +
| 11:25-11:45
 +
| Brian D. O'Connor
 +
| [Cloud Computing/HT 'omics Data] [[Media:39_BOSC2010.pdf | SeqWare Query Engine: Storing and Searching Sequence Data in the Cloud]] [http://www.slideshare.net/bosc2010/o-connor-bosc2010 ***SLIDES***]
 +
|-
 +
| 11:45-12:00PM
 +
| Judy Qiu
 +
| [Cloud Computing/HT 'omics Data] [[Media:40_BOSC2010.pdf | Hybrid Cloud and Cluster Computing Paradigms for Life Science Applications]] [http://www.slideshare.net/bosc2010/qiu-bosc2010 ***SLIDES***]
 +
|-
 +
| 12:00-12:15
 +
| Ben Langmead
 +
| [Cloud Computing/HT 'omics Data] [[Media:42_BOSC2010.pdf | Cloud-scale genomics: examples and lessons]] [http://www.slideshare.net/bosc2010/langmead-bosc2010-cloudgenomics ***SLIDES***]
 +
|-
 +
| 12:15-12:30
 +
| Enis Afgan
 +
| [Cloud Computing/HT 'omics Data] [[Media:43_BOSC2010.pdf | Deploying Galaxy on the Cloud]] [http://www.slideshare.net/bosc2010/afgan-bosc2010-galaxycloud ***SLIDES***]
 +
|-
 +
| '''12:30-2:00'''
 +
|
 +
| '''Lunch'''
 +
|-
 +
| 2:00-2:20
 +
| Steffen Möller
 +
| [Cloud Computing] [[Media:26_BOSC2010.pdf | Community-driven computational biology with Debian and Taverna]] [http://www.slideshare.net/bosc2010/moeller-bosc2010-debiantaverna ***SLIDES***]
 +
|-
 +
| 2:20-2:40
 +
| Darin London
 +
| [Cloud Computing/HT 'omics Data] [[Media:3_BOSC2010.pdf | Dealing with the Data Deluge: What can the Robotics Community Teach us?]] [http://www.slideshare.net/bosc2010/london-bosc2010 ***SLIDES***]
 +
|-
 +
| 2:40-3:00
 +
| Nyasha Chambwe
 +
| [HT 'omics Data] [[Media:19_BOSC2010.pdf | The Goby framework: towards efficient next-generation sequencing data analysis]] [http://www.slideshare.net/bosc2010/chambwe-bosc2010 ***SLIDES***]
 +
|-
 +
| 3:00-3:15
 +
| Dana Robinson
 +
| [HT 'omics Data] [[Media:10_BOSC2010.pdf | BioHDF: Open binary file formats for NGS data - current status and future directions]] [http://www.slideshare.net/bosc2010/robinson-bosc2010-biohdf ***SLIDES***]
 +
|-
 +
| 3:15-3:30
 +
| Jens Lichtenberg
 +
| [HT 'omics Data] [[Media:28_BOSC2010.pdf | Concurrent Bioinformatics Software for Discovering Genome-wide Patterns and Word-based Genomic Signatures]] [http://www.slideshare.net/bosc2010/lichtenberg-bosc2010-wordseeker ***SLIDES***]
 +
|-
 +
| 3:30-3:38
 +
| [http://gmod.org/wiki/User:Chemmeri Chris Hemmerich]
 +
| [HT 'omics Data] [[Media:30_BOSC2010.pdf | Automated Annotation of NGS Transcriptome Data using ISGA and Ergatis]] [http://www.slideshare.net/bosc2010/hemmerich-bosc2010-isgaergatis ***SLIDES***]
 +
|-
 +
| '''3:38-4:00'''
 +
|
 +
| '''Coffee Break'''
 +
|-
 +
| 4:00-4:20
 +
| Mark Wilkinson
 +
| [Semantic Web] [[Media:4_BOSC2010.pdf | From Moby to SADI - Modeling Semantic Web Services with the Semantic Automated Discovery and Integration Framework]] [http://www.slideshare.net/bosc2010/wilkinson-bosc2010-mobytosadi ***SLIDES***]
 +
|-
 +
| 4:20-4:35
 +
| Aravind Venkatesan
 +
| [Semantic Web][[Media:21_BOSC2010.pdf | ONTO-ToolKit: enabling bio-ontology engineering via Galaxy]] [http://www.slideshare.net/bosc2010/venkatesan-bosc2010-ontotoolkit ***SLIDES***]
 +
|-
 +
| 4:35-4:45
 +
| Kazuharu Arakawa
 +
| [Semantic Web] [[Media:6_BOSC2010.pdf | G-language Bookmarklet: a gateway for Semantic Web, Linked Data, and Web Services]] [http://www.slideshare.net/bosc2010/arakawa-bosc2010-glanguatebookmarklet ***SLIDES***]
 +
|-
 +
| 4:45-4:55
 +
| Christian M Zmasek
 +
| [Semantic Web] [[Media:25_BOSC2010.pdf | Connecting TOPSAN to Computational Analysis]] [http://www.slideshare.net/bosc2010/zmasek-bosc2010-topsan ***SLIDES***]
 +
|-
 +
| 4:55-5:10
 +
| Jianjiong Gao
 +
| [OS Software] [[Media:20_BOSC2010.pdf | Musite: Global Prediction of General and Kinase-Specific Phosphorylation Sites]] [http://www.slideshare.net/bosc2010/gao-bosc2010-musite ***SLIDES***]
 +
|-
 +
| 5:10-5:18
 +
| Hervé Ménager
 +
| [Lightning Talk] [https://projets.pasteur.fr/wiki/mobyle/ Mobyle Bioinformatics Web Portal: project update] [http://www.slideshare.net/bosc2010/menager-bosc2010-mobyle ***SLIDES***]
 +
|-
 +
| 5:18-5:26
 +
| Stuart Owen
 +
| [Lightning Talk] [http://www.taverna.org.uk/ The Taverna 2.2 Workflow Workbench with a case study using it for Next Gen Sequencing of African cows] [http://www.slideshare.net/bosc2010/owen-bosc2010-taverna22cows ***SLIDES***]
 +
|-
 +
| 5:26-5:34
 +
| Jiten Bhagat
 +
| [Lightning Talk] [http://www.biocatalogue.org/ BioCatalogue - the Public Curated Registry of Life Science Web Services] [http://www.slideshare.net/bosc2010/bhagat-bosc2010-biocatalogue ***SLIDES***]
 +
|-
 +
| 5:34-5:42
 +
| Christian M Zmasek
 +
| [Software Demo] [http://phylosoft.org/archaeopteryx/ Evolutionary tree visualization and analysis with Archaeopteryx] [http://www.slideshare.net/bosc2010/zmasek-bosc2010-aptx ***SLIDES***]
 +
|-
 +
| 5:42-5:50
 +
| Aleksi Kallio
 +
| [Lightning Talk] [http://chipster.sourceforge.net/ Connecting Chipster genome browser to the cloud] [http://www.slideshare.net/bosc2010/kallio-bosc2010-chipstercloud ***SLIDES***]
 +
|-
 +
| 5:50-5:58
 +
| Christopher Bottoms
 +
| [Lightning Talk] [http://search.cpan.org/~molecules/Bio-SNP-Inherit-0.00100001-TRIAL/lib/Bio/SNP/Inherit.pm SNP Allele Designations (Bio::SNP::Inherit)] [http://www.slideshare.net/bosc2010/bottoms-bosc2010-biosnpinherit ***SLIDES***]
 +
|-
 +
| 5:58-6:06
 +
| Tomasz Puton
 +
| [Lightning Talk] [http://github.com/krother/biopython BioPython modules for handling RNA sequences containing modified nucleosides] [http://www.slideshare.net/bosc2010/puton-bosc2010-biopythonmodulesrna ***SLIDES***]
 +
|-
 +
| 6:06-6:15
 +
| Brad Chapman
 +
| [Lightning Talk] [http://www.open-bio.org/wiki/Codefest_2010 Codefest 2010 Report]
 +
|-
 +
| 6:15-6:45
 +
| &nbsp;
 +
| [[BOSC_2010/Birds-of-a-Feather | Birds of a Feather]]
 +
|-
 +
| 6:45
 +
| &nbsp;
 +
| <nowiki>OBF</nowiki> Board Meeting and No-host Dinner; Location: Legal Seafood
 +
|-
 +
|
 +
|
 +
|
 +
|-
 +
| '''Day 2'''
 +
| '''Saturday'''
 +
| '''July 10''': Hynes Convention Center room 207
 +
|-
 +
| 9:00-9:15AM
 +
| Kam Dahlquist
 +
| [Announcements]
 +
|-
 +
| 9:15-10:15
 +
| Ross Gardler
 +
| [Keynote] [[BOSC_2010#Ross_Gardler | Community Development at the Apache Software Foundation]] [http://www.slideshare.net/bosc2010/gardler-bosc2010-communitydevelopmentattheasf ***SLIDES***]
 +
|-
 +
| '''10:15-10:45'''
 +
|
 +
| '''Coffee Break'''
 +
|-
 +
| 10:45-11:05
 +
| Christopher Fields
 +
| [Bio* Update] [[Media:22_BOSC2010.pdf | Towards a Modern BioPerl: BioPerl Update 2010]] [http://www.slideshare.net/bosc2010/fields-bosc2010-bioperl ***SLIDES***]
 +
|-
 +
| 11:05-11:20
 +
| Raoul J.P. Bonnal
 +
| [Bio* Update] [[Media:15_BOSC2010.pdf | BioRuby 2010 updates: moving to agile bioinformatics]] [http://www.slideshare.net/bosc2010/bonnal-bosc2010-bioruby ***SLIDES***]
 +
|-
 +
| 11:20-11:35
 +
| Peter Rice
 +
| [Bio* Update] [[Media:14_BOSC2010.pdf | EMBOSS: The European Molecular Biology Open Software Suite]] [http://www.slideshare.net/bosc2010/rice-bosc2010-emboss ***SLIDES***]
 +
|-
 +
| 11:35-11:50
 +
| Brad Chapman
 +
| [Bio* Update] [[Media:16_BOSC2010.pdf | Biopython Project Update 2010]] [http://www.slideshare.net/bosc2010/chapman-bosc2010-biopython ***SLIDES***]
 +
|-
 +
| 11:50-12:05PM
 +
| Tiago Antao
 +
| [OS software] [[Media:13_BOSC2010.pdf | interPopula: Database and tool integration for population genetics using Python]] [http://www.slideshare.net/tiago/inter-popula ***SLIDES***]
 +
|-
 +
| 12:05-12:20
 +
| Laurent Gautier
 +
| [Bio* Update] [[Media:2_BOSC2010.pdf | Bioconductor with Python, What else ?]] [http://www.slideshare.net/bosc2010/gautier-bosc2010-pythonbioconductor ***SLIDES***]
 +
|-
 +
| 12:20-12:30
 +
| Eric W Talevich
 +
| [Bio* Update] [[Media:8_BOSC2010.pdf | Bio.Phylo: A unified phylogenetics toolkit for Biopython]] [http://www.slideshare.net/etalevich/biophylo-phylogenetics-in-biopython-bosc-2010 ***SLIDES***]
 +
|-
 +
| '''12:30-2:00'''
 +
|
 +
| '''Lunch'''
 +
|-
 +
| 2:00-2:20
 +
| Simon Mercer
 +
| [OS Software Framework] [[Media:9_BOSC2010.pdf | The Microsoft Biology Foundation]] [http://www.slideshare.net/bosc2010/mercer-bosc2010-microsoftframework ***SLIDES***]
 +
|-
 +
| 2:20-2:40
 +
| William Crawford
 +
| [OS Software/Code Generation] [[Media:36_BOSC2010.pdf | Building Bioinformatics Web Application with Clickframes]]
 +
|-
 +
| 2:40-3:00
 +
| Morris A. Swertz
 +
| [OS Software/Code Generation] [[Media:24_BOSC2010.pdf | MOLGENIS: rapid prototyping of biosoftware at the push of a button]] [http://www.slideshare.net/bosc2010/swertz-bosc2010-molgenis ***SLIDES***]
 +
|-
 +
| 3:00-3:10
 +
| Alexandros Kanterakis
 +
| [OS Software/Code Generation] [[Media:17_BOSC2010.pdf | Generating a data platform for microarray gene expression experiments using MOLGENIS and MAGE-TAB]] [http://www.slideshare.net/bosc2010/kanterakis-bosc2010-molgenis ***SLIDES***]
 +
|-
 +
| 3:10-3:25
 +
| Sebastian J. Schultheiss
 +
| [Web Services] [[Media:5_BOSC2010.pdf | Long-term availability of bioinformatics web services]] [http://www.slideshare.net/bosc2010/schultheiss-bosc2010-persistancewebservices ***SLIDES***]
 +
|-
 +
| '''3:25-4:00'''
 +
|
 +
| '''Coffee Break'''
 +
|-
 +
| 4:00-4:15
 +
| [http://gmod.org/wiki/User:Lstein Lincoln Stein]
 +
| [Visualization] [[Media:34_BOSC2010.pdf | GBrowse2]] [http://prezi.com/xwpsks7tnnd8/gbrowse-20-bosc-talk/ ***SLIDES***]
 +
|-
 +
| 4:15-4:35
 +
| Gary D. Bader
 +
| [Visualization] [[Media:12_BOSC2010.pdf | Cytoscape Web: An interactive, customizable web-based network browser]] [http://www.slideshare.net/bosc2010/bader-bosc2010-cytoweb ***SLIDES***]
 +
|-
 +
| 4:35-4:50
 +
| Nobuaki Kono
 +
| [Visualization] [[Media:38_BOSC2010.pdf | Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API]] [http://www.slideshare.net/bosc2010/kono-bosc2010-pathwayprojector ***SLIDES***]
 +
|-
 +
| 4:50-5:05
 +
| James A. Morris
 +
| [Visualization] [[Media:7_BOSC2010.pdf | Evoker: a visualization tool for genotype intensity data]] [http://www.slideshare.net/bosc2010/morris-bosc2010-evoker ***SLIDES***]
 +
|-
 +
| 5:05-5:20
 +
| Pavel Tomancak
 +
| [Visualization] [[Media:11_BOSC2010.pdf | Fiji Is Just ImageJ - an Open Source platform for biological image analysis]]
 +
|-
 +
| 5:20-5:30
 +
| Iddo Friedberg
 +
| [Visualization] [[Media:32_BOSC2010.pdf | IPRStats: visualization and analysis of InterProScan Results]] [http://www.slideshare.net/bosc2010/friedberg-bosc2010-iprstats ***SLIDES***]
 +
|-
 +
| 5:30-6:00
 +
|
 +
|[[BOSC_2010/Birds-of-a-Feather | Birds of a Feather]]
 +
|}
  
−
'''''Clouds: all fluff and no substance?'''''  Cloud architectures have made plenty of impact in the press over the
+
[[Category:BOSC]] [[Category:Conferences]]
−
past 18 months, but have they made any impact in solving real bioinformatics challenges? This talk will detail the Sanger Institute's experiences with the cloud, both good and bad, and ask what needs to be done to prepare the cloud for the era of commodity sequencing and $500 genomes.
+
[[Category:BOSC Conferences]]
−
 
 
−
=== Ross Gardler ===
 
−
 
 
−
Our other keynote speaker will be [http://www.linkedin.com/in/rossgardler Ross Gardler], Vice President for Community Development at the Apache Software Foundation and Manager for OSS Watch (University of Oxford), which helps institutions and projects in the UK that are using or developing free and open source software.  He has also performed Computer Science and Management research and teaching in both the UK and West Indies.  In his talk, he will share with the O|B|F community the insights he has gained in community building for Apache and other open source projects.
 
−
 
 
−
== List of confirmed speakers from submitted abstracts ==
 
−
 
 
−
This list is in no particular order, the exact schedule of talks will be forthcoming.
 
−
 
 
−
Click on the talk title to view the abstract as a PDF file.
 
−
 
 
−
* Christopher Fields and Mark Jensen: [[Media:22_BOSC2010.pdf | Towards a Modern BioPerl: BioPerl Update 2010]]
 
−
* Raoul J.P. Bonnal: [[Media:15_BOSC2010.pdf | BioRuby 2010 updates: moving to agile bioinformatics]]
 
−
* Peter Rice: [[Media:14_BOSC2010.pdf | EMBOSS: The European Molecular Biology Open Software Suite]]
 
−
* Peter Cock/Brad Chapman: [[Media:16_BOSC2010.pdf | Biopython Project Update]]
 
−
* Laurent Gautier: [[Media:2_BOSC2010.pdf | Bioconductor with Python, What else ?]]
 
−
* Tiago Antao: [[Media:13_BOSC2010.pdf | interPopula: Database and tool integration for population genetics using Python]]
 
−
* Eric W Talevich: [[Media:8_BOSC2010.pdf | Bio.Phylo: A unified phylogenetics toolkit for Biopython]]
 
−
* Ronald Taylor: [[Media:29_BOSC2010.pdf | An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics]]
 
−
* M. Hanna: [[Media:18_BOSC2010.pdf | The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data]]
 
−
* [[Media:40_BOSC2010.pdf | Hybrid Cloud and Cluster Computing Paradigms for Life Science Applications]]
 
−
* [[Media:26_BOSC2010.pdf | Community-driven computational biology with Debian and Taverna]]
 
−
* [[Media:39_BOSC2010.pdf | SeqWare Query Engine: Storing and Searching Sequence Data in the Cloud]]
 
−
* [[Media:3_BOSC2010.pdf | Dealing with the Data Deluge: What can the Robotics Community Teach us?]]
 
−
* [[Media:4_BOSC2010.pdf | From Moby to SADI - Modeling Semantic Web Services with the Semantic Automated Discovery and Integration Framework]]
 
−
* [[Media:5_BOSC2010.pdf | Long-term availability of bioinformatics web services]]
 
−
* [[Media:6_BOSC2010.pdf | G-language Bookmarklet: a gateway for Semantic Web, Linked Data, and Web Services]]
 
−
* [[Media:21_BOSC2010.pdf | ONTO-ToolKit: enabling bio-ontology engineering via Galaxy]]
 
−
* [[Media:25_BOSC2010.pdf | Connecting TOPSAN to Computational Analysis]]
 
−
* [[Media:20_BOSC2010.pdf | Musite: Global Prediction of General and Kinase-Specific Phosphorylation Sites]]
 
−
* [[Media:36_BOSC2010.pdf | Building Bioinformatics Web Application with Clickframes]]
 
−
* [[Media:24_BOSC2010.pdf | MOLGENIS: rapid prototyping of biosoftware at the push of a button]]
 
−
* [[Media:17_BOSC2010.pdf | Generating a data platform for microarray gene expression experiments using MOLGENIS and MAGE-TAB]]
 
−
* [[Media:10_BOSC2010.pdf | BioHDF: Open binary file formats for NGS data - current status and future directions]]
 
−
* [[Media:30_BOSC2010.pdf | Automated Annotation of NGS Transcriptome Data using ISGA and Ergatis]]
 
−
* [[Media:12_BOSC2010.pdf | Cytoscape Web: An interactive, customizable web-based network browser]]
 
−
* [[Media:38_BOSC2010.pdf | Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API]]
 
−
* [[Media:34_BOSC2010.pdf | GBrowse2]]
 
−
* [[Media:11_BOSC2010.pdf | Fiji Is Just ImageJ - an Open Source platform for biological image analysis]]
 
−
* [[Media:32_BOSC2010.pdf | IPRStats: visualization and analysis of InterProScan Results]]
 
−
* [[Media:9_BOSC2010.pdf | The Microsoft Biology Foundation]]
 
−
* [[Media:28_BOSC2010.pdf | Concurrent Bioinformatics Software for Discovering Genome-wide Patterns and Word-based Genomic Signatures]]
 

Latest revision as of 18:13, 7 September 2015

  • Return to BOSC 2010 main page.
  • BOSC 2010 Proceedings: The Proceedings have been published as of 21 December 2010 in BMC Bioinformatics.
  • Click here to download the BOSC 2010 program and schedule as a PDF file (5 pages, 300k)
  • Click here to download all abstracts compiled into one PDF file (2 MB).
  • Important Information for Speakers
  • Slides for both days' talks are up on SlideShare under the username "bosc2010". Individual links to each talk are posted on the schedule below.

Schedule

Click on the talk title to view the individual abstract as a PDF file.

Day 1 Friday July 9: Hynes Convention Center room 207
7:30-9:00AM Registration Pick up badges for BOSC 2010, Hynes Convention Center (early arrival is recommended as there are usually long lines)
9:00-9:15AM Kam Dahlquist [Welcome] Introduction to the OBF and Welcome to BOSC 2010
9:15-10:15 Guy Coates [Keynote] Clouds: all fluff and no substance? ***SLIDES***
10:15-10:45 Coffee Break
10:45-11:05 Ronald Taylor [Cloud Computing/HT 'omics Data] An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics ***SLIDES***
11:05-11:25 M. Hanna [Cloud Computing/HT 'omics Data] The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data ***SLIDES***
11:25-11:45 Brian D. O'Connor [Cloud Computing/HT 'omics Data] SeqWare Query Engine: Storing and Searching Sequence Data in the Cloud ***SLIDES***
11:45-12:00PM Judy Qiu [Cloud Computing/HT 'omics Data] Hybrid Cloud and Cluster Computing Paradigms for Life Science Applications ***SLIDES***
12:00-12:15 Ben Langmead [Cloud Computing/HT 'omics Data] Cloud-scale genomics: examples and lessons ***SLIDES***
12:15-12:30 Enis Afgan [Cloud Computing/HT 'omics Data] Deploying Galaxy on the Cloud ***SLIDES***
12:30-2:00 Lunch
2:00-2:20 Steffen Möller [Cloud Computing] Community-driven computational biology with Debian and Taverna ***SLIDES***
2:20-2:40 Darin London [Cloud Computing/HT 'omics Data] Dealing with the Data Deluge: What can the Robotics Community Teach us? ***SLIDES***
2:40-3:00 Nyasha Chambwe [HT 'omics Data] The Goby framework: towards efficient next-generation sequencing data analysis ***SLIDES***
3:00-3:15 Dana Robinson [HT 'omics Data] BioHDF: Open binary file formats for NGS data - current status and future directions ***SLIDES***
3:15-3:30 Jens Lichtenberg [HT 'omics Data] Concurrent Bioinformatics Software for Discovering Genome-wide Patterns and Word-based Genomic Signatures ***SLIDES***
3:30-3:38 Chris Hemmerich [HT 'omics Data] Automated Annotation of NGS Transcriptome Data using ISGA and Ergatis ***SLIDES***
3:38-4:00 Coffee Break
4:00-4:20 Mark Wilkinson [Semantic Web] From Moby to SADI - Modeling Semantic Web Services with the Semantic Automated Discovery and Integration Framework ***SLIDES***
4:20-4:35 Aravind Venkatesan [Semantic Web] ONTO-ToolKit: enabling bio-ontology engineering via Galaxy ***SLIDES***
4:35-4:45 Kazuharu Arakawa [Semantic Web] G-language Bookmarklet: a gateway for Semantic Web, Linked Data, and Web Services ***SLIDES***
4:45-4:55 Christian M Zmasek [Semantic Web] Connecting TOPSAN to Computational Analysis ***SLIDES***
4:55-5:10 Jianjiong Gao [OS Software] Musite: Global Prediction of General and Kinase-Specific Phosphorylation Sites ***SLIDES***
5:10-5:18 Hervé Ménager [Lightning Talk] Mobyle Bioinformatics Web Portal: project update ***SLIDES***
5:18-5:26 Stuart Owen [Lightning Talk] The Taverna 2.2 Workflow Workbench with a case study using it for Next Gen Sequencing of African cows ***SLIDES***
5:26-5:34 Jiten Bhagat [Lightning Talk] BioCatalogue - the Public Curated Registry of Life Science Web Services ***SLIDES***
5:34-5:42 Christian M Zmasek [Software Demo] Evolutionary tree visualization and analysis with Archaeopteryx ***SLIDES***
5:42-5:50 Aleksi Kallio [Lightning Talk] Connecting Chipster genome browser to the cloud ***SLIDES***
5:50-5:58 Christopher Bottoms [Lightning Talk] SNP Allele Designations (Bio::SNP::Inherit) ***SLIDES***
5:58-6:06 Tomasz Puton [Lightning Talk] BioPython modules for handling RNA sequences containing modified nucleosides ***SLIDES***
6:06-6:15 Brad Chapman [Lightning Talk] Codefest 2010 Report
6:15-6:45   Birds of a Feather
6:45   OBF Board Meeting and No-host Dinner; Location: Legal Seafood
Day 2 Saturday July 10: Hynes Convention Center room 207
9:00-9:15AM Kam Dahlquist [Announcements]
9:15-10:15 Ross Gardler [Keynote] Community Development at the Apache Software Foundation ***SLIDES***
10:15-10:45 Coffee Break
10:45-11:05 Christopher Fields [Bio* Update] Towards a Modern BioPerl: BioPerl Update 2010 ***SLIDES***
11:05-11:20 Raoul J.P. Bonnal [Bio* Update] BioRuby 2010 updates: moving to agile bioinformatics ***SLIDES***
11:20-11:35 Peter Rice [Bio* Update] EMBOSS: The European Molecular Biology Open Software Suite ***SLIDES***
11:35-11:50 Brad Chapman [Bio* Update] Biopython Project Update 2010 ***SLIDES***
11:50-12:05PM Tiago Antao [OS software] interPopula: Database and tool integration for population genetics using Python ***SLIDES***
12:05-12:20 Laurent Gautier [Bio* Update] Bioconductor with Python, What else ? ***SLIDES***
12:20-12:30 Eric W Talevich [Bio* Update] Bio.Phylo: A unified phylogenetics toolkit for Biopython ***SLIDES***
12:30-2:00 Lunch
2:00-2:20 Simon Mercer [OS Software Framework] The Microsoft Biology Foundation ***SLIDES***
2:20-2:40 William Crawford [OS Software/Code Generation] Building Bioinformatics Web Application with Clickframes
2:40-3:00 Morris A. Swertz [OS Software/Code Generation] MOLGENIS: rapid prototyping of biosoftware at the push of a button ***SLIDES***
3:00-3:10 Alexandros Kanterakis [OS Software/Code Generation] Generating a data platform for microarray gene expression experiments using MOLGENIS and MAGE-TAB ***SLIDES***
3:10-3:25 Sebastian J. Schultheiss [Web Services] Long-term availability of bioinformatics web services ***SLIDES***
3:25-4:00 Coffee Break
4:00-4:15 Lincoln Stein [Visualization] GBrowse2 ***SLIDES***
4:15-4:35 Gary D. Bader [Visualization] Cytoscape Web: An interactive, customizable web-based network browser ***SLIDES***
4:35-4:50 Nobuaki Kono [Visualization] Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API ***SLIDES***
4:50-5:05 James A. Morris [Visualization] Evoker: a visualization tool for genotype intensity data ***SLIDES***
5:05-5:20 Pavel Tomancak [Visualization] Fiji Is Just ImageJ - an Open Source platform for biological image analysis
5:20-5:30 Iddo Friedberg [Visualization] IPRStats: visualization and analysis of InterProScan Results ***SLIDES***
5:30-6:00 Birds of a Feather
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