BOSC 2010 Schedule

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Keynote Speakers

Guy Coates

Guy Coates, Group leader of the Informatics Systems Group at the 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:

Clouds: all fluff and no substance? Cloud architectures have made plenty of impact in the press over the 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.

Ross Gardler

Our other keynote speaker will be 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.

Schedule

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

Day 1	Friday	July 9
9:00-9:15AM	Kam Dahlquist	[Welcome] Introduction to the O|B|F and Welcome to BOSC 2010
9:15-10:15	Guy Coates	[Keynote] Clouds: all fluff and no substance?
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
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
11:25-11:45	Brian D. O'Connor	[Cloud Computing/HT 'omics Data] SeqWare Query Engine: Storing and Searching Sequence Data in the Cloud
11:45-12:00PM	Judy Qiu	[Cloud Computing/HT 'omics Data] Hybrid Cloud and Cluster Computing Paradigms for Life Science Applications
12:00-12:15	Ben Langmead	[Cloud Computing/HT 'omics Data] Cloud-scale genomics: examples and lessons
12:15-12:30	Enis Afgan	[Cloud Computing/HT 'omics Data] Deploying Galaxy on the Cloud
12:30-2:00		Lunch
2:00-2:20	Steffen Möller	[Cloud Computing] Community-driven computational biology with Debian and Taverna
2:20-2:40	Darin London	[Cloud Computing/HT 'omics Data] Dealing with the Data Deluge: What can the Robotics Community Teach us?
2:40-3:00	Nyasha Chambwe	[HT 'omics Data] The Goby framework: towards efficient next-generation sequencing data analysis
3:00-3:15	Dana Robinson	[HT 'omics Data] BioHDF: Open binary file formats for NGS data - current status and future directions
3:15-3:30	Jens Lichtenberg	[HT 'omics Data] Concurrent Bioinformatics Software for Discovering Genome-wide Patterns and Word-based Genomic Signatures
3:30-3:38	Chris Hemmerich	[HT 'omics Data] Automated Annotation of NGS Transcriptome Data using ISGA and Ergatis
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
4:20-4:35	Aravind Venkatesan	[Semantic Web] ONTO-ToolKit: enabling bio-ontology engineering via Galaxy
4:35-4:45	Kazuharu Arakawa	[Semantic Web] G-language Bookmarklet: a gateway for Semantic Web, Linked Data, and Web Services
4:45-4:55	Christian M Zmasek	[Semantic Web] Connecting TOPSAN to Computational Analysis
4:55-5:10	Jianjiong Gao	[OS Software] Musite: Global Prediction of General and Kinase-Specific Phosphorylation Sites
5:10-6:00		[Lightning Talks] Birds of a Feather
6:30		O|B|F Board Meeting and No-host Dinner; Location TBA
Day 2	Saturday	July 10
9:00-9:15AM	Kam Dahlquist	[Announcements]
9:15-10:15	Ross Gardler	[Keynote] Community Development at the Apache Software Foundation
10:15-10:45		Coffee Break
10:45-11:05	Christopher Fields	[Bio* Update] Towards a Modern BioPerl: BioPerl Update 2010
11:05-11:20	Raoul J.P. Bonnal	[Bio* Update] BioRuby 2010 updates: moving to agile bioinformatics
11:20-11:35	Peter Rice	[Bio* Update] EMBOSS: The European Molecular Biology Open Software Suite
11:30-11:45	Brad Chapman	[Bio* Update] Biopython Project Update
11:45-12:00PM	Tiago Antao	[Bio* Update] interPopula: Database and tool integration for population genetics using Python
12:00-12:15	Laurent Gautier	[Bio* Update] Bioconductor with Python, What else ?
12:15-12:25	Eric W Talevich	[Bio* Update] Bio.Phylo: A unified phylogenetics toolkit for Biopython
12:25-2:00		Lunch
2:00-2:20	Simon Mercer	[OS Software Framework] The Microsoft Biology Foundation
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
3:00-3:10	Alexandros Kanterakis	[OS Software/Code Generation] Generating a data platform for microarray gene expression experiments using MOLGENIS and MAGE-TAB
3:10-3:25	Sebastian J. Schultheiss:	[Web Services] Long-term availability of bioinformatics web services
3:25-4:00		Coffee Break
4:00-4:15	Lincoln Stein	[Visualization] GBrowse2
4:15-4:35	Gary D. Bader	[Visualization] Cytoscape Web: An interactive, customizable web-based network browser
4:35-4:50	Nobuaki Kono	[Visualization] Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API
4:50-5:05	James A. Morris	[Visualization] Evoker: a visualization tool for genotype intensity data
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
5:30-6:00		Birds of a Feather