5th Annual Cytoscape Retreat and Symposium

Programme

Find a printable pdf version of the detailed programme and directions here:

Click on the names of the Speakers to find their resumes and abstracts of their talks.
The plugin names are also hyperlinked to their descriptions
The main event is the Public Symposium on November 8^th entitled: Integrative Bioinformatics: At the cutting edge of network analysis and biological data integration. Preceding the symposium is a Tutorials and Application Showcase day (November 7^th) that will be filled with hands-on training sessions and demonstrations of plugin developers.

Surrounding these are the development days; 6^th and 9^th. These are targeted at the core-development team of Cytoscape and (plugin-)developers.

Programme outline

Monday	November 5th	Arrivals Day (development team, organization)
1: Tuesday	November 6th	Software Development Discussions
2: Wednesday	November 7th	Tutorials and Application Showcase day
3: Thursday	November 8th	Public Symposium Integrative Bioinformatics: At the cutting edge of network analysis and biological data integration
4: Friday	November 9th	Cytoscape Development Planning

Detailed Programme

Arrivals Day

Monday November 5th	Arrivals Day (development team and organization)
Where	Amsterdam old city center
09:00-12:00	Potential Development team discussion breakfast
12:00-17:00	Afternoon informal hackathon
17:00-19:00	Meet and greet for development team and organization and other eary arrivals in Cafe de Jaren (next to Doelen Hotel) View Map

Day 1: Software Development Discussions

Tuesday November 6th	Software Development Discussions Suggested Attendees - Cytoscape (plugin-)developers, Scientific Advisory Board(SAB), Cytoscape Board of Directors and other interested parties
Where	AMC Lecture room K 01-123
0845:-09:15	Welcome - Registration - Coffee
09:15-11:00	Overview programme 2.6 Status + Release date 2.7 Possibilities
11:00-11:15	Coffee break
11:15-13:00	3.0 Overview o Motivations o Current problems o Philosophical changes 3.0 Goals 3.0 Timeline
13:00-13:30	Lunch
14:00-15:30	Input process, RFC-s Layering o Model changes o Event handling Plugin Rearchitecture o OSGi o Present Plugin Proto-API Data Integration
15:30-15:15	Coffee and tea break
15:15-18:00	Workflow Process/planning improvements o RFC-s
19:00-(...)	Drinks and dinner for attendees of Day 1 Special surprise event!!!

Day 2: Application showcase and hands-on tutorial sessions

Wednesday November 7th	Application showcase, hands-on tutorial sessions and Cytoscape developers hackathon
Where	Lecture rooms K 01-123	AMC Conference Hall (Collegezaal)2	Lecture rooms K 01-122
Tracks (parallel)	I Tutorials	II Plugins and Application showcase Chair: Gary Bader	III Hackathon/Developers tutorials
08:45-09:15	Welcome - Registration - Coffee
09:15-09:30	Chairman's Welcome: Gary Bader
09:30-11:00	Tutorial Session I	o Mario Albrecht: NetworkAnalyzer o Dorothea Emig: DomainGraph, BiLayout o Ben Hitz: SgdInteractionsPlugin o Maital Ashkenazi: EnhancedSearch o Willem Ligtenberg: Reconn	Kei Ono - Mike Smoot: Vizmapper
11:00-11:20	Coffee break
11:20-13:15	Tutorial Session II	o Aaron Barsky: Cerebral o Sabry Razick: Bioscape o Eugene Rakhmatulin: Metacore o Thomas Kelder: GPML-plugin o Evrim Itir Karac: Molecular Interaction Maps	Scooter Morris: CyGroups, Layout
13:15-13:45	Lunch
13:45-15:45	Tutorial Session III	o Yves Deville: BioEdge o Robert Kincaid: VistaClara o Alan Kuchinsky: Literature search, Hyperedges, Workflow o Alex Pico: BubbleRouter o Christoph Schwarz: Vispara	Kei Ono: Webservices API
15:45-16:00	Coffee and tea break
16:00-18:00	Tutorial Session IV	o Steven Maere: BinGO o Gary Bader: PathwayCommons, GoSlimmer, Thematic Maps o July Dickerson: MetNet tools o Matthias Reimann: EagleVista o Scooter Morris: CyGroups, StructureViz, SFLDLoader	Breakout/Hackathon sessions
19:00-(...)	Guided City tour through Amsterdam

Day 3: Public Symposium (click on name for abstract and resume)

Thursday November 8th	Integrative Bioinformatics: At the cutting edge of network analysis and biological data integration
Where	AMC Conference Hall (Collegezaal) 1
08:45-09:15	Welcome - Registration - Coffee
09:15-09:30	Opening by chair Trey Ideker
09:30-10:15	Keynote Speaker: Leroy Hood: Biological networks and disease
10:15-10:45	Andrew Hopkins: Network Pharmacology: chemical opportunities for systems biology
10:45-11:15	Coffee break
11:15-11:45	Rogier Versteeg: Oncogenic networks of cancer pathways in childhood cancer
11:45-12:30	Chris Sander: Systems Biology of Cancer Pathways: from Molecular Perturbations to Cellular Phenotypes
12:30-13:15	Peter Sorger: Modeling Mammalian Death and Survival Pathways
13:15-14:15	Lunch (separate Cytoscape Board Meeting at lunch)
14:15-15:00	Ruedi Aebersold: Protein-centered networks in systems biology: Analysis and visualization
15:00-15:30	Benno Schwikowski: Computational tools increasing sensitivity and reliability of mass spec-based proteomics
15:30-16:00	Jean-Daniel Fekete: Visualizing Dense Networks with Enhanced and Hybrid Matrices
16:00-16:30	Coffee and tea break
16:30-17:15	Ewan Birney: Reactome, Networks and Genomes
17:15-17:45	Trey Ideker: Gaining power in gene association studies with Cytoscape
17:45-19:00	Drinks reception
19:30-(...)	Dinner for invited guests: Speakers, Organization, SAB/Board , Development team

Day 4: Cytoscape Development Planning

Friday November 9th	Discussions about the next steps for Cytoscape Suggested Attendees - Cytoscape (plugin-)developers, Scientific Advisory Board, Cytoscape Board of Directors and other interested parties
Where	AMC Lecture room K 01-123
9:30-11:00	Programme dependent on Tuesday; updated during retreat
11:00-11:15	Coffee break
11:15-13:00	Tba
13:00-13:30	Lunch
13:30-15:00	Tba
15:00-17:00	Work on Roadmap 2007/ Match Core Developers to Action Items
17:00-18:45	Wrap-up: SAB Input, Board Issues & Future Vision
18:45-(...)	Night out in Amsterdam for attendees of Day 4 A museum night at the van Gogh