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Agenda
• Motivation
• Introduction to Google Wave
• SynBioWave Main Robot
• Add-on Robots
• Live Demo
Motivation
Scientist in Germany
Scientist in India
Scientist in the USA
SynBioWave offers collaboration for Biologists
Online
Motivation → Introduction Google Wave → Architecture → SynBioWave Main Robot → Add-on Robots → Live Demo
Free
Documentation
Live
Google Wave
• Online collaboration platform
• combines e-mail, chat, forum, etc.
• Web based
• Introduced in 2009
• Customizable
Motivation → Introduction Google Wave → Architecture → SynBioWave Main Robot → Add-on Robots → Live Demo
Google Wave
Motivation → Introduction Google Wave → Architecture → SynBioWave Main Robot → Add-on Robots → Live Demo
Robots and Gadgets
Robots
• Automated chat participant
• Runs on a server (Appengine)
• Can read and write to the wave
Gadgets
• Client-side java script application
• Mostly used for GUI
• Limited access to wave content
Architecture
Motivation → Introduction Google Wave → Architecture → SynBioWave Main Robot → Add-on Robots → Live Demo
• Extends the features of wave
• Can be added like a normal contact
SynBioWave Main Robot [email protected]
Motivation → Introduction Google Wave → Architecture → SynBioWave Main Robot → Add-on Robots → Live Demo
Add-on Robots
• Extend the main robot
• Can be combined in a custom way
• Developers can create their own robots
Motivation → Introduction Google Wave → Architecture → SynBioWave Main Robot → Add-on Robots → Live Demo
Translation Robot
• Finds open reading frames
• Translates sequences
Motivation → Introduction Google Wave → Architecture → SynBioWave Main Robot → Add-on Robots → Live Demo
REBase Robot
• Finds restriction enzyme binding sites
Motivation → Introduction Google Wave → Architecture → SynBioWave Main Robot → Add-on Robots → Live Demo
Codon Usage Robot
• Analyzes codon usage of sequences
• Compares it to codon usage of Human, E.coli and Yeast
Motivation → Introduction Google Wave → Architecture → SynBioWave Main Robot → Add-on Robots → Live Demo
Alignment Robot
• Compares sequences using alignment algorithms
• Global and local alignments
Motivation → Introduction Google Wave → Architecture → SynBioWave Main Robot → Add-on Robots → Live Demo
Primer Designer Robot
• Calculates primers for PCR
Motivation → Introduction Google Wave → Architecture → SynBioWave Main Robot → Add-on Robots → Live Demo
BLAST Robot
• Uses NCBI BLAST
• Submits jobs and evaluates results
Motivation → Introduction Google Wave → Architecture → SynBioWave Main Robot → Add-on Robots → Live Demo
Live Demo
Motivation → Introduction Google Wave → Architecture → SynBioWave Main Robot → Add-on Robots → Live Demo
Prospects
• Google discontinues Wave servers
Wave internal comunication
HTTP/HTTPS Request
User I/O (local)
User Gadget
Wave Client
Wave Server
SynBioWave RobotAdd-on Robots
Wave
External Server
e.g. NCBI BLAST
SynBioWave API
Go
ogle
Wave
AP
I
Acknowledgement
Other Freiburg_Software team members:
• Paul Staab
• Jörg Walossek
• Katja M. Arndt
• Kristian M. Müller
Thank you for your time!
Team Wiki: 2010.igem.org/Team:Freiburg_Software Project Website: www.synbiowave.org http://sourceforge.net/projects/synbiowave/ Or find us on facebook "synbiowave "
