Re-engineering DNA Surveillance - University of Auckland · Re-engineering DNA Surveillance obiasT...
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Re-engineering DNA Surveillance
Tobias [email protected]
Department of Medical- and Bioinformatics
Upper Austria University of Applied Sciences
Softwarepark 11, 4232 Hagenberg, Austria
Version 1·00·−2 � 26. Mai 2010 � Tobias Ehrenberger
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Outline
1 About DNA Surveillance
2 Motivation and Aims
3 Tasks
4 Architecture
5 The New User Interfaces
6 Conclusion
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
About DNA Surveillance
What is DNA Surveillance?
A species identi�cation tool
using phylogenetic methods
available on the internet.
How does it work?
Input: Unknown Sequence + Reference Alignment
Output: Phylogenetic Tree
Statistical Support
Bootstrapping
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
About DNA Surveillance
What is DNA Surveillance?
A species identi�cation tool
using phylogenetic methods
available on the internet.
How does it work?
Input: Unknown Sequence + Reference Alignment
Output: Phylogenetic Tree
Statistical Support
Bootstrapping
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
About DNA Surveillance
What is DNA Surveillance?
A species identi�cation tool
using phylogenetic methods
available on the internet.
How does it work?
Input: Unknown Sequence + Reference Alignment
Output: Phylogenetic Tree
Statistical Support
Bootstrapping
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Motivation and Aims
Why Re-engineering?
No sources available.
Current system can not be maintained.
Aims
Maintainability
Usability
Flexibility
Modularity
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Motivation and Aims
Why Re-engineering?
No sources available.
Current system can not be maintained.
Aims
Maintainability
Usability
Flexibility
Modularity
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Motivation and Aims
Why Re-engineering?
No sources available.
Current system can not be maintained.
Aims
Maintainability
Usability
Flexibility
Modularity
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Motivation and Aims
Why Re-engineering?
No sources available.
Current system can not be maintained.
Aims
Maintainability
Usability
Flexibility
Modularity
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Motivation and Aims
Why Re-engineering?
No sources available.
Current system can not be maintained.
Aims
Maintainability
Usability
Flexibility
Modularity
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Motivation and Aims
Why Re-engineering?
No sources available.
Current system can not be maintained.
Aims
Maintainability
Usability
Flexibility
Modularity
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Motivation and Aims
Why Re-engineering?
No sources available.
Current system can not be maintained.
Aims
Maintainability
Usability
Flexibility
Modularity
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Tasks
Modules
Database Schema
WebApp for Reference Alignment Setup
Option for auto-generating DNA Surveillance Instances
WebApp for Users
Phylogenetics Server
Preceding Work
Re-engineering started by Waltraud Sichart in 2009
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Tasks
Modules
Database Schema
WebApp for Reference Alignment Setup
Option for auto-generating DNA Surveillance Instances
WebApp for Users
Phylogenetics Server
Preceding Work
Re-engineering started by Waltraud Sichart in 2009
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Tasks
Modules
Database Schema
WebApp for Reference Alignment Setup
Option for auto-generating DNA Surveillance Instances
WebApp for Users
Phylogenetics Server
Preceding Work
Re-engineering started by Waltraud Sichart in 2009
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Architecture
Current DNA Surveillance
New version
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Architecture
Current DNA Surveillance
New version
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
The New User Interface
WebApp for Reference Alignment Setup
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
The New User Interface
User Input Environment
Required:
Reference Alignment
Unknown Sequence
or File of Sequences
Optional:
Bootstrap Analysis
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
The New User Interface
Output:
Results:
Phylogenetic TreeDistance MatrixBS-Results
In addition:
BLAST-Result
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Conclusion
In a nutshell. . .
New DNA Surveillance
consists of modules
provides extended functionality and
is maintainable
Open Tasks
More Tests (+ Bug�xing)
Final Release
. . .
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
Conclusion
In a nutshell. . .
New DNA Surveillance
consists of modules
provides extended functionality and
is maintainable
Open Tasks
More Tests (+ Bug�xing)
Final Release
. . .
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
That's it!
Thank you for your attention!
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Introduction Motivation and Aims Tasks Architecture The new UIs Conclusion
That's it!
Questions?
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