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SUSTC-Shenzhen B
iGEM 2013 Asia Regional Jamboree October 5, 2013
SUSTC-Shenzhen B
iGEM 2013 Asia Regional Jamboree October 5, 2013
How to visit our software
SUSTC-Shenzhen B Asia Regional Jamboree October 5, 2013 How to - - PowerPoint PPT Presentation
SUSTC-Shenzhen B Asia Regional Jamboree October 5, 2013 How to - - PowerPoint PPT Presentation
iGEM 2013 SUSTC-Shenzhen B Asia Regional Jamboree October 5, 2013 How to visit our software iGEM 2013 SUSTC-Shenzhen B Asia Regional Jamboree October 5, 2013 Problem 1:Synthetic Biology calls for more sharing openwetware.org Sharing
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What’s next? Sharing genetic circuits!
Problem 1:Synthetic Biology calls for more sharing
Background—Demo—Software –Future—Human Practice—Team--Acknowledgement
- penwetware.org
Sharing protocols, course and lab notebook partsregistry.org Sharing Biobrick™ igem.org Sharing student wiki
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Problem 2:Genetic circuit is not well defined, not standard
Background—Demo—Software –Future—Human Practice—Team--Acknowledgement
But genetic circuits are not defined in partsregistry!
Four categories in partsregistry:
- Promoter
- RBS
- Coding sequence
- Terminator
Part:BBa_K228101 Composite parts
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Background—Demo—Software –Future—Human Practice—Team--Acknowledgement
Data from parts.iGEM.org
Promoter 18% RBS 3% Protein Domain 2% Protein Coding Regions 39% Transcriptional Terminators 3%
Composite Parts 35%
PARTS DISTRIBUTION
Problem 2:Genetic circuit is not well defined, not standard
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Problem 3: Genetic circuit data is scattered
Background—Demo—Software –Future—Human Practice—Team--Acknowledgement
Genetic Circuit
Papers Others Synthetic Biology website iGEM teams’ wiki
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Our solution
Background—Demo—Software–Future—Human Practice—Team—Acknowledgement
More sharing Central database Circuit Standard Form
A registry of standard genetic circuit
Sharing platform
Central database Logical Genetic Designer
An online software for sharing
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Background—Demo—Software –Future—Human Practice—Team—Acknowledgement
Demo
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Feature 1: Sharing platform ——Mind Road
Background—Demo—Software –Future—Human Practice—Team—Acknowledgement
A novel approach to show the Synthetic Biology projects
- Online platform
- Systematic Category
- Brainstorming Mode
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Background—Demo—Software–Future—Human Practice—Team—Acknowledgement
Description Protocol Circuit Reference Comment
Feature 1: Sharing platform ——Mind Road
- The standard project information
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Feature 2: Central Database—— Circuit Registry
Background—Demo—Software–Future—Human Practice—Team—Acknowledgement
- A genetic circuit is composed of genetic Coding-frame(s)
- A Coding-frame is composed of four types of Biobrick™:
Promoter, RBS, coding sequence, terminator
- Different coding frame can set up a logical regular system.
- A genetic circuit should be given some labels in order to sort
into the Mind Road.
BBF RFC 97 Genetic Circuit Standard (version1.0)
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Background—Demo—Software–Future—Human Practice—Team—Acknowledgement
Evaluation system
The circuit is reported to be functional in peer-reviewed journals. The circuit is reported by one iGEM team and independently successfully reproduced by another iGEM team. The circuit is reported by one iGEM team.
- Feature 2: Central Database—— Circuit Registry
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Feature 3: Logical Genetic Designer (LGD)
Background—Demo—Software–Future—Human Practice—Team—Acknowledgement
- LGD is a computer aided designer for synthetic biology
- The Structure of a Genetic Circuit in the standard significance.
Genetic Circuit Coding-frame Biobrick™ Large Small
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Feature 3: Logical Genetic Designer (LGD)
Background—Demo—Software–Future—Human Practice—Team—Acknowledgement
- preliminarily redesign the existing circuit in BioMiao.
The LacI is at a highly expression restraining all the promoters and the GFP is at a low level for araC is lowered by LacI the expressivity of LacI is becoming lower. So arac increase with GFP While araC increasing the expression of LacI is increasing to. Then it came back to the first stem and the GFP is at a low expression.
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How to upload a project and run it
Background—Demo—Software–Future—Human Practice—Team—Acknowledgement
Sharing your circuit by submitting!
Submit Validation Display & share Comment & Exchange
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Result
Background—Demo—Software–Future—Human Practice—Team—Acknowledgement
70+ previous iGEM projects 5 projects which were published in papers like CELL, etc. ALL the iGEM 2013 Asian wetware projects.
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User experience
Background—Demo—Software–Future—Human Practice—Team—Acknowledgement
- FEEDBACK from Prof. King Chow of 2013 HKUST iGEM team
The idea of sharing the projects is good. But pay attention to the verification of the submitted projects, it’s a rough work and need some professional volunteers to help you.
- FEEDBACK from 2013 iGEM team Peking:
“The surface of the page is great! The most impressive part is the animation of the mind road. This summary is highly significant because the iGEM community desperately need a sorting software. We will upload our information when this software is complete.”
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Technology support Online design Project sharing Genetic circuit database Experimental experience
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Future
Background—Demo—Software–Future—Human Practice—Team—Acknowledgement
Amateur Researchers iGEMers
Realization
Idea Idea
Idea
Idea
Idea
Idea
Idea
Support
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Human practice
Background—Demo—Software –Future—Human Practice—Team--Acknowledgement
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Team
Background—Demo—Software–Future—Human Practice—Team—Acknowledgement
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Acknowledgement
Background—Demo—Software–Future—Human Practice—Team—Acknowledgement
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Thank Y hank You!
- u!
BioMiao
A registry of standard genetic circuit
http://www.sustc- genome.org.cn/igem2013/index.html