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 protocols, course and lab notebook partsregistry.org Sharing Biobrick ™ igem.org Sharing student wiki What’s next? Sharing genetic circuits! Background — Demo — Software – Future — Human Practice — Team--Acknowledgement

Problem 2:Genetic circuit is not well defined, not standard Four categories in partsregistry: • Promoter • RBS Composite parts • Part:BBa_K228101 Coding sequence • Terminator But genetic circuits are not defined in partsregistry! Background — Demo — Software – Future — Human Practice — Team--Acknowledgement 4

Problem 2:Genetic circuit is not well defined, not standard PARTS DISTRIBUTION Promoter Composite 18% Parts 35% RBS 3% Protein Domain 2% Transcriptional Protein Coding Terminators Regions 3% 39% Data from parts.iGEM.org Background — Demo — Software – Future — Human Practice — Team--Acknowledgement 5

Problem 3: Genetic circuit data is scattered Papers iGEM teams’ wiki Genetic Circuit Synthetic Biology Others website Background — Demo — Software – Future — Human Practice — Team--Acknowledgement 6

Our solution Circuit Standard Form More sharing Central database A registry of standard genetic circuit An online software for sharing Central database Sharing platform Logical Genetic Designer Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 7

Demo Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 8

Feature 1: Sharing platform —— Mind Road A novel approach to show the Synthetic Biology projects • Online platform • Systematic Category • Brainstorming Mode Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 9

Feature 1: Sharing platform —— Mind Road The standard project information •  Description  Protocol  Circuit  Reference  Comment Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 10

Feature 2: Central Database —— Circuit Registry  BBF RFC 97 Genetic Circuit Standard (version1.0) • 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. Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 11

Feature 2: Central Database —— Circuit Registry - - -  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. - - - - - Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 12

Feature 3: Logical Genetic Designer (LGD) • LGD is a computer aided designer for synthetic biology • The Structure of a Genetic Circuit in the standard significance. Large  Genetic Circuit  Coding-frame  Biobrick ™ Small Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 13

Feature 3: Logical Genetic Designer (LGD) • 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. Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 14

How to upload a project and run it Sharing your circuit by submitting! Submit Validation Display & share Comment & Exchange Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 15

Result  70+ previous iGEM projects  5 projects which were published in papers like CELL, etc.  ALL the iGEM 2013 Asian wetware projects. Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 16

User experience  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.” Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 17

Future Technology support Researchers Idea Support Idea Experimental Online design experience iGEMers Idea Idea Idea Amateur Idea Realization Genetic Project Idea circuit sharing database Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 18

Human practice Background — Demo — Software – Future — Human Practice — Team--Acknowledgement 19

Team Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 20

Acknowledgement Background — Demo — Software – Future — Human Practice — Team — Acknowledgement 21

BioMiao A registry of standard genetic circuit http://www.sustc- genome.org.cn/igem2013/index.html Thank Y hank You! ou!