Software tools for iGEMers: BioBrick / Past Project Search & - - PowerPoint PPT Presentation

Software tools for iGEMers: BioBrick / Past Project Search & Tutorials

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Background

In iGEM... Important part is: “Think & decide your project” iGEM Start to Finish

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Background

Lots of time is spent on finding information required for “Think & decide your project” part Such as ...

• Learning about essential iGEM concepts
• Searching past projects relevant to yours
• Deciding what BioBrick parts to use

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Our Software - More efficiency!

• Learning about essential iGEM concepts
• Search past projects relevant to yours
• Decide what BioBrick parts to use

➡ Tutorials … Obtain knowledge easily! ➡ New Search System … Save your time & labor! ➡ Web base … Easy & speedy to use!

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Our Software

• Tutorial
• Search

BioBrick Puzzle Gene Network Game Past Project Search BioBrick Search

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Our Software

• Tutorial
• Search

BioBrick Puzzle Gene Network Game Past Project Search BioBrick Search

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Tutorial - Concept

• Target
• iGEM beginners
• Subject
• BioBrick Standard Assembly
• Dynamics of Genetic Network

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Tutorial - Background

• Beginners
• Many of iGEM participants are new-comers
• Spend a lot of time learning about iGEM
• BioBrick / Genetic Network
• All teams must learn
• No adequate educational materials

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Tutorial - Feature

• Interactive … Learning efficiently
• Game … Keeping users interested
• Contents relevant to iGEM

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Let's watch the Video: BioBrick Puzzle & Gene Network game

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(Video part)

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Text (Video part)

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Tutorial - text-based guides

Text-based guides describing

• Background knowledge useful to understanding the games

For the BioBrick Puzzle,

• Principles and characteristics of BioBricks

For the Gene Network Game,

• Background knowledge of genetic networks & modeling

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Tutorial - Conclusion

• BioBrick Puzzle
• Learn BioBrick Standard Assembly
• Gene Network Game
• Learn genetic networks
• Understand & design constructs
• Acquire basic skills to conduct modeling
• Beginners can learn proper knowledge efficiently

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Our Software

• Tutorial
• Search

BioBrick Puzzle Gene Network Game Past Project Search BioBrick Search

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Our Software

• Tutorial
• Search

BioBrick Puzzle Gene Network Game Past Project Search BioBrick Search

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Past Project Search - Background

Past team information is scattered

• Any of these pages do not contain enough information
• These pages are divided by years

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Past Project Search - Features

• Search across multiple years
• Integration of scattered information
• Title, Abstract, School info, Presentation materials ...
• Filtering by
• Track, Medal, Year, Award & Region
• Simple & user-friendly interface

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(Video part)

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Past Project Search - Conclusion

Improved the accessibility to past iGEM teams’ data

• Across multiple years
• Displayed all at once
• Can be narrowed down as necessary

Likely to be useful for

• iGEMers studying previous researches
• Any people who interested in iGEM

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Our Software

• Tutorial
• Search

BioBrick Puzzle Gene Network Game Past Project Search BioBrick Search

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BioBrick Search - Introduction

BioBrick Search

• is a novel BioBrick Search tool
• provides more efficiency and reliability

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TOKYO

S O F T W A R E

BioBrick Search - Background

Conventional Search at partsregistry.org

• Not very useful
• Problems we spotted:
• Results are not sorted by

reliability or relevance

• Information given in the

result list is insufficient

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BioBrick Search - Video

(Video part)

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Methods for retrieving data

We made scripts for retrieving data & storing them into server

• They automatically collect necessary data from:
• Past Project Search ... wiki, team info, jamboree result page
• BioBrick Search ... partsregistry database and wiki

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• Publicly available since this August
• Made a community post at iGEM official page
• Accessed from 16 different countries
• Received favorable responses
• “We successfully found the appropriate parts from their

functions”

• “We took into account the "reliability" score to determine

which BioBrick parts to use”

• Made improvements based on feedbacks from users
• Search history at the top of the page
• Direct link to the partsregistry.org wiki page

Collaboration

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Our Software

• Tutorial
• Search

BioBrick Puzzle Gene Network Game Past Project Search BioBrick Search

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Attributions

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