Software tools for iGEMers: BioBrick / Past Project Search & Tutorials Saturday, November 3, 12 1
Background In iGEM... Important part is: “Think & decide your project” iGEM Start to Finish Saturday, November 3, 12 2
Background Lots of time is spent on fi nding 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 Saturday, November 3, 12 3
Our Software - More efficiency! • Learning about essential iGEM concepts ➡ Tutorials … Obtain knowledge easily! • Search past projects relevant to yours • Decide what BioBrick parts to use ➡ New Search System … Save your time & labor! ➡ Web base … Easy & speedy to use! Saturday, November 3, 12 4
Our Software • Tutorial BioBrick Puzzle Gene Network Game • Search Past Project Search BioBrick Search Saturday, November 3, 12 5
Our Software • Tutorial BioBrick Puzzle Gene Network Game • Search Past Project Search BioBrick Search Saturday, November 3, 12 6
Tutorial - Concept • Target ‣ iGEM beginners • Subject ‣ BioBrick Standard Assembly ‣ Dynamics of Genetic Network Saturday, November 3, 12 7
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 Saturday, November 3, 12 8
Tutorial - Feature • Interactive … Learning e ffi ciently • Game … Keeping users interested • Contents relevant to iGEM Saturday, November 3, 12 9
Let's watch the Video: BioBrick Puzzle & Gene Network game Saturday, November 3, 12 10
(Video part) Saturday, November 3, 12 11
Text (Video part) Saturday, November 3, 12 12
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 Saturday, November 3, 12 13
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 e ffi ciently Saturday, November 3, 12 14
Our Software • Tutorial BioBrick Puzzle Gene Network Game • Search Past Project Search BioBrick Search Saturday, November 3, 12 15
Our Software • Tutorial BioBrick Puzzle Gene Network Game • Search Past Project Search BioBrick Search Saturday, November 3, 12 16
Past Project Search - Background Past team information is scattered • Any of these pages do not contain enough information • These pages are divided by years Saturday, November 3, 12 17
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 Saturday, November 3, 12 18
(Video part) Saturday, November 3, 12 19
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 Saturday, November 3, 12 20
Our Software • Tutorial BioBrick Puzzle Gene Network Game • Search Past Project Search BioBrick Search Saturday, November 3, 12 21
BioBrick Search - Introduction BioBrick Search • is a novel BioBrick Search tool • provides more e ffi ciency and reliability Saturday, November 3, 12 22
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 insu ffi cient TOKYO S O F T W A R E Saturday, November 3, 12 23
BioBrick Search - Video (Video part) Saturday, November 3, 12 24
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 Saturday, November 3, 12 25
Collaboration • Publicly available since this August ‣ Made a community post at iGEM o ffi cial page ‣ Accessed from 16 di ff erent 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 Saturday, November 3, 12 26
Our Software • Tutorial BioBrick Puzzle Gene Network Game • Search Past Project Search BioBrick Search Saturday, November 3, 12 27
Attributions Saturday, November 3, 12 28
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