Bioinformatics meets Go

by otiai10

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Bio- informatics meets Go #gocon 2017 Autumn @otiai10

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whoami ● 落合展 ○ github.com/otiai10 ○ DRYな備忘録 ○ WETな備忘録 ● Prev: Dev Agency in Deu. (RoR, Swift, React/ReactNative) ● Now: Academical Inst. (Go, Electron)

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Product we’re making Genome Analysis Platform “SeqPod” is a desktop app for non-IT biologists, by which they can easily execute massive and complex analysis. is a protocol for bioinformaticians, by which they can easily publish workflows: and cli tools for that.

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Bio- informatics meets Go Pros

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Easy to Write ● Static Types ○ Support by Editors ■ GoLand ■ Atom + go-plus + … ■ Vim + vim-go ■ etc … ● even fast compiling ←

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Fast Enough ● Fast itself // TODO: source required ● Need to parse huge sized files ○ DNA, RNA, Proteins… ~10TB ● by using massive “Super Computer” ○ CPU cores: 1200 ○ Memory max: 2TB ○ Disk: 12PiB ● Good match to write goroutines ○ all I can use!!

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Portability ● Go itself ○ easy to start writing Go, just with locating go/src and setting PATH ● To deliver CLI tools to customers ○ Amazing Cross Compiling ○ you can shut them up who always say “it doesn’t work in my Python version”

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Bio- informatics meets Go Cons

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Nobody Helps Especially in Japan https://github.com/seqpod

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Packages Missing https://github.com/search?q =bioinformatics&type=Repo sitories

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Ambiguity of Biology

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Ambiguity of Biology ● ex) File extensions ○ .fasta .fa .fna .ffn .faa .fra ○ are ALL THE SAME THING ● One of global standard data structure of Bio ○ has a field which is dictionaries sometimes, lists sometimes, array of list sometimes, or simple strings sometimes ■ so hard to decode to Go struct ;(

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Wrapping up feelings Go in Bio-info

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Wrapping up feelings Go in Bio-info Non-Web Context

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Wrapping up feelings Go in Bio-info Non-Web Context 1. First-mover Advantage

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Wrapping up feelings Go in Bio-info Non-Web Context 1. First-mover Advantage 2. Good match with strict protocoled industry/market

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Wrapping up feelings Go in Bio-info Non-Web Context 1. First-mover Advantage 2. Good match with strict protocoled industry/market 3. Excellently Easy to deliver CLI a. Even for server application, GAE/Go is very good for private web-app, cz it’s so economic

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1. First-mover Advantage 2. Good match with strict protocoled industry/market 3. Excellently Easy to deliver CLI a. Even for server application, GAE/Go is very good for private web-app, cz it’s so economic 4. Except for low salary Wrapping up feelings Go in Bio-info Non-Web Context

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終わ

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終わらない

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How to make carrier and SURVIVE

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Salary is God

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Salary is /Go{1,2}d?/

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すなわちインカム

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学習

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習得

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NOT ONLY

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BUT ALSO

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どう活かすか

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どう活かすか

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How to Leverage

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不足

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経歴

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insufficiency

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即ち個性

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即ち希少性

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insufficiency is identity and rarity

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「もっと◯◯だったら...」

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否

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◯◯ではないこと（□□であること）が優位性となるフィールドがある