Resources to learn more about efficient large-scale computing skills
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This page has a long list of resources to learn about efficient large-scale computing.
Blog posts
2022
生物情報科学科での学部教育
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私は，生物情報科学という，生物学と情報科学の融合分野について，学部生の段階で先進的な教育を受ける機会に恵まれました。私が在籍したときは，学年の学生人数は10人程度，一方で教授陣も約10人ほどと，学生定数：教員数がほぼ 1:1 というとても恵まれた環境で，最先端の学問分野を指導していただくことができました。
2021
Stanford での大学院生活・大学院出願準備に関するリソース
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This post is written in Japanese. Yosuke explains his life at Stanford.
News (2021)
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Here are the exciting moments in 2021! We have other news posts.
2020
Notes on Apache Columnar format
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There are several column-oriented data formats. To store and query large table files, we explor those modern technologies. Here, I have some snippets.
高校生への科学アウトリーチ活動
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Occasionally, Yosuke performs science outreach talks. This post explains an example of such activities targeted for Japanese high schoolers.
Egronomics
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Kinesis Advantageous 2 keyboard.
Using tmux on mac
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Terminal multiplexer software, such as tmux and screen, is a useful tool. When using tmux on mac, I encountered the following error.
GWAS and genetic analyses with PLINK2 and pgenlibr
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PLINK is a well-established software for genetic analysis. In many projects, we use plink2 for genome-wide association studies (GWAS) and other genetic analyses using the raw genotype matrix.
Working with very small values in R
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When you’re working on extremely small floating numbers in R (such as when you have strong p-values), there are a few options.
船井情報科学振興財団による Funai Overseas Scholarship
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This post is written in Japanese. Yosuke explains his fellowship support from the Funai Foundation for Information Technology, which supports Japanese citizens and permanent residents. You may have some luck with DeepL translator.
Using Bundler via Docker on mac
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Ruby bundler is a convenient tool to manage the Ruby environments. This website, for example, is built with Jekyll.
figshare API
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Figshare is a data hosting service to make the scientific results available. While they have a nice web interface to upload your files, you sometimes want to upload a large file (> 5GB, for example). For that purpose, they provide an API access. Here is my example on how to use their API.
Useful links
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Here, I list publicly available resources.
Commonly used commands in high performance cluster computing with Slurm workload manager
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SLURM is one of the most common job scheduler used in many high performance cluster computing severs (HPC). Here, I summarize useful SLURM commands.
COVID-19 host genetics に関する研究
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This post is written in Japanese. Please check my post on our recent preprint, Tanigawa, Y. & Rivas, M. Initial Review and Analysis of COVID-19 Host Genetics and Associated Phenotypes. (2020). Also, you may have some luck with DeepL translator.
News (2020)
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Thanks to my colleagues and supports from the community, we had several exciting moments in 2020! We have other news posts.