Another Japan in the World

Jun Aruga's blog.

Genomics

A bio hackathon - Cambridge UK

Last month, I traveled Cambridge and London again 2nd time this year, then South of London, Brighton and Isle of Wight. I experienced so many things. As it was hard to clear my thoughts by the travel, I was delayed to output it on the blog…

Synthetic Biology and Microsoft

I did read the book "The impact of Synthetic Biology". Unfortunately, this book is only written in Japanese. It's about Synthetic Biology, that is to write a genome. The world first Artificial Cell, Minimal Cell was created by Craig Venter…

Sequencing: Run mapping by bowtie2 and view it on IGV

Previously I ran mapping by Hisat2, and did view it by IGV Sequencing: Run mapping - Another Japan in the World Sequencing: view mapped genome on IGV (Integrative Genomics Viewer) - Another Japan in the World This time, I try to do mapping…

Sequencing: view mapped genome on IGV (Integrative Genomics Viewer)

Install Integrative Genomics Viewer (IGV) [1] to view mapped genome. Use bam file that was created previously. See the blog page. java is used. Install it if it is not installed. $ java -version java version "1.8.0_25" Java(TM) SE Runtime …

Sequencing: Run mapping

This is the next article from Sequencing: Install mapping tools - Another Japan in the World. Try to do mapping by Hisat2 with previous fastq files trimmed by FastQC. Go to Hisat2 official web [1], click H. sapiens GRCh38 "genome" link, an…

An age of DIYBio

I found an interesting open science community. That is Mozilla Science Lab [1]. You can see several projects there. In the past posts on my blog, maybe I have introduced similar communities Elixir Europe [2] and GA4GH [3]. Also I found an …

Sequencing: Install mapping tools

I tried to do mapping the genome data I used before. I tried to install a tool for mapping of the genome. I tried 2 tools: TopHat 2 [1], HISAT2 [2] for that. The result is TopHat 2: I could not install it. HISAT 2: I could install it. This…

Sequencing: Trimming FASTQ file

This article to trim .fastq files. .fastq files outputted from a sequencer can include data with a bad quality score. In the case, we would do trimming the bad data. Use the data used in previous blog post. Genome Sequening: Quality Check …

Sequencing: Quality Check by fastqc

This article to demonstrate how to do quality check for the data from Illumina Sequencer. Download FASTQ file Use publicly uploaded sequencing data on DRA (DDBJ Sequence Read Archive) [1]. You can also download same data from SRA (NCBI Seq…

Reading "実験医学" as e-book

It is no doubt that Amazon and the Kindle store have changed how to read books. Nowadays, people can easily buy and read not only books in their region but also English books, and other books in any region around the world, if those books …

Developments in NGS

X axis: Read length => Read length for each reads Y axis: Gigabses per run => Total read bases per run (unit: Giga) Detail is [1] [1] Detail: Developments in high throughput sequencing – July 2016 edition | In between lines of code

The World first portable genome sequencing device NinION supporting Linux

This is not new information. I just found it today. Oxford Nanopore mobile portable genome sequencer MinION is supporting not only Windows and Mac but also Ubuntu Linux partly! [1][2] MinION Video: MinION: a portable, real-time DNA/RNA seq…

The World Economic Forum at Davos

Recently I was reading a book of Jennifer Doudna who is a RNA biologist and discovered how to edit gene with Crisper Cas9, the revolutional way for genome editing. [1] The book I am reading is the Japanese translation edition. It is a quit…

The most cited genes

This person is ... [1] A software engineer with some training in bioinformatics, he was pursuing a PhD and thought it would really help to know some fundamentals of biology. "A software engineer with some training in bioinformatics" is lik…

Understanding Longevity Industry

To understand it, longevity.international: http://longevity.international/ The reports are good. Juvenescence: Investing in the age of longevity: https://www.amazon.co.jp/dp/B075WXX93Q Just started reading, the book and the structure of co…

Visualization is a key for learning

I realized it recently. I am saving my memory's main structure as an image. It is something like the Tree trunk: saving as an image or sense. Small branches and leaves: saving as an text. To get information from my brain. Maybe I am access…

シークエンサー

日本語で書きます。 理由は、日本語のゲノムの資料を今日読んで、「なんだ、そういうことだったのか」ということがあったからです。 残念なことに、まだまだ日本語の文章を読んだ方が格段に理解ができる、ということがわかりました。 国際ヒトゲノム参照配列…

Amazon and Genomics

Google Genomics, Microsoft Genomics, And now Amazon Web Services with Genomics. Partnership with DNAnexus, Illumina, and Seven Bridges. Getting to Know APN Genomics Partners BioTeam, DNAnexus, Illumina, and Seven Bridges | AWS Partner Netw…

GWAS Catalog webinar

It is really a cool video and etc. The NHGRI-EBI GWAS Catalog, a curated resource of SNP-trait associations | EMBL-EBI Train online

Barcelona Conference

Hello, nice to see you again! This rail is used by tram. My favorite street. It’s near Barcelona Zoo. I attended 2 days genome conference in Barcelona this month. It was a really inspired one. Traveling anywhere, attending conference/works…

Video site for GWAS, and Ensembl

Recently, I am checking SNP/Genotype, Phenotype reference DB about Genomics. Because understanding actual structure in DNA looks easier than understanding behavior inside of DNA. It’s a kind of approach from IT Object Oriented. First I hav…

Thinking of SNP and Personal NGS at a suburb

If living, a suburb is better than central of the city. If staying at hotel for not sightseeing, the suburb is also better. Today is a good day. I got idea there. A Park BIOLOGICKE CENTRUM (= Biology Centre) There is 1 million SNP (Single …

GA4GH Oct 2016 meeting

Put the link here, as it is hard to look for it from the top page. Summary of 4th Plenary Meeting — October 18 | Global Alliance for Genomics and Health

Lab in London, Google & Death

Just memo for myself. Super lab opens in London This news issued this month. Francis Crick Institute Crick is of Watson & Crick DNA helix model. The lab is near KingsCross station. Also DeepMind office is near KingsCross station. That is a…

University Campus in Brno, Czech Republic

There was a biology event at University Campus area in Brno. There were 3 key buildings. CEITEC - Central European Institute of Technology [1] Masaryk University [2] Shopping mall: OC Campus Square Brno [3] It is upscale Office (AT&T and e…

Institutions in Barcelona, Spain

I have visited 2 institutions in Barcelona. That is one of my hobby. Parc de Recerca Biomèdica de Barcelona (PRBB) It is in front of the beach. Near Ciutadella | Vila Olímpica station (L4, T4) Parc Científic de Barcelona It is in Technology…

Upgrade Human, End Aging

There are 2 videos about upgraded human. Gregory Stock [1] To upgrade is human www.ted.com Aubrey de Grey [2][3][4][5][6] A roadmap to end aging In 2005 www.ted.com Undoing Aging In 2013 youtu.be Seeking immortality In 2014 youtu.be What i…

Mendel Museum & Czech traditional show

Mendel Museum It was sunny. 2008: Project 1000 Genomes - the aim is to map variations in the human genome and its comparison. It is the map of all possible SNP and comparison for ethnic and genotype? It looks exciting. [1] Czech traditiona…

Describe Genome as a Animation

It helps to understand Genome behavior to describe it as a animation. See its presentation, and videos.www.ted.comyoutu.beyoutu.beyoutu.be

Genomics 101 - Barry Schuler

A presentation about Genomics in 2008. I am excited and motivated for that. It is also good as a gate to the Genome World.www.ted.com