Another Japan in the World

Jun Aruga's blog, who lived in Japan, Singapore, live in Czech Republic. Mainly about IT and travel.

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 …

Cambridge, UK

London King's Cross station => Cambridge station => Stansted Airport

Oxford, UK

London Paddington station => Oxford station Oxford station The biggest only shopping mall in Oxford A street A popular Jamaican restaurant A covered market A Market A park

London, UK

Stansted Airport => Train (Stansted Express) => Liverpool station South Kensington station, Museums => Walking => Hyde Park => Walking => Green Park station => KIng's Cross station

Clay to drink

To care and clean my intestine. A cup of spoon every morning, with water. So far, I could see the good effect.

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…

Install TensorFlow from source on Fedora 27

IT

I tried to install TnsorFlow from source seeing the official page [1]. The source is on GitHub [2]. Install build dependency RPM packages $ sudo dnf install python-devel Install a build tool Bazel. Bazel is necessary to build TensorFlow fr…

Install TensorFlow on Fedora 27

IT

This article is about how to install TensorFlow binary package on Fedora Linux. I referred the install document for Ubuntu Linux on official page [1] $ cat /etc/fedora-release Fedora release 27 (Twenty Seven) $ python3 --version Python 3.6…

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 …

Lucerne, Switzerland

Lucerne is very good and beautiful place for the sightseeing and relaxing. You can go to the mountain casually and enjoy the nature. It takes around 60 minutes from Lucerne to Zurich. In front of Lucerne main station Mount Pilatus Swiss Mu…

Zug, Switzerland

Zug is a silent city. In Switzerland, tax rate is different for each region. Zug has an advantage for the tax.

Bouldering gym in Basel, Switzerland

B2 - Boulders & Bar Address: Hardstrasse 46, 4133 Pratteln, Switzerland Near Pratteln train station or near tram line 14 Pratteln, Schlossstrasse station. URL: https://www.bzwei.ch/ Price: 20 CHF / 1 time It's not near Basel main station. …

Basel Switzerland facing Germany and France

Basel is interesting city. The city is facing along the border of Germany and France. The area is around the border is very interesting. I can imagine people life is unique. We can easily reach to outside of the border of Switzerland by Ba…

Basel, Switzerland

Basel main station Basel exhibition centre. Huge.

Davos, Switzerland

As I had interest for Yuval Harari's talk at Davos World Ecnomic Forum 2018, I visited the place in Davos. Anyone can join the event for free. https://www.weforum.org/open-forum/pages/faq The Open Forum is accessible to everybody. If you a…

Zurich, Switzerland

Zurich Airport. It looks like shopping mall or train station building. It takes only 12 minutes from Zurich airport to Zurich main station by train. Market in Zurich main station. Zurich main station Yuval Harari's books are popular in Zur…

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…

Install RPM 4.8.0 on CentOS6

IT

I investigated how default running RPM v4.8.0 [1] is built and installed on CentOS6, because my application [1] needs to support CentOS6. Very old version RPM v4.8.0 is running as a default on CentOS6. We can use CentOS6 environment, downl…

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…

Canary Islands

The islands have 7 islands mainly. This time the route I visited is Gran Canaria -> Tenerife -> Gran Canaria Tenerife: Largest island in Canary island. Santa Cruz on north east is a center of the island. Gran Canaria: 2nd largest island. I…

2017年の振り返り

近況 2018年、あけましておめでとうございます。 今回は、年末年始の恒例行事として、日本語で、これを読まれているどなたかのために記事を書きたいと思います。 昨年の年末から今まで、半分は、締め切りが迫っていた仕事、もう半分は、自分で決めたタスクに…

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…

Air Berlin and Niki filed for bankruptcy

The LCC airline companies was bankruptcy. Niki https://www.flyniki.com/en/start.php The flight operations of NIKI Luftfahrt GmbH under the IATA airline code HG were suspended on Thursday, 14th December 2017. Air Berlin https://www.airberli…

Sending pull-request to Mercurial repository

IT

A way to send pull-request to Git repository is deeply in my mind and body. In case of git repo. I would show this as a comparison of Marcurial repo. $ git clone <repo url> $ git remote add junaruga <forked repo url> $ git checkout -b feature/foo $ vi something $ gi</forked></repo>…

Anaconda and Jupyter

IT

When talking with researchers, they like using Anaconda to install Python and other Python packages to build Python environment. Anaconda is a collection or all in one for Python and other Data Science (Analysis) packages. People do not ha…