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…

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…

news.harvard.edu My favorite parts in the speech. "I’ve sat with children in juvenile detention and opioid addicts, who told me their lives could have turned out differently if they just had something to do, an after school program or some…

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 …

The Future Starts Here I found interesting event " The Future Starts Here" in Victoria and Albert Museum, in London. Maybe I am going to visit there soon. You can feel what's interesting from below URLs. Victoria and Albert Museum (now unt…

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…

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 …

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

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

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

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

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…

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 …

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…

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…

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…

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

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 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 main station Basel exhibition centre. Huge.

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 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…

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

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: https://vimeo.com/211467532 I want it and…

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…

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…

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…

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…