Another Japan in the World

Jun Aruga's blog.

Nanopore Day@EMBL Heidelberg

The reason I visited Heidelberg was because of Nanopore Day, the community event held by Oxford Nanopore Technologies. The event was held at the EMBL office. That was good opportunity to know both EMBL Heidelberg and Nanopore. Easy route i…

Heidelberg, Germany

This time's route: Brno, Czech - bus (student agency) or train - Prague, Czech: 2 hours 40 mins (same time for bus and train) Prague, Czech - bus (Flixbus) - (Germany, Frankfurt - bus (Flixbus) -) Germany, Heidelberg: 7 hours or 8 hours 30…

How to convert PDF file to PNG file with high quality on Fedora

IT

Here is the way to convert PDF file to PNG files (1 PNG for 1 page of the PDF) with convert command, according to [1]. Maybe output image file type are recognized automatically from the file extension name ".png". $ convert \ -verbose \ -d…

South of London

From the UK travel 1 month ago. Brighton Seven Sisters Near Brighton Isle of Wight This time the route is Brighton -> (Train) -> Portsmouth and Southsea Station -> (Bus) -> Southsea Hoverport stop -> (Hovercraft) -> Ryde In the island, the…

"The Future Starts Here" in London

I wrote a blog about how attractive "Future starts here" in Victoria and Albert Museum was 2 month ago. Last month I visited there. It was one of the most interesting and affected experience. Let's see the photos together. That is to under…

Camridge, UK

I like Mill Rd in Cambridge, UK. A variety of country's restaurants. Chinese, Korean, African, and etc restaurants.

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…

Install Perl 5.28.0 with thread on Mac

IT

I would note how to install perl with thread, as I needed it to use RNA Sequencing tool: Trinity [1]. I needed to upgrade Perlbrew [2] itself, as I got an error to install perl. Upgrade Perlbrew. $ \curl -L https://install.perlbrew.pl | ba…

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…

Mark Zuckerberg's Speech at Harvard

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…

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 …

Victoria and Albert Museum - The Future Starts Here

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…

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.