Another Japan in the World

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

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…

English pronunciation and the used mascle

I am not good at speaking with good pronunciation. But recently I checked each pronunciation of mine. And I found that especially the physical motion opening a mouse widely with side was my challenging. According to International Phonetic …

Talk: Yuval Harari

Historian Yuval Harari’s Talk. Very interesting. Also how to speak, and the used words. How to make a sentence. How to express a dense content by short words in short time. Those are so helpful for me. www.ted.com And his book is also writ…

Wateched The Linguistic Genius of Babies

Today what I learned from below video in English lesson is I understood why my listening to English is so hard to me :) Taking the statistics of sounds from English and Japanese language, Japanese language does not have sounds like English…

Brown Rice in Brno Finally..

I found the shop and e-shop to buy brown rice in Brno. Maybe we can buy it stably! “RÝŽE KULATOZRNNÁ NATURAL”. This word is a key to to find the brown rice in Czech. BRNĚNKA Address: Purkyňova 35d, 612 00 Brno-Královo Pole In front of tram…

Appearance and Personality

That may be surprising people. Living in Czech, my problem is that it’s still hard for me to distinguish most local people from appearance. For detail, I might be able to do it. But I am not confident for that. Of course each people has a …

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…

Install Docker on Mac 10.9

IT

I installed Docker on my Mac. The situation is the latest Docker does not support my old Mac. But by installing Docker toolbox including Docker, I could use Docker on Mac. To install the toolbox, see this page. https://store.docker.com/edi…

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

Love Avinguda Diagonal (Diagonal street) in Barcelona

Avinguda Diagonal (Diagonal street). This street may be the most favorite area so far. Why? I can relax because of a few people, a big space, many cafe with enough space, nice fitness gym with pool, healthy cafe and market, shopping malls,…

Brown Rice in Barcelona

Let me share you where we can buy brown rice in Barcelona El Corte Inglés The “El Corte Inglés” in front of Catalunya station is very crowded. So, I will recommend other El Corte Inglés shops in other area to buy brown rice. At the top of …

Barcelona east tram area

I walked from Hotel W Barcelona to shopping mall Diagonal Mar (Address: Avinguda Diagonal, 3, 08019 Barcelona, Spain). There are 2 tram areas on west and east of Barcelona. Those area are an local / business area. My impression is West: fo…

Barcelona La Boqueria foot market

Accustomed Boqueria foot market. I visited many times there. The photo is from my past several travels this month, last month and last year. Let me introduce my favorite shops and an restaurant.

Barcelona Vegetarian Restaurant

Teresa Carles Near Catalunya station Maybe very popular restaurant. Address: Carrer de Jovellanos, 2, 08001 Barcelona, Spain Black rice. There are many UK people. Maybe I have heard UK English there. Teresa Carles Healthy Foods Aguaribay M…

Everything that has a beginning has an end, Neo.

The title is a line from Oracle in Matrix (Revolutions). In general, it is hard to find people who are working from their passion. If you see people who are working from the passion, they made an effort to get the skills so much in their p…

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…

Python Best Practices & Cython

IT

This is a memo for Python’s Best Practices and C extension from Python. I have heard that from my colleague. Python’s Best Practices The Hitchhiker’s Guide to Python! — The Hitchhiker's Guide to Python : So far, this site is the best. PEP …

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 …

Moving residence is solving several problems

Moving residence is solving several problems at same time. Recently I moved my apartment. There are 2 purposes mainly. Moving near office to save the time and simplify my life more. Moving bright place to get more sunshine for my health. W…

Brown Rice in Brno

Brown rice in vegetarian restaurants Brno, Czech Republic is a city that has many vegetarian restaurants regardless of the small city. But there is a challenging for that. That is that Brown Rice (Rice Natural) [1] is not popular in the ci…

Český Krumlov, Czech

I would recommend this beautiful and clean city if you have a chance to go to Czech Republic. I would recommend below cities for the people who travel in Czech Republic at first time. Prague to know city area. Český Krumlov to know traditi…

České Budějovice, Czech

České Budějovice, this hardly pronounced city is a gateway city to Český Krumlov, and also has more populations in the region. The feature of the city is that the old buildings have been saved in a clean status. The city is clean. I had no…

Python, Bio Tools and me

IT

My idea Needless to say, recently bio industry’s development is remarkable. After finishing first human genome’s full sequence, the investment by governments and big company, related services. I am a fascinated person for that. I have lots…

Install RPM from source on Fedora

IT

When I used Fedora 23, I was not able to build RPM due to errors. However today when I tried to do it on Fedora 25, I was able to build and install. Great. I will note the build success day here. Install $ git clone git@github.com:rpm-soft…

Prague Japanese Restaurant

These photos are in 2015. I found those when I checked my past photos. Both are delicious. Katsura Katsura http://katsura.cz Ramen Bar Ramen Bar https://www.yelp.com/biz/ramen-noodle-bar-praha

San Sebastian, Spain - Bar near Hill/other foods

Bar near Hill When I had stayed on the Hill (Munto area), this Bar/Cafe was a part of my life. I really felt it was my life. La Taberna del Cuélebre Address: Calle Goiko Galtzara Berri, 2, 20009 San Sebastián, Guipúzcoa, Spain A Vegetarian…

San Sebastian, Spain - Bar@Donostia

The Bar that I would introduce is near Iglesia de Santa María, on Abuztuaren 31 Kalea street, Donostia. I do not know the restaurant/Bar name. This area was very crowded. But we can eat “Sea urchin” there. A Bar near Iglesia de Santa María…

San Sebastian, Spain - Bar Bergara@Gros

Let me introduce foods in San Sebastian, dividing same articles. Today is my most favorite restaurant in San Sebastian. Pincho[1] is representative food in San Sebastian. We can eat it at Bar. Bar Bergara [2] This Bar is in Gros area that …

San Sebastian, Spain - Beach, Hill

I had been in San Sebastian, Spain in last year end. I thought I wanted to go to warming place at that time. After considering several places as a candidate, I decided to go to San Sebastian, finally. San Sebastian has several faces in it.…

Upgrade Fedora 24 to 25

IT

Yesterday I upgraded Fedora 24 to 25 reading below article that I used last time. [1] Unfortunately I have faced several issues after that. I want to take note for that here. There are some articles about Upgrading Fedora [2][3]. Later I w…

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

もうすぐ2017年

年末のこの時期、昔なら年賀状を書いていたこの時期であるが、 その年を振り返り、来る年を思う気持ちは変わらない。 2016年は、旅行では、欧州を中心に8カ国、訪れた。 チェコがこの時期の気温がマイナスになるのに対して、 今旅行中のスペインでは、気温が…

Install Python 2.7.13 from source on Mac

IT

Continuing from previous article. $ cd ~/hg/cpython Check latest version in v2.x. v2.7.13 is latest version for that. $ hg tags | grep 'v2\.7' Below command hg update -r something is like a git checkout something. $ hg update -r v2.7.13 31…

Download cpytyon with Mercurial

IT

I wanted to compile python from source code, reading a document[1]. However I was failed to do it last time. [2] hg clone was failed because of the issue. It may be because of my PC’s poor memory environment. $ hg clone https://hg.python.o…

Mercurial training

IT

I started to use Mercurial that is another source code management (SCM) tool such as Git. Nowadays there are many SCM tools, such as CVS, SVN, VSS, Git, Mercurial. CVS, SVN, and VSS is central repository management tool. Those are already …

Git Tips

IT

I will summarize tips that I learned after reading a Git book. git describe Show the most recent tag that is reachable from a commit For example, we know a commit hash that a bug was fixed. And we can find fixed version base on the commit …

Think about the Python environment like Ruby Bundler

IT

Want to use Python environment like Ruby Bundler! Ruby Bundler is very convenient. Below process is so common before starting development for a RugyGem package. $ git clone GIT_URL/foo.git $ cd foo $ bundle install --path vendor/bundle $ b…

Install Python 3.5.2 from source on Mac

IT

Python Install latest stable version Python 3.5.2 on Mac. Seeing official site [1]. However as I was not able to download with Mercurial (hg command), that is on the official site, get the source from git mirror. [2] Install from Git sourc…

Install Ruby 2.3.3 from source on Mac

IT

Install Ruby 2.3.3 from source on Mac. Use git to get the source. $ cd ~/git/ruby $ git pull --tags $ git checkout v2_3_3 $ autoconf $ ./configure --prefix=/usr/local/ruby-2.3.3 \ --with-openssl-dir=`brew --prefix openssl` 2>&1 \ | tee -a …

Boulder Bar again in Prague, Czech Republic

I have visited Prague again. After I have been accustomed to Czech, then I visited to Prague. This is 2nd time. The situation that I had seeing were different from previous one. I went to Vietnam restaurant and Japanese restaurant. Boulder…

Bouldering gym and Vietnamese restaurant in Berlin

There are 2 impressed points in Berlin. Bouldering gym It is "Magic Mountain". Maybe I came here after 2 years. There are both Bouldering and Lead. This gym has clear grade for the course for Bouldering. Interesting point is a mixture with…

Future of Brno Centre

I have found a board about “Future of Central of Brno” in front of a big tram station. There were pictures for the future. And schedule to 2045! The south area of Brno will be renovated. Brno has an advantage about train course. So, maybe …

Linux Conference in Berlin

This week I have been in Berlin for Linux Confernce Europe 2016. 15 years ago I attended Linux Confernce. I was a student. But the price for the ticket was still acceptable. But now it has been changed. It is expensive for them to buy it. …

Future of Fedora

IT

Current Technology https://fedoraproject.org/wiki/Releases Check ChangeSet about Fedora 23, 24. https://fedoraproject.org/wiki/Releases/23/ChangeSet https://fedoraproject.org/wiki/Releases/24/ChangeSet Culture See those great presentations…

Upgrading Fedora 23 to Fedora 24

IT

Recently I upgraded Fedora 23 to 24. GUI did not work for me. But below CUI commands worked. Upgrading Fedora 23 Workstation to Fedora 24 - Fedora Magazine

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…

Formentela, Spain

I went here and there in the island by bicycle. But the island had the suitable size for motorbike or car.

Ibiza, Spain

It was a special island.