Indo-Pacific Fish Conference (IPFC)

9th Indo-Pacific Fish Conference (IPFC) is going to be held in Okinawa in June 2013.

Bioinformatician position advertised!

My unit is looking for an individual skilled with large-scale sequence data handling.

The detail is found here:
http://seqanswers.com/forums/showthread.php?t=23818

http://www.nature.com/naturejobs/science/jobs/286326-A-bioinformatician-postdoc-or-technical-staff-at-sequencing-core-unit-of-RIKEN-Center-for-Developmental-Biology

Please feel free to contact to the email address therein for questions etc.

Recent addition to my collection

After I moved to Japan in early Spring, I visited aquarium parks in Japan several times. The most impressive one was that in Okinawa, Churaumi Aquarium.

The newest one I visited was that in Tokyo, Sumida Aquarium. This one was just opened in May 2012, beside the Tokyo Skytree also just opened at the same time.

The below are the miniature figures I bought in the souvenir shop in the Sumida Aquarium. On the left you see the zebra shark (Stegostoma fasciatum), and on the right, the leopard shark (Triakis semifasciata).

The one on the right is my favorite. I didn't expect that I can find figures for these species at all. I got very excited and ended up with spending two thousand yen for them.

EEA 2012 in Milan, Italy

European Elasmobranch Association’s 16th Annual Conference will be held in Milan, Italy, 22th-25h November 2012. [ conference web site ]

My education restarted - Day 1

About 6 months after I quited working in a university in Southern Germany, I gave the first lecture in front of students this week. It was part of the 1-week-long undergrad internship program that the institute hosted. I had students raise their hands for several questions.

They included a basic question, 'Have you had any bioinformatics lecture in your university study?'

Out of 23 very keen students (primarily interested in developmental biology, though), .......................... only 3 raised their hands.

It will take time, but I have to seriously think about how to change this reality.

History to make ... - from Olympic games

I am quietly excited about the rise of Japanese soccer - both mens' and womens'. I did not imagine that the day like this really comes. But, what is really new and what has changed? In my sense, nothing really. Especially, in the mens' team, there is not a single special player. They just have unity, patience and skills. These elements are also what I truly respect in my work, especially in what I am now trying to achieve in my new position in Japan.

Nonsense to compare, but ...

I always get puzzled when I am asked 'which do you like, life in Germany or Japan?'. But, I can easily list differences between them.

On the other hand, there are many things that I previously did not take as advantage of living in Japan. New discoveries!! One of them is that I can access to every kind of research expertise in the country because many, many people live in the small islands (=Japan).

When I was in southern Germany, I felt that I was in the middle of many pretty cities with various research centers and researchers in Switzerland, France, Austria, and of course Germany. But, in fact they were scattered throughout the vast land.

Here in Japan, in the small islands, we have access to all kinds of things, and that is convenient. But, this is the reason why the country tends (or I should say 'we tend'?) to become isolated from the rest of the world. I am seeing all the pros and cons of this tendency.

from Yokohama

Skate genome resource

The journal DATABASE published an article about skate genome annotation. It includes links to the project website and sequence resources .

6 - 0 for Japan

The match between Japan and Jordan was played in Saitama, Japan. The number 10 of the Japanese team, Shinji Kagawa, is moving to Manchester United after scoring 13 goals this year for Borussia Dortmund (BVB!) in Germany. He also scored one goal tonight.

RIKEN CDB Graduate School Guidance

On May 26th, RIKEN CDB in Kobe, Japan, will hold the first annual guidance session for students who want to start developmental biology research for master or doctor program.

Because targeted participants are probably already in Japan, I paste below the official advertisement written in Japanese. I will also join this event and introduce my unit.

----

神戸にある理研 発生・再生総合研究センター（CDB）では、５月２６日（土曜午後）に連携大学院説明会を開くことになりました。http://www.cdb.riken.jp/daigakuin/

この説明会は、理研 発生・再生総合研究センター（CDB）中で、大学院の講座として、大学院生も行ける研究室を紹介しようというもので、今年が初めての試みです。遠隔地からも参加してもらえるよう、午後１２時５０分から開始します。CDBを代表するサイエンティストのレクチャーや連携大学院の教員を兼ねているラボの訪問の機会ももうけてあります（プラス懇親会）。

大学院を決めようとしている学部学生（４年）と修士の学生に広くこの説明会の存在を知ってもらいたいので、mailing list, twitter、facebookを使っている方、あるいは、みなさんのラボの後輩や、そのまた後輩の学部学生に、この情報を伝えていただければ大変ありがたく思います。

ぜひよろしくお願いします。

'Oktober'-fest in Kobe, Japan, in April/May

It was rainy today in Kobe, my new base in Japan. I visited a place called 'Kobe Harborland', a big attraction on the seashore with my family. We happened to find an event related to Germany. Yes, the traditional 'Oktoberfest' !

But, why in April/May? In Japan, we are now right in the middle of the year's biggest holiday season, called 'Golden week'. Probably, organizers chose this period due to this holiday season.

Did we, after 5-year-long life in Germany, enjoy ourselves in this late spring Oktoberfest in Kobe this time? No, we did not enter the event area and stayed in a different roofed area with more in-door shops. I am sure food and drinks at such a place are outrageously expensive. Moreover, we don't really miss German stuffs yet.

Special Issue about Elasmobranchs Biology

Here is the table of contents of the special issue of the Journal of Fish Biology, titled 'The Current Status of Elasmobranchs: Biology, Fisheries and Conservation'.

No.1 (in computics) in my neighborhood

The other day, I took a walk alone from my working place in a lunch time. It took only 10 minutes for so to reach another branch of RIKEN with which I am affiliated, namely RIKEN Advanced Institute for Computational Science (AICS). This center hosts the world's fastest supercomputer (as of November 2011 - see the ranking). Both this center and my working place as well as many other institutes, university campus and biomedical companies are located on an artificial island, called Port Island. To be honest, the main purpose of my walk on the day was to look for any nice restaurant or canteen because that is always the issue in our life on the artificial industrial island. Unfortunately, mission not really completed.

Heading for north from the area with RIKEN AICS. This promenade with cherry blossom tree is really attractive, with all concrete.

A snapshot of Japanese precision which I have to learn

Below you see the label showing collection time on a mailbox in my neighborhood in Kobe. You see how precise Japanese postmen are or are trying to be! I got very surprised at this.

'Currywurst' in Japan

Today I had a lunch at a small restaurant in Kobe serving "Currywurst" which is famous among German people.There seemed no German employee.

The book 'Evolutionary Genomics .... ' coming soon!!

A collection of valuable chapters about evolutionary genomics will be published in two volumes by Springer [ see the product page at amazon.com: volume 1 volume 2]

I also contributed to a chapter in this book and am expecting a free copy.

 

Deutschland - Japan

A woman's football (=soccer) competition, Algarve Cup, is going on in Portugal.

Tomorrow the final between Germany and Japan will be played. In the world cup 2011 held in Germany, Japan defeated Germany . Let us see what happens in this big match tomorrow.

German elements in Japan

Bakery KÖLN in Sannomiya, Kobe

VOGEL Animal hospital, in Rokkomichi, Kobe

Bakery GUTEN APPETIT in Yokkaichi, Mie

Lineup of various bread sold in GUTEN APPETIT in Yokkaichi, Mie

Restarting in Japan

I arrived in Japan this Sunday (19th) and am setting up new life here. My new base is Kobe near Osaka (but distant from Tokyo). I learned in Europe that this city is famous for its delicious beef as well as for the big earthquake in 1995. Regarding this beef, most people have not tried to eat, but just heard cows that produces 'Kobe beef' are fed beer.

Special last days in Konstanz

I have only two more days in Konstanz. It has been hectic to pack at home and send out, while working on some residual burocuracy etc. Unexpectedly we had a lot of snow although the temperature arose quite a bit. My winter shoes were already sent out in a package for surface mail. I have to survive with my favorite lether shoes, but they are already quite damaged.

This morning we had emotional moments to say goodbye to our 6-year-old son's teachers and friends. It is unbearable when I imagine what this move means to him. Apart from this, I mostly can stay calm, probably because I know what the life is in my next place. But, people saying goodbye to me would feel that I am moving away to an unknown world. I really want to stay in touch with them (you!?) and show how I start in Japan.

Rehabilitation effort (1)

I now need to work on filling out forms for contracting for my position in the next working place. I found a few Japanese traditions (that I need to recover) in this kind of formalities.

1) In Japan, we are based on a unique way of counting years in official documents. For example, this year 2012 is the 24th year in the Japanese way after the previous emperor passed away. I lost the habit to stick to this Japanese year count system. Often I mistakenly write '12' in some blanks instead of 24, for example.

2) A very basic thing. I am accustomed to write and recognize the digit 7 in the European way. This European handwriting is hard to recognize by Japanese people, and the Japanese normally write it in the way shown here (mostly #1). I know this well, but I am so familiar with the European way and spontaneously write 7 in that way. I always realize this after my hand automatically makes a mistake, and say to myself 'These 5 years made a big difference!'

It should not take a lot of time to recover the habits, though. Let's see.

Croc genomes

A paper reporting results and plans of crocodile genome sequencing is out in Genome Biology.

The consortium page is here. One can also run BLAT searches at the UCSC site.

A course at NHGRI

I have just found a web page containing the schedule of a course running at NHGRI in US. The course is titled 'Current Topics In Genome Analysis 2012'. This should be a great overview of where we stand in genomics.

New year's shock

I am preparing hard to clean up things here in Konstanz and prepare for new life in Japan, while still taking care of a lot of teaching especially this month.

Over the Christmas holidays, I was expecting a set of documents for apartment rent contract I am going to make through a real estate agency in Kobe, Japan. The contact person at that agency told me that he sent out the envelope containing the documents on December 22, with a relatively quick mailing method. Normally, with this method, an envelope arrives at my place in 4-5 days.

I watched crazy fireworks from the balcony of my apartment on the Silvester day (Dec 31), ...... still waiting for the envelope.

The new year came, and I could not wait any more. It was already two weeks - too long! I requested the shipment code from the sender, and contacted a central post office in Frankfurt, because the sender in Japan told me that he confirmed that the envelope was already in Germany. At the post office, the person who answered my phone call was totally unfriendly, maybe because of my awkward Germany. She said 'schon zugestellt !' (means already in its way to my home). It was weird because even if the envelope is really in its way, it is too slow. But, ....... the envelope did not arrive for the next 5 days. ........... what?

Finally, yeasterday, I called the post office again with the help of a German colleague at my working place. She explained my situation well, and found out that the envelope came to the building including my apartment, but the postman could not find the right recipient, because he could not read my name which was written .............. in Japanese. When we made this second call, the envelope was right back at the post office. We told her my name in alphabets, and got an expected delivery time range. This morning the envelope finally arrived. It turned out that the tag for delivery did not even have the names of the countries on both the sender's and recipient's sides. It was lucky that the envelope was first sent to the right country (probably with the help of my phone number included there). It is simply shocking that the sender, a Japanese, did not have any international mind - wrote no destination country and included the recipient's name in Japanese (more precisely, in Chinese letters). On the other hand, he looked very able and resourceful when I got a lot of help to look at some apartments in Kobe in my last visit to Japan. Yes, he is able but probably within the country - very symbolic in the geographically and culturally isolated country, if I may say this.

One more shock of today was that my application to open a new bank account in Germany was rejected, possibly because of my nationality. I prepared some documents for this. It is very discouraging - tough life as a non-European continues until the last moment. I know, it is not a big deal. This (rejection like this) is not the first time in Germany. I will say at last 'Nein Danke & Nicht mehr !'