Trip to Munich - Part 2

While I am in Europe, I am establishing as many connections with people as I can.  I would like to work in Europe for a couple years after graduating.  It is something I have always wanted to do and now, being a cheap source of labor again, I have an opportunity to fulfill that dream.  I am visiting different labs in different cities to get the feel for the areas, people in the labs, professors, and general environments. I treat these as pre-interviews where both sides get to evaluate the possibility of collaborating on a project.  It is very important to me to feel a part of the lab and that there is good chemistry between the people.

Monday I made a presentation to the bioinformatics group of Professor Raul Zimmer at Ludwig-Maximilians-Universitaet-Muenchen (LMU).   I was a bit nervous because this was the first time I have presented to a computational group. I was not sure how much detail or background to give.  I  assumed that they would ask questions if there was not enough detail.  It was a bit surprising when at the end they all started rapping their knuckles on the table.  Evidently it is used in Germany, Austria, and parts of Switzerland instead of clapping at the end of an academic presentation. 


I noticed that everyone in the group seemed to have fun and enjoyed being with the each other.  There seems to be a mutual respect that flows from the top down.  I have to admit that I had a much more intellectually stimulating time in Munich than in all my time so far in France.  I certainly was much more comfortable speaking a little German and I can read more German than French.  There is also a lot of English everywhere in the city, from signs to the announcements in the trains and trams.  It is a much more friendly city in general than Lyon.  People can look you in the eye and even smile at you while they are sitting at the restaurants and cafes.  This is something I rarely see in Lyon.  I think that the German philosophy of work and play fit better with what I am accustomed to in Boulder.


I spent the next day walking around the city and visited a museum for a few hours.  Looked at some of the masters and other paintings.  Looked at the styles and methods they used to create their art.  It was interesting to see all the kids listening to the explanations of these works of art.

If and when I graduate, I will talk again to Professor Zimmer about project possibilities, and it may including teaching.  There are many international students and courses can be taught in either language (German or English).  I think with a little intense study, my German may make a stay here easy and fun.

The day I was returning to Lyon, there was a major storm that closed the Frankfurt airport, but it was only raining in Munich and we were not delayed taking off.  We arrived in Lyon at 11:00 pm and I headed for the train.  I watched it pulling out while walking out to the station and had to wait another half hour.  By the time I got into the city it was midnight and I caught the last subway train of the night to my apartment.  At least I didn't have to walk that three miles. 

Trip to Munich - Part 1

I am headed to Munich, Germany to visit the Bioinformatics group of some students that I met at a conference last April.

Even on the plane and train descending into Munich I could tell it is different here.  There were no giant skyscrapers and the buildings all have color.  I have been told that Munich is a series of villages that have grown together, but that it still maintains a village atmosphere.  The city is only 20 km across (12.4 miles) and is nearly a circle.   My nephew, Dakota, was here last summer and I heard that he did not like Munich because it is a large city, but after 6 weeks in Lyon, Munich does feel like a village. There are wide open spaces with paths, large boulevards and walkways, and a great transportation system to make getting around without a car easy.

I arrived on Saturday and Franziska picked me up from the train station.  She is the administrator for the department and was nice enough to volunteer to let me stay at her house during my visit.  Her two oldest kids are out of the house and she let me stay in one of their rooms.  We toured the city in her car and she showed me the major sites, explained public transportation on the U-bahn and tram systems, and talked about the history of the bioinformatics group.  She made me dinner at her house and we talked for hours.  She warned me when we were making arrangements that she likes to talk.  She told me stories about her family, travels to foreign countries in an old VW camper van, and about Munich.

On Sunday Franziska had a brunch to attend outside of town and she dropped me off at the BMW headquarters where I met up with Thomas. I met Thomas in Barcelona last year at a Bioinformatics conference. We walked around the BMW displays for both cars and motorcycles and then walked over to the Olympic village.  There is a large hill next to the stadium.  I don't know if it is natural or man made, but from the top you can see across the whole city, as you can see in the first picture on this page. From there we caught the U-bahn over to the Marienplatz, which is a nice pedestrian plaza in a retail district.  On this sunny morning it was full of people strolling. We walked over to the Glockenspiel to see the tourists and then climbed the church tower in Peterskirche (St. Peter's Church). 

Once we climbed the 15 stories of narrow stairs (one person wide, had to turn sideways at times), taking turns climbing and letting the people coming down pass us, we arrived at the crowded top.  I have a bit of a fear of heights and I don't like crowded places.  This was both.  The balcony around the top of the tower is almost as narrow as the stairway and was packed with people.  I made it outside, but could not get myself to move very far, staying within 5 feet of the doorway.    After about two minutes I went inside.  Tried again, but with a large number of people out there, I could not easily pass and it was more than I could manage.  I finally gave up and stayed inside looking out through the doorway and windows.  You can see across the whole city and even see the Alps in the distance.  I need to go back on a less crowded day so I can hug the wall and walk all the way around the outside. It really was a spectacular site. 

Thomas is a fantastic photographer and he showed me some of his compositions.  He has already had one of his pictures on a magazine cover.  The owner of a local bicycle shop is also a fan of his work and has offered to have a showing of Thomas' photographs.  He needs to pick about 10 works to show.  I hope he will be able to post some images of the showing to share with those of us that cannot attend.

From there we went to lunch and it was the only time that I actually ate German food.  I ordered the Schweinebraten with Kartoffelknödel and sliced cabbage in a vinegar.  Schweinebraten is a Bavarian pork roast that was very tender and flavorful.  Kartoffelknödel is a potato dumpling that is the size of a baseball.  It was a very filling meal.

During lunch we were joined by Gergley, with whom I have been emailing and Skyping during the last year.  It was his efforts that allowed me to make this trip.  When we met last year in Barcelona, we had an instant connection because we have taken similar paths to being graduate students.  We both spent a number of years in industry and consulting before finding our desire to pursue research.  His journey is more difficult than mine as he and his wife have three children at home all under the age of 10.  His mind is always active and he seeks answers to the questions that continually arise. 

Gergely took over as tour guide from Thomas for the rest of the afternoon. We walked around the area where the University is centered and along the wide open boulevard. We headed for the Englischer Garten, a large public park, to stroll with hundreds of couples and families.  It was nice to have such a large park inside the city and we must have passed 10 different groups playing football in the grass.  Gergley is originally from Hungary and I talked about the differences between the cities we are living in.  We talked about his research, my research, the recent results of the ENCODE project, and possible projects for the future.

It started to rain and we even saw a few flakes of snow as we walked, so we hopped on a bus and headed back to his car.  Gergely received a special release from parental duties for the evening and we met up with Thomas for an evening out.   They wanted to go bowling.  We ate Mexican food at the restaurant in the bowling alley.  Not bad.  I have been told that there is good Mexican food in the area.  It was nice and spicy.  We bowled for a couple hours and they, being the perfect hosts, let me win two games and tie for high score in a third game out of the four we played.   

Here are some sketches

Everyone has been asking to see some of my sketches.  Well, maybe not everyone, but I have had a few requests.  The problem is that I am not been self confident enough to show them.

I have lots of empty time, time that I need to get away from the research and allow my brain to rest.  I spend a lot of time sitting in my apartment, so I decided to try pencil drawings.  I have always loved the drawings I would see on the streets of Paris or Rome where people are capturing the feeling of a place.  Photographs usually capture the physical but not the emotional feel of a place. 

I am amazed at the amount of time and concentration it takes to create a drawing. I can spend a couple hours just creating the outline of the scene, buildings, but not any of the details.  Maybe as I do it more often I can speed up the process. After spending all that time, I must still go back and fill in the details, someday.  I am good at starting them, not so good at finishing. I usually pick a scene with too much going on.  I have taken photographs of places without any people to use for practice drawings.

It is hard to let others see, and therefore judge, something coming from my emotional side.  No problem with letting people see my computer code because it comes from the logical side of my brain.  That side is well versed in critical analysis of problems and solutions, even when they are mine.  But the emotional side is still unprotected and has not developed any protection from the harsh words and subjective analysis.  I still feel that all my work is very juvenile and lacks any real talent, but it represents where I am in my progression as an artist.

My ability and technique is all self taught.  I have never really spent time with art, so there is a lot of experimentation with different pencil hardness, how to capture my vision, perspective, shading, foreshortening … everything.  I guess I should have taken an art class when I was in school.  Well, before grad school.

Okay.  Now that I have couched my ability and told you all to be nice, below are some sketches. You should be able to click on them to get bigger images. The building is St Georges, a small church below the massive Fourviere and down the street from the large St Jean's. The image to the right is a practice sketch with attempts to capture the depth and 3D feel of fabric draped on the ground. The hands are my hands, they kept getting in the way.  The girls are all from photographs of life models I found online.

Explaining American Ideals via "Lincoln"

 The internal self image that defines who each of us are is not diminished by time or any physical changes.  When we are allowed to examine our own minds and beliefs, which happens when you spend a lot of time explaining your way of life to someone else, we can see what it is that actually makes us who we are as an individual.

I went with a couple of the other students to the movie "Lincoln" last week.  Many of the Hollywood films are shown with the original voices (movies listed with VO) and French subtitles, which means I can watch and understand the dialogue.  But, all the titles and explanation text is in French and I was guessing at the exact context.  For instance, one of the captions said something about re-election, but I can only assume it was saying this scene was after his election to a second term.

Lincoln was a bit slow for me, with Spielberg trying to make a "pretty" film.  Long panoramic shots, Gone with the Wind styled scenes, and long dramatic pauses.  Most of the people in the theater were dozing off and I saw their heads drop.  I even had trouble sitting through the twenty minutes of commercials before the film and then two and half hours of film time.  The story only took one and half hours to tell, but stretched out forever. 

It is interesting to see the different reactions and what they took away from the movie.  They don't have the same background information as we were all taught in school.  My recollection of this president is he was a backwoods Illinois raised, self educated lawyer, with high ideals who became president, chopped his own firewood, and liked to tell stories and make short speeches.  Not much depth of a background as history was never a subject I was ever interested in enough to read.  But, it does give me a different starting point than someone raised in another country.

Their impression of the movie was "So what was the big deal?"  Another comment (paraphrased by me) "The Brits had abolished slavery without a civil war about 30 years earlier and they were making lots of money in the slave trade at the time." and "The whole movie was about buying votes." 
They also did not understand the story telling and short speeches, they felt that any man that was commander of the United States must be a great orator, with a deep and resonating voice that can be heard across the whole world.  Our fairy tale view of Lincoln is a soft spoken man with lots of self deprecating humor, who used stories to highlight values and actions of others, before telling you what he wanted or was going to do, using the stories to support or contrast his views.  A grandfatherly figure who should be on the porch in a rocking chair with children at his feet.  WAIT, that was in the movie, without the rocking chair, but it did have an old potbelly stove and coffee pot.

I have rambled on enough for today.  I believe this movie was nice, wholesome and pretty.  But its messages are lost in the translation for other countries without a built-in admiration for this president.

Off to play soccer

It is indoor soccer, but with outdoor rules, including sidelines and endlines, so you must keep the ball in play. US indoor uses a hockey style playing area, and you can play off the walls, and the wall around the goal area puts shots that are wide back into play.  The goals are handball goals (used in European and the Olympic team sport of handball), about 6 feet tall and 8 feet wide.  I have not played in a couple of months, and it has been at least four months since I was running around playing.  I am so excited.

I arrived about 10 minutes early.  I was practically skipping on my way in.  We were scheduled to play at 10:30 French time, which means a start nearer to 11:00, but it takes me a while to warm up.  It takes me a lot longer to warm up than the young guys.  They are in their late twenties and early thirties, which means most of them could be my kids.  I was, of course, the first to arrive.  The gym was empty except for a couple of workers vacuuming the floors.  You enter on the second floor and look down onto the playing surface.  It is the size of a basketball court.  If fact, it is a basketball court outlined in red and has baskets at both ends suspended from the ceiling.  Basketball is a very popular sport in France, as is volleyball, so there is also the  smaller volleyball court drawn with white lines.  One of the works came over to me and started speaking French. 

Major disappointment.  They closed the gym this morning to paint for a week.  At least 8 days until I can play indoor.  I was like a kid thinking it was Christmas day, waiting to open presents and POW … I am told that Christmas is not until next week at the earliest.  I will now go into the corner and cry. :,(

Well, maybe I can find the old guys playing in the park this weekend.  It will be cold, 0 Celsius (32 F) but cold never stops the addicted from getting out on the field. 

Added a reading chair to my apartment

After about two weeks here, my back was killing me from laying on the bed/couch to read.  I either read books downloaded to my phone or journal articles.  But I could never get in a comfortable position on the couch and the desk chair does not recline.  What I miss is my nice, comfy, leather recliner.  I could easily sit, lean back, put my feet up and read.  Of course it is also easy to fall asleep, especially when reading the technical papers.

I decided I needed a better chair for reading here in France.  I tried to find used furniture stores here in Lyon, but could only find one and it had a sign saying it would close in January.  It seems like with nearly a million people there would be places to trade-in furniture.  I needed a nice secondhand shop like the one my aunt created up in Sandpoint Idaho.  They have donations of all kinds and some furniture.  I guess if I could read French better I would  be able to find something.

No problem.  It seems that everyone here shops at IKEA for furniture.  In fact, all of the furniture in my apartment is from IKEA, including the kitchen area and bathroom sink.  I have never been to one, although there is one in south Denver, but there is one just a short walk from a stop along Tram 2.  So, off I went.  IKEA is in a big retail area with a Home Depot type store at one end and IKEA at the other.

In between, there are other clothing and electronics stores, as well as a small mall and a Carrefour, which is a Walmart equivalent.  Carrefour has everything from cameras and computers to toilet paper and laundry soap.  They also have food of every kind, including a butcher and fish market in the store.

I went to IKEA on a Thursday afternoon because I was told it gets really busy on Saturday.  There were only a couple of people around as I entered. It was love at first sight.

There are a million things to buy at decent prices.  And they make sure that you look at it all.  The stores are set up so you wander through the store in a single direction.  It felt a little like a Disneyland river ride where you travel a long way in very little space with hairpin turns taking you back and forth in a tight maze.  I found the chairs at the beginning of the river cruise and the one I liked was on sale.  Regularly 70 euro, it was only 39 euro if you got the white seat pad.  The chair is nice because you can lean back and read in comfort, but it also rocks a little bit.

Having found what I wanted, I wandered on down the river and found all kinds of exciting things.  When I came in I had decided that I was not going to buy anything, so I did not grab a cart or bag at the entrance.  Good thing.  I started picking up items and would have bought more, but my hands quickly became full.  I got out spending only 30 euro.

I also ate lunch at the cafeteria.  They have all kinds of food : salads, entrees, desserts and main courses.   They are known for their Swedish meatballs, so I decided to get that. A nice plate of 15 meatballs with two sides, a dessert, and a drink were only 8 euro, about half the cost of a meal in a restaurant.  I don't know how much has been in the news in the US, but they are investigating how horse meat was found in some frozen lasagna here in France.  A few days later I read they had also found some in meatballs from IKEA.  Don't know if the ones I ate had some, but they sure were tasty.

Now the only problem was getting the chair from the store and back to my apartment.  I can take a bus C22 to catch the Tram 2 to take me to IKEA. Or I can take the Metro line B to Line D out to catch the Tram.  Either way it is at least one transfer.  The chair comes unassembled, but it is still a large box and I needed to also get the chair pad.  I thought I would use my rolling suitcase to cart the stuff, but the chair was too large to fit inside.  I needed to lash it to the outside.

On Saturday I grabbed my suitcase and headed back to IKEA.  I was told that it is much more crowded, but I did not realize how much more crowded it would be. Most of the stores in France are only open Saturday and not Sunday.  When I was here before, I strolled in and wandered with out anyone else around.  Today was totally different.  Millions of people must have been here today.  I joined the throng of people entering the building.

Once inside I was immediately stopped as security walked up to me, putting his hand out and rapidly speaking to me wouldn't let me pass.  I told him I didn't understand and asked if he spoke English, which he replied in the negative.  He pointed to my suitcase and I immediately understood, he needed to check the bag.

Today the isles are packed with people, strollers, carts, kids running in and out of the people.  You are a fish in a large school and can only keep going at the speed of the fish ahead of you, which is at a snail's pace.  The chairs are displayed near the front, but of course, you pick up the boxes in the warehouse at the end of the river as you reach the sea of cashiers.

As I wandered along, I found yet a couple more items to add to my load.  Finally, I reached the warehouse, found the boxes, and lashed the box and the pad to my suitcase and went to stand in line.

They have not figured out how to use a queuing system like a bank uses, so you stand in line and if there is a problem you just sit there and wait.  That is what I did.  It took about 20 minutes from the time I entered a line until I finished paying.  Then for the fun part, getting on the tram and the bus.

Luckily the store is near the end of the tram line and the tram was not very full when I got on.  I could maneuver the bulky package into an out of the way place.  As the tram passed one of the many universities in Lyon, it became more and more crowded.  As we approached the stop where I needed to get off, the tram was packed.  I had to knock over people to get my three foot wide package out of the door.  A short walk to the waiting bus and I loaded it into the wheelchair location with ease.  The nice thing about the bus is that it drops me off 50 feet from the door to my apartment.  It takes twice as long as catching the metro, but it was much easier than hauling the cart down to the subway.  Thirty minutes later I was at the door of the apartment.

Now I had a box of parts and a chair pad.  It took me about an hour to assemble the chair and now I can sit and read in comfort. 

They live with the way things are

I have found that the French and other socialist states are content with living with the way things are.  They don't think about how to change it to be better.  Changes might put someone out of a job, or if you do something that is not your job, you are taking away the opportunity for someone else to do his or her job and gain satisfaction.

That means that they work around everything.  For instance, in the markets they have the same small baskets that you carry and the small carts that we have in the US.  They also have some in-between sized rolling baskets (like a small laundry basket on wheels).  You leave the carts at the check out and during the busy hours they stack up.

People were just moving around an empty cart sitting in the middle of the small path to the register.  I watched 4 or 5 people struggle to reach over the cart to place their items on the counter and shuffle past it.  When I got there, I just moved it out of the way, into an empty space by the unused register next to us.  Something so simple, yet it was not an apparent option to anyone else.

There are some differences in the supermarkets that I like.  You must weigh and tag all the vegetables and fruits with a tag like the deli puts on your package.  That way when you get to the cashier, they are already to be scanned.  All of the cashiers are seated and can scan items and take payments.  I also like their credit cards.  It is a PIN and CHIP system that is a debit card.  But, your card is always in your possession and you must enter a PIN code with every transaction.

They also have the saying that "you can't have everything" which to me is the completely wrong attitude.  You can have everything, but you have to work for it.  I just assume that we can have it all and it is up to me to decide how much effort, or money, I want to expend to achieve it.

I finally did my own laundry

I have been taking my laundry over to a cleaners.  They wash and dry and fold my laundry for about 15 euro.  It has saved me time and effort, but it is a bit expensive.  I have been trying to use the washers and dryer in the building where I live.  They have a machine that accepts credit cards, but I think it is either broken or only accepts the pin and chip cards used here in Europe.  Either way, I needed to take my bundle of dirty clothes over to the laundromat.  They are usually small with 3 to 5 washers and one or two dryers.  A lot of people wash the clothes in the washers, but take the damp clothes home to line dry.  I did already buy some soap so I could wash clothes in the sink, so I was ready to give it a try.

There is a single payment station on the wall with buttons for each of the machines. I was not sure exactly what procedure was required to make it all work. Most of the time when I pass this laundromat it is empty.  But luckily this time, there were people already in there and one was just loading his clothes into the washer.

They pack the washing into the front load washers much more than I thought possible. Clothes kept falling out until they were stuffed back into the washer. I watched as he placed the soap into the machines and then walked up to the pay station.   He dropped the coins into the machine, the credit being shown on an led readout and then pressed the button.  Voila, the money disappeared and the washer started.  Okay, so it is not so dramatic, but when all of the instructions are in French and your English-French dictionary does not have those words in it, it seems much more dramatic.

My turn, I stuff the laundry, fill the soap, pay, and press.  I am washing my clothes.  It takes about a half an hour for the cycle, so I head off to the grocery store to get some supplies, and stop at the bakery to get my daily loaf of bread.  When I get back, the laundry is still going, but soon the high speed spin is removing most of the water from the clothes.

But, now both dryers are occupied.  So I have to wait until someone is done with the dryer.  Only waited about 15 minutes before a dryer was available. You pay for the dryer in 4 minute increments for 60 euro cents, which is about 20 cents US per minute.  I dried the clothes for about 24 minutes which got most of the stuff almost dry.  Brought it home and spread it out on all the chairs and counters to finish drying while I went out to explore another part of Lyon.

The cost was less than 10 euro, but I needed to dedicate one to two hours for sitting around and waiting.   I will still use the cleaners to wash my shirts and press them.  The owner is very kind and patient with me and my limited french, so I will still take business his way.  Including my wash if I get lazy again.

Bad Day

Evidently I was suppose to mail a form to the French bureaucracy when I got here. The OFII, the local immigration office, needs to verify that I am actually here.

I still need to make copies of my passport, visa, and other papers but cannot because I don't have a code for the copier.

 I need to get yet another stamp for my passport in order to make the visa valid.  If I don't, I may not be able to get back into France if I leave to visit other countries.

But I don't understand what I need to do to finish filling out the form.  I am very frustrated.  I am also frustrated because the washing machines in the building do not take any of my credit cards.  Ugh!

Today, everything sucks!

Now that a few days have passed, it does not look as bleak.  I have completed making copies and mailing the information off.  Now I wait for them to call.  They need to come visit me in my residence before I receive the final stamp.

Oh, that and I have to pay a fee.  I think that is the real reason for all the paperwork and the visit, to justify the large fee they will charge.  I will try to get the local French lab to cover the cost of the scientific visa when the officials actually come to get it.

 

100 days left in Europe

I have already been here 33 days or one quarter of my trip.  It has passed faster than I thought.  I am concerned that I have a lot of work to do and only 100 days left to do it. 

The research has been progressing at a reasonable pace and I know it will all come together in the end.  I have planned three trips to visit other universities while I am over here: Munich Germany, Leuven Belgium, and Strasbourg France.

Trip to Munich in March

I met a group of researchers from Munich Germany when I was in Barcelona last April for a Computational Biology Conference.  I hit it off with one of them.  He is an older student with a wife and three children.  We both spent a number of years working in industry before returning to school to chase the PhD.  

Gergely is originally from Hungary but has been in Germany for the past few years.  He's just about to finish his PhD.  He has arranged for me to visit, found me a room and an interview with his professor who has a post-doc position available for a bioinformatican. 

There are some interesting possibilities that could be imagined with this group.  Their group consists mainly of computer scientists that are processing biological data.  This is a group that I feel much more at home with than the biologists.  When I am with the biological groups, I am usually the only computational person and I must interact within a subject I am much less familiar.

Even though I have spent a bit of time in Europe and studied German for years in high school, I have never been there.  I did stay one night in Germany when I was eighteen, but it was a tourist town on the Rhine and everyone spoke English.  We will see how much of my German I can remember after 35 years. 

Trip to Leuven outside of Brussels, Belgium at beginning of April

I have been introduced to a colleague of my thesis advisor.  She indicated that I am in Europe and would like to visit interesting labs.  Kevin Verstrepen was at MIT and Harvard when my advisor was at MIT.  He was happy to have me come visit and even hooked me up with another grad student that has a bed available.  I found some cheap flights and should be able to keep the costs down for a four day trip.

I have never been to Belgium and have no idea what the country is like.  I do know that Brussels is the center of the European Union and NATO.  Therefore it is a very international city and I have been told that most of the people can converse in English, so I don't need to learn Flemish.

The Verstrepen Lab is a molecular biology lab that is similar to the lab I am a member of in Boulder.  They endeavor to understand how the transcription process works by experimenting with yeast cells.  We usually use either the strain of yeast used in baking or the strain used in making beer.  These cells are easy to grow and we are able to measure the processes that are going on in within the cells.  Yeast cells are very adaptive and their genome can change within a very few generations.  We can control the changes to the DNA and then measure the changes that occur within the cell. 

Of course we cannot "see" any of this.  The data from an experiment is hundreds of thousands, millions, or billions of individual pieces of information.  This is where I, as a computational biologist, come into the picture.  We take all this information and arrange and organize it into a set of usable information.  We can tell if the changes from one experiment are statistically different from another, we can visualize the information and allow the biologist to "play" with the data, viewing it from different perspectives.  We can use this information to build models of how the cell is performing the processes and we can see what outcomes might occur from changes we are planning in the future. 

Planning a trip to Strasbourg France in mid April

I met a very well known professor from Strasbourg last year in Boulder.  He is also a friend of my thesis advisor and I will be visiting his lab in mid-April.  Strasbourg is a smaller city, about the size of Boulder, and has a large number of students at the different universities in the area.  It will be nice to visit somewhere besides big cities.