Dublin

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Another day, another new city and country! I arrived early for a full day in Dublin. The museum highlight of the day was definitely the bog bodies at the National Museum of Ireland Archaeology. These bodies are burials or sacrifices discovered in peat bogs in Ireland – most of them accidentally. Due to the low temperature and acidic and anoxic water, features like hair and fingernails are preserved on these burials.

Incredible preservation. Hair, fingernails and jewelry are still visible on some of these bodies.

Selfie with a bog body? Why not…


After getting my fill of museums and walking around the city, I stopped by the Guinness storehouse for a tour, a lesson on tasting, and a pint on their sky-high “gravity bar.”

A 360 view of the city with a Guinness in hand, what could be better.


That night, I found a small pub with a bunch of local musicians cycling through. They were sitting in a circle with uilleann pipes, fiddles, a banjo and a concertina, all playing traditional Irish tunes. Cobblestone is off the beaten tourist path and definitely recommended if you’re looking for a more local spot in Dublin. There’s only so much banjo I can take in one night, so I later headed to Temple Bar in the city center. Well known for attracting travelers from all over the world, I met a couple from Connecticut and listened to cover songs with an Irish twist til the morning hours.

Temple Bar is a Dublin icon

I had a few hours to kill before my flight the next morning. Dublin has an upcoming craft coffee scene, which was actually quite impressive. I wandered around the city, trying different shops and sending my caffeine level sky-high. No napping on this plane ride!

But first, breakfast. The full Irish from Third Space

First Draft Coffee for a pourover and a few work things to catch up on. Points if you recognize a t-SNE plot when you see one!

Delicious pourover from Two Pups coffee.

Espresso from Container Coffee. I’m sensing a trend after Brixton…

Cardiff

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After the short time in Lonon, I was on a bus to Cardiff. This was my first time in Wales, and it was nice to be in a calmer place. I was staying with two friends from the ISCB Student Council who showed me around the downtown and Harbor of Cardiff. It was raining when I got there, which I found to be quite common in Wales. I was actually happy for the cool weather and rain – after Istanbul’s constant 33°C sun, this was the first time I had to wear the sweater and rainjacket I brought!

The next morning I had an early flight across the way to Dublin. Last city in Europe!

From simit and kebabs to tea and crumpets

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After a tearful goodbye with Lauren and Selen, I hopped on a Turkish Air flight and was headed for London. This was my first time in the city, so I was looking forward to the museums, history and … Not to mention trying to pass off my British accent as authentic!

I was staying in Brixton, a neighborhood in South London known for the street market and Caribbean influences . I’m calling Brixton the Somerville of London – super hip these days, gentrifying rapidly, and full of young people who think adding ‘craft’ to the start of everything is a good idea. Brixton still has some of it’s old character, as I saw walking around during the opening hours of the market.

Setting up market stalls in the morning.

Brixton’s covered market. Coffee shops getting warmed up for the day.

Pop Brixton, a collective of restaurants, bars and shops assembled out of shipping containers. Come 6PM this place was packed!

Morning coffee and some blogging.


Museums for the day included the British Museum (Rosetta stone and ancient Egyptian sarcophagi) and the Imperial War Museum. The later had the best collection of WWI and WWII artifacts I’ve ever seen, laid out in a way that felt like your were walking through a history of the war.

The tail fin from Heinz Schnaufer’s Bf110 fighter. The most successful German night pilot in the war, he shot down 121 British bombers and was responsible for 850 RAF casualties.


Later activities included seeing the sights in London, taking selfies with famous buildings and bar trivia at one of Brixton’s craft beer pubs.

Big Ben and Little Ben!

Best tap handle I’ve seen. And a decent beer, too!

 

Doseluna winery

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I realized I’ve been neglecting to talk about the vineyard we were staying on! Doseluna winery is completely owned and operated by Selen’s family. They produce a red, white and rose wine from the grapes grown here. Vines sprawl down the hill from the house, ripening in the Mediterranean sun. The harvest of this season’s grapes won’t happen for another month, but we were lucky enough to tour the winery and help out with production.

Rows and rows of green and red grapes

Aging the Cabernet in oak barrels

Fully stocked and temperature-controlled storage


There’s a fully operational lab in the winery. Winemaking is a science, and precise monitoring of pH, sugar, alcohol and sulfate levels is crucial to a consistent and delicious wine. Here, we were adding potassium metabisulfate, a necessary preservative, to a red wine in a steel tank.

Adding sulfate to the tanks

Lauren measuring out metabisulfate to add to the wine


Earlier that day, Lauren and I set out to hike a nearby peak (okay, more of a hill). It was a long walk through olive groves and miles of thornbushes, but worth it for the views!

Sunrise in the olive grove

A wall surrounding a dead tree. Who built this shrine, and why?

 

Scrambling up some rocks on the way up.

Exhausted and scratched, but happy to be at the top!

The vineyard, as seen from the peak.

Assos day two – market day

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In a nearby town there was a local outdoor market on Fridays. Everyone seemed to show up – buying, selling, exchanging and conversing. You could find everything from clothes to power tools and quail eggs to live chickens. Lauren and I were most excited about the fresh produce, and made a beeline for those stalls.

Need a chain for your boat? We got that.

Mountains of fresh parsley and dill

Tomatoes, eggplant, fruit – everything you could ever want.


The fruit was the most notable. The best strawberries I’ve ever had – fresh, small and packed with flavor. We got 2kg for 14 Lira, about $4. That’s less than a dollar per pound. Incredible. Every exchange was happening in Turkish, but we managed to make it work with the basics we knew, and plenty of pointing!

Proud owner of a mountain of strawberries

If you know me, you know why I was excited by this stand.


What do you do when you have kilos and kilos of fruit you couldn’t possibly eat? Make jam, of course! After a laborious pitting and pruning operation we had the stove full, cooking down three different pots. Sour cherry, strawberry-basil-balsamic (my favorite), and strawberry-peach.

Slightly less fruit after all the sampling that was happening

Jam cooking down

The final product. Well worth the effort!

Arriving in Assos

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How lucky are we? Selen’s family runs a vineyard in Assos, on the Turkish coastline near the Greek island Lesvos. We piled in the car — six hours of driving and a ferry ride later we arrived at the vineyard. And just in time! We welcomed a thunderstorm rolling in from the Aegean. We all huddled under the porch to watch the lightning. Soon enough it was hailing fairly large pellets — the first time that’s happened in Assos since Selen’s family has been here.

Lightning over the Aegean

After the storm – ancient Assos in the background


The next day we explored Assos, the ancient village built on a hill over the sea. The construction dates back to 530BC, and much of it is still standing. There’s no mortar holding the walls and tower together, only perfectly carved stone blocks interlocking an supporting each other. At the top of the hill was a large temple to Athena, the god of war and wisdom. Only a few column pieces remained, reassembled here with some modern cast sections. Stand among the columns and imagine the Greeks using this temple, right where you are, 2500 years ago. And then snap out of it and pose for a photo.


Further down the hill is an amphitheater, still standing with the same timeproof construction.

We walked town to the old harbor town of Assos afterwards. It’s now a popular tourist destination, filled with hotels, restaurants, and a place to get ice cream by the water. We saw some locals serving “fish bread” to tourists from their boat. Doesn’t get fresher than this!

No trickery from this ice cream man!

Thanks for telling us you are taking a photo, Lauren!

Olive trees grow like weeds around here. Unfortunately they are nowhere near ripe. Still, we got a great sunset over the ocean and a perfect end to the day.

Not the best idea I’ve had this trip.

Harbor at sundown

Cycling around Büyükada

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After so much city time, Lauren and I wanted something more quiet and active for today. Selen recommended Büyükada, the largest of the Princes’ Islands in the sea of Marmara. The day started with another boat ride, this one much longer than the last.

Cruising down the Bosphorus

We rented bikes from a local shop and set out to explore the island. There are two peaks, one topped by an old Greek orphanage that is now in decay. Fun fact: this is (or was before it starting apart) the largest wooden building in Europe and the second largest in the world! Now, it’s all blocked off.

View of the orphanage from the higher peak

The highest point on the island was a major challenge to cycle up on the poorly maintained rentals, so we had to walk most of the way. The views of the sea of Marmara and the Turkish coastline were worth it!



On the way down we found a nice secluded swimming hole. A dip, a nap and a snack later we were feeling refreshed!

The sea of Marmara was cool and clear

Later, in town, we got dinner at a seaside restaurant. They let us choose which freshly caught fish we wanted cooked up.

One freshly caught sea bass, please!

The winding route we took around the island


On the boat ride home, we had an exceptional sunset over the old city. Aya Sofia and the blue mosque looking regal here.

Istanbul’s Old City

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Monday, Lauren and I were up early the next morning for a full day in Istanbul’s old city. We caught a boat from a terminal near Selen’s house and rode it all the way down the Bosphorus. Getting around by boat is common and efficient here. The terminal runs just like a metro stop – swipe your Istanbulkart to get in – and we noticed many local commuters boarding at stops from both the European and Asian sides of the Bosphorus.

Simit for breakfast!

I caught Lauren having tea and contemplating the spirit of travel

Morning fog over Anatolia

Today was the day to be tourists in the old city. First up was Hagia Sophia (pronounced Aya Sofia here), the towering monument to religion constructed by the Byzantine Emperor Justinian in 537AD.  It was a Greek Orthodox church back then, and many mosaics and symbols of Christianity are still visible inside the building. With the conquering of Constantinople (Istanbul) by the Ottoman Empire in 1453, out went Christianity and Aya Sofia was converted into a mosque. It remained a place of active worship until the 1930’s, when it was opened to the public as a museum.

Notice the massive calligraphic panels (recent additions), with the names of Allah, Muhammad and other important Islamic characters.

Across the way is the Blue Mosque, a towering building with a distinctive red carpet that is still actively used as a place of worship.

Men still kneel on the red carpet to pray at the Blue Mosque today. Lauren had to cover up to go inside!

In desperate need of snacks after only simit for breakfast, we searched the Hippodrome (a circus and chariot racing pavilion in the times of Constantinople) for some street food. Luckily a vendor selling freshly roasted chestnuts and corn was more than happy to oblige. We took a trip through the Grand Bazzar after, one of the oldest covered markets still in operation today. We stopped to peruse the hand-made silk rugs, gasp at the gold salesman and sample Turkish delight from vendors eager to take our Lira.

Service with a smile! I think we were his first customers of the day.

Wearing your wealth on your sleeve is a thing here.


Afterwards, we toured Topkapı Palace, where Ottoman Sultans lived and ruled from the 15th century onward. Most interesting was the Harem, the private quarters of the Sultan and his family. The Sultan’s mother (Queen Mother) had a ton of power back then! She dictated which women could be part of the Harem, and actually had a room between the Sultan and his wives (no doubt to keep tabs on their comings and goings).

Only the Sultans family and servants were allowed inside. A palace within the palace.

Imperial hall of the Harem.


Finally, we had to try a Turkish bath (hamam). Baths have been a staple of Istanbul’s culture since the 16th century. Walk into the bath room wearing only a towel. Çemberlitaş Hamam is one of the oldest and the obvious choice. Lay down on the hot marble slab and wait 15 minutes for your skin to soften. When your masseuse enters, roll over and try to convince yourself it’s fun as they scrape your body of its outer layers with what is basically a brillo pad. Enjoy a hot massage and soap bath following, and end with a cold shower. Wow.

You will be scrubbed clean of every single dead skin cell while laying on a marble slab from 1584. Source


Tired, but cleaner than we’ve been in days, we rode back up the Bosphorus in another commuter boat.

Arriving in Istanbul

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“Why Turkey?” I was asked this question many times by friends and family as I prepared to travel further East than I’ve ever been before. Turkey has made international headlines many times the past year, not often for good reasons. The country is increasingly conservative and repressive. What can it offer to an American traveler? Is it safe for Westerners?

The main reason for this trip to Turkey is to visit Selen, a good friend from Brown who grew up in Istanbul and is currently completing a Master’s program here while applying to medical school. Lauren, another good friend from Brown, and I both had the time off. What a great excuse to travel and visit a new place! Selen reassured us that Turkey was still was still worth a visit — She spun tales of thick coffee, fragrant food, boat rides up and down the Bosphorus and trips to visit some of the world’s oldest and grandest mosques and churches. Plus, her family runs a vineyard on the coast of the Aegean, a 6-hour drive from Istanbul. We would get a chance to visit and sample their wine and olive oil. What more could I possibly want?

I’m glad I listened to Selen.

Our first day in the city began with brunch at Emigran Sütiş, a bustling restaurant near Selen’s house. We sat on the balcony and our table was quickly filled with Turkish coffee, freshly baked bread, vegetables, honey and kaymak (Turkish cream/butter). We ordered 3 types of menemen, eggs scrambled in a pan with tomatoes, spices and cheese or sausage for the main course. We watched boats motor up and down the Bosphorus as Lauren, Selen and I got each other caught up on where our lives were going. It had been a year since Selen moved from Boston back to Turkey!

The first of many Turkish coffees!

Sipping my troubles away


After breakfast we walked along the Bosphorus, taking in the new sights, sounds and smells of Istanbul. Fisherman casting into the blue water and men selling simit (circular sesame bread, hugely popular in Turkey) filled the path. One thing you notice immediately about Istanbul is the number of stray cats and dogs wandering around. People actually seem to enjoy and care for the strays here – it’s not uncommon to see trays of water and food set out on the street.

Cats by the Bosphorus. Photo credit Lauren C.

One of many Simit stands. Photo credit Lauren C


Later that day we toured the Istanbul naval museum, where we learned about Caïques: gilded boats that Sultans of old used to parade around the Bosphorus. Many had Kiosks for the Sultan and his family in the back – just like a floating palace. One Sultan even had a smaller caïque solely to bring him coffee and tea. Talk about luxury!


Next was Dolmabahçe, a grand palace on the Bosphorus built in 1856 and used as the center of the Ottoman empire for decades. We toured the lavish interior, much of it filled with rooms too big and gaudy to be practical. We had a relaxing afternoon in the park, with plenty of time to (literally) smell the roses.

Getting up close and personal

The famous view: Ortaköy Mosque with the pier and bridge in the background


A dinner of köfte (Turkish meatballs) and Tuborg (Turkish beer) I was ready to call the first day in Istanbul a success. More to come tomorrow!

ISCB Student Council Symposium 2017

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Each year, the International Society for Computational Biology Student Council (ISCB-SC) organizes a conference for students and early career scientists in computational biology. The Student Council Symposium (SCS) is typically the day before the Intelligent Systems for Molecular Biology conference and welcomes scientists from all over the world. As one of the organizers of SCS this year, I had to be in Prague to administer the conference and deal with last-minute . Check out these links if you’re interested in the Student Council (twitter), or want to read some writing I’ve done on planning an international conference in the past.

We had 3 excellent keynotes this year:

  • Dr. Christine Orengo, professor at UCL and protein structure expert. Dr. Orengo gave an overview of her research, but spent most of the time speaking about advice for young scientists. A major point she stressed was to carve out your own niche in the research world. Find an area that combines what you’re good at, what interests you, and where the field isn’t too crowded. There, you can maximize the impact of your work and can be the most successful without excessive competition. Dr. Orengo also spoke about how important good relationships with your competitors are. I took this away from the lecture, “keep your collaborators close, but keep your competitors closer.” Not to compare scientific research to The Godfather, but the point was that you should treat your competitors well. You can learn from them, be motivated by them, and might even end up joining forces in the end!
  • Dr. Johannes Söeding, professor at the Max Planck Institute for Biophysical Chemistry and another protein sequence, structure and homology expert. His lecture was more focused on research his team had been doing. Quite successfully, I might add, as we had two of his students presenting at SCS!
  • Fiona Nielsen, founder and CEO of Reopositive. Fiona talked about her transition from academia to private industry. Deep in the research process, she found it almost impossible to identify or access datasets that would support her project. It’s a problem I’ve seen over and over again in my own research: there are many databases of genotyping or gene expression data, each with their own datasets, formats and access rules. After identifying the data you need, it can take months to be approved if the dataset has restricted access (for patient sensitive information or germline mutation status). Majorly frustrated by these repetitive roadblocks, Fiona was driven to solve this problem. She first established a charity (DNAdigest) and then a company (Repositve). It was interesting to hear Fiona’s take on this winding career path, and helpful to be reminded that pure research isn’t the only path that can have a positive impact on patients.

Another highlight of this year was the flash presentations: 5 minutes, 2 slides and 1 chance to sell your work to the crowd. Flash presentations gave many more people a chance to speak – we had 12 this year. I was worried that keeping people to the 5 minute time limit would be difficult, but everyone stayed on track and they were a big success. We’ll definitely have more flash presentations at future SCS.

This was also the largest SCS I’ve ever attended or organized — we had 75 poster presentations and even more people registered for the symposium! I enjoyed helping to organize an event that brought people from such diverse and far-reaching backgrounds together. A lot of time and effort goes into SCS, but it’s rewarding and worth it in the end.

Finally, we moved the crowd to a nearby restaurant and bar for the “networking event,” which is a chance to let off some steam and enjoy a good meal while avoiding the topic of research entirely. It was great fun, even if Bart did hog all the beer!

A huge thanks to the other SCS organizers, it takes a big team effort to pull off an event like this: Julien Fumey, Mehedi Hassan, Bart Cuypers, Aishwarya Alex Namasivayam, Nazeefa Fatima, Alexander Monzon, Farzana Rahman, Sayane Shome, Dan DeBlasio, R. Gonzalo Parra and Alex Salazar all made invaluable contributions and were a pleasure to work with.