Arriving in Assos

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

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

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.

What’s next: Stanford Genetics!

After a long process of PhD applications, interviews and waiting for results, I’m happy to announce that I’ve settled on a home for the next 5 years. Stanford’s PhD program in genetics was exactly the right fit for my scientific, career and lifestyle interests.

I chose the genetics program over the biomedical informatics program for a few reasons. First, BMI proclaims to be focused on algorithm development and expects students to draw their main interests from algorithms. Although I find algorithm development interesting, it has to be motivated by an underlying biological problem. The genetics program will allow me to work on biological problems that excite me (probably related to chromatin structure and conformation) from a computational angle. Second, when I searched for faculty that I want to work with, they were most commonly in genetics or other biology-focused departments. That being said, I plan to do an entirely computational PhD if I can manage it. That’s where my interests and expertise lie.

Students typically complete 3 rotations their first year. At the top of my list are chromatin biologists William Greenleaf and Alistair Boettiger, and Computer Science/Genetics expert Anshul Kundaje.

A few months to finish up at the Broad, a few months of travel and a big move out west are in my future. It’s an exciting time.

Vineyard 70.3 – 4th place!

After months of training for the Vineyard 70.3 triathlon, the weekend of the race was finally here! I was slightly nervous, but mostly excited to test my training against the course and the other competitors. I took the ferry from Woods Hole to the Vineyard Saturday afternoon, had a carb-y dinner with my friend Jordan who was also competing, and got to sleep very early. Up at 5:30 on Sunday and ready to race!

The morning was cold and windy – whitecaps lapped against the beach as the sun came up. Shortly after 7:00 the race started and we were off! The swim was tough – the choppy water made it hard to sight and it took me a few minutes to get settled into a comfortable rhythm. The bike section was much better, I passed a ton of people while maintaining a reasonable level of effort. Finally, it was time to run and I was still feeling strong. I kept passing people while only being passed by a one person (who went on to take first place for the women, so I’m not even mad). I really had to push through the pain in the last few miles, especially running along the beach in a headwind.

When I crossed the line I was shocked at my time  – 5:15! I thought 6 hours was a realistic goal for the race… I blew that out of the water! I ended up placing 4th overall and 1st in the 20-24 age group. I was thrilled with the results and enjoyed a persistent runner’s high for a while after crossing the line.

Here’s a race report about what I did well and what I can improve on for future races.
Swim: 29 min. Course was short, garmin showed it as 1600yd
Bike: 2:53 (19.3 mph)
Run: 1:49 (8:23min/mi)
Total: 5:15
What I did well: Biked hard but didn’t overdo it. Hydrated and ate frequently and regularly. Ran at a consistent pace and pushed through a crushing mile 10-12 with a headwind. Transitions were smooth, especially T2.
To improve: Swim – more time in the pool, ocean swims in choppy water would have made a difference in the time. I was in the bottom half of swim finishers. I’m on a Specialized Allez roadie I bought used and also commute on. I think the move to a tri bike would make a big improvement.
Training: Averaged 8-10 hours a week for the past 5 months. Typically 1 swim/wk. Two week vacation at start of August with only 4 runs for workouts.

What’s next? Not sure. For now some R&R and big meals will do me well. I’m considering pursuing triathlon seriously depending on where I end up for grad school, but that remains to be seen. A huge thanks to everyone who supported me taining for this race, especially my parents who came to the Vineyard and cheered me on!

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4 things I learned from keynote lectures at SCS2016

SCS2016 featured keynote lectures by two senior scientists in computational biology. John Quackenbush and Janet Thornton each shared scientific findings and expert advice to the students listening eagerly in the audience. I came away from the lectures with a few ideas I will keep in mind for both my daily research work and future career planning:

  1. “All models are wrong, but some are useful.” John Quackenbush opened his talk with this well-known quote attributed to George Box. He explained that many of the network models researchers in his group create are inherently flawed — and that’s OK! No model is perfect, but good ones can solve the problem at hand.
    This is definitely something I can apply to my research — It’s easy to get bogged down thinking about the small flaws in models I come up with or methods I use. It’s better to ask “is this useful?” than “is this perfect?”
  2. “You have to work hard, and it only gets harder.” Tough words to hear from Janet Thornton, who described her path from student, to PI, to eventual director of European Bioinformatics Institute. Janet described how she thought each career advancement would bring a decrease in the amount of work required for success. Just the opposite, she discovered. Each transition brought more work and more responsibilities, but these were balanced out by an increase in excitement. Higher-level responsibilities and mentoring younger students made the increased workload worth it.
  3. “Every revolution in science has been driven by one and only one thing: access to data.” John Quackenbush described how data used to be siloed away in the towers of the elite. Access was hard to obtain — due to both policy and logistical constraints — and science moved slowly as a result. We are slowly entering a culture of data sharing, driven by the obvious results of collaboration and the means to be able to share globally and instantaneously. John was excited about the potential for science in the future as data sharing becomes even more common, and I am too!
  4. “Communication is the hardest part, and the most important.” Janet Thornton selected communication as the single most difficult part of her career. She named it the sole factor that could make or break a project, collaboration or organization. I thoroughly agree with this statement (enough to make it the theme of my blog on organizing SCS2016) but was surprised that she still considers it a challenge. Effective communication takes practice, but can be very rewarding — whether it’s a Nature paper, innovative collaborative project or a successful international symposium!

The keynote lectures of SCS2016 were special. Senior scientists gave us a view not only into their thoughts on research, but also their ideas about careers, communication and the scientific process as a whole. Students have a lot to learn from mentors like John Quackenbush and Janet Thornton, and these lessons will stick with me for a long time.

This post was originally posted in the PLOS Computational Biology Field Reports Blog.

How do you organize an international symposium?

One word: communication.

I was approached by the ISCB Student Council leadership almost a year ago with an invitation to work as the co-chair for SCS2016. Yesterday, students from around the globe came together to share their research in computational biology here in Orlando. Throughout the many month-long organizing process, one theme stayed constant: the importance of communication.

It’s communication that convinces senior faculty to travel and give keynote lectures. Communication that persuades pharmaceutical and publishing companies to sponsor travel fellowships and our networking event. Communication that gets the word out to students around the world, communication that enables us scientist to speak in a common language despite different backgrounds, educations, accents and opinions. And most importantly, communication that allows students in different time zones come together and work to put an event like SCS2016 together.

To this end, a few practical tips: Doodle polls with timezone support are key for organizing meetings with people from different parts of the world. Skype or other web-based group calls keep people together and on track. To-do lists and documents of people’s responsibilities prevent you from forgetting what was decided at the last meeting. Gentle reminders via email are sometimes needed to make sure deadlines are met.

I learned a lot about the way I work with people. I’m quick to take on additional responsibilities if I feel I can complete a task quicker than delegating it out to someone else. I had to learn that “fast” or “better” isn’t always the end goal. It can be much more rewarding to give the responsibility to someone else and let them learn from it.

Inevitably, communication will break down at some point in the process. At this time, responsibilities fall on the head organizers to complete what needs to be done, even if it involves losing sleep!

Organizing SCS2016 was a lot of work, especially in the few weeks before the conference. Was it worth it? Without a doubt. I’m grateful for the opportunity I had to learn and work with other motivated students, and I’m proud of the event we pulled off yesterday!

This post was originally posted in the PLOS Computational Biology Field Reports Blog.

Martha’s Vineyard 70.3 triathlon

I’ve been interested in doing a triathlon for a while now – the combination of swim, bike and run is an excellent test of fitness, endurance and skill. Last week I finally pulled the trigger and signed up for the half-ironman distance triathlon on Martha’s Vineyard in September. It’s a beautiful course (the bike is basically a tour of the whole island) and will be a good event to focus my training on over the next few months. I think this is a good event for me for a few reasons:

  • 70.3 will be a challenge but not impossible with training. That’s a 1.2 mile swim, 56 mile bike and 13.1 mile run. I’m more interested in the endurance aspect than how fast I can finish the course.
  • It’s over six months away. I plan to train seriously for four months. This will give me plenty of time to work out the kinks in my training and do a sprint/olympic tri to practice.
  • Training will happen in the summer. It’s tough to find a pool to swim in around Boston, so I’m planning to do a lot of my training in Walden Pond, Upper Mystic Pond and the ocean when I’m back on Cape Cod.


    Just look at that bike route!

I plan to start training for the 70.3 in May. Until then I’m focusing on lifting and seeing how far I can push my squat, bench, deadlift and press. It’s fun to set goals and see your progress! You can follow me on the blog and Strava.