Arriving in Istanbul

“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 Muslim. 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

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.

Cesky Raj (Czech Bohemian Paradise)

Cesky Raj is the first Nature Reserve in the Czech Republic. Two hours North of Prague by train, it’s a great day trip to get out of Prague. You’ll find towering sandstone rock gardens, ancient castles built atop weathered outcroppings, swimming holes at every other turn and Czech locals out enjoying the warm weather.

I spent an entire day in the Bohemian Paradise, taking the train to Turnov in the morning and returning in the evening. You can walk to the major sites, espicially if you take bus back to the train station. However, any path walked is much better biked! After a little trouble and miscommunication finding the shop, I rented a bike for the day and was cruising down the cycle tracks. An early stop at the inforamtion center gave me a map of all the roads, hiking paths and cycling routes that was invaluable for the trip.

Here are some photos of what I saw over the course of the day.

http://Start%20of%20the%20tour.%20Cycle%20tracks%20and%20maps%20are%20easily%20found.

Start of the tour. Cycle tracks and maps are easily found.

http://Warm%20water%20and%20willow%20trees!

Warm water and willow trees!

http://Rock%20garden%20outlook

Rock garden outlook

http://Looking%20over%20the%20rock%20garden

Looking over the rock garden

http://Valdštejn%20Castle.%20A%20nice%20stop%20with%20a%20pub!

Valdštejn Castle. A nice stop with a pub!

http://Another%20swimming%20hole

Another swimming hole

http://A%20nice%20water%20supply%20coming%20out%20of%20the%20rocks?

A nice water supply coming out of the rocks?

http://Guess%20not.%20I%20think%20this%20means%20it's%20bad...

Guess not. I think this means it's bad...

http://You%20just%20come%20across%20this%20in%20the%20woods!

You just come across this in the woods!

http://One%20of%20many%20village%20churches

One of many village churches

I don’t think I heard another lick of English after the information center – most people were visiting from other parts of the Czech Republic. For a good part of the trip I played leapfrog with a couple: her on a mountain bike and him in a tricked-out handcycle. Carbon frame, a huge climbing gear and fat mountain wheels. Watching him climb the steep roads to the castles was impressive and inspiring. We passed each other stopping for sights, snacks and swimming holes.

The route took me through some of the major sites: Var castle, Hubra Skala, Vysker. Some of the marked cycle routes were winding dirt roads through the forest, others were long and steep switch backed climbs. A bike gives you so much freedom in where you can go – so much quicker than walking, easy to conquer rough terrain and no problem to park against a signpost for a visit to castle or for an afternoon beer! I recommend Cesky Raj to anyone visiting Prague with a day to kill and a desire to get outside the city.

 

Summer travels start NOW!

The past few weeks have been a whirlwind. Since the end of June, I have:

  • Quit my job at the Broad Institute (yet somehow I’m still working)
  • Moved out of my apartment in Somerville
  • Given away or thrown away approximately 50% of my possessions
  • Said goodbye to the great friends I’ve made in Boston

A lot is in flux right now, but the newfound free time has been enjoyable. I’m especially looking forward to the ~2 months of traveling before I have to start grad school in September. Here’s a quick rundown of what’s to come.

Tomorrow, I fly to Prague for some solo travels and the 2017 International Society for Computational Biology Student Council Symposium, which I help organize. Then, on to Istanbul. Meeting friends, visiting mosques and drinking plenty of Turkish coffee are on deck. Flying back through London and Dublin to knock a few new cities off the list.

Turn around with a fully loaded car (including mountain bike) and drive North, making a left turn after Toronto, and heading to Banff and Jasper National Parks. Spend a few weeks in the parks mountain bike touring and exploring the beautiful blue lakes.

THIS is what I want (stock photo bland-ness not included)

I’m going to make a few posts along the way, so stay tuned!

 

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.