Cold Spring Harbor, New York — We’ve submitted our reports, given our final presentations and reminisced over our slide show. We’ve exchanged our photos, moved out of our room and said our goodbyes. My research experience as a URP at CSHL has drawn to a close. What a defining summer it has been! From attending weekly faculty talks to giving my own talks, and from auditing seminars in the Gene Expression course to competing against that course’s team in the annual Plate Race, I discovered that I really feel at home in a dynamic research environment. From barbequing with graduate students to dining with renowned scientists, and from sailing in the lab’s “Double Helix” sailboat to climbing the Double Helix sculpture, I found that I thoroughly enjoy living and playing with scientists. I now know, more than ever, that I want to be a scientist. And what’s more, I’ve been blessed with everything an aspiring scientist could want: research experience, career advice and a support group.

My research project has been more successful than even I initially anticipated. I completed my project goal, a new visualization interface for the gene expression data in WormBase. WormView, as we call it, is available at http://dev.wormbase.org/db/gene/expression for demonstration. Type in a gene name, and my Perl program will find the gene’s expression data and draw an image that visualizes the data. In addition, the worm image is an entry point for a new search tool. WormMap, as we call it, searches by tissue, rather than by gene. Just scroll your mouse over the worm image and click! There is still much room for improvement, but this summer, I’ve shown that the concept really can work. As more and more data is added to databases like WormBase, scientists will be increasingly pressed for digestible and efficient ways to access that data, and it’s this growing need that my project directly addresses. I hope WormView and WormMap will help researchers in the future!

In addition to learning bioinformatics firsthand, I’ve gained advice and insight about applying to graduate schools and pursuing a scientific career from some of the leading scientists of the world. I’ve dined and conversed with the CSHL chancellor, president and dean in their homes! I’ve met countless other scientists in all different stages of their careers: graduate students, postdocs and principal investigators. Most have been more than willing to share their stories and offer me advice. I now believe that a scientific career is an achievable goal for me.

Finally, I’ve bonded with a support group of 23 other URPs who share the same interests and goals. I am really going to miss everyone! We’ve already made plans to meet in the coming year, and we all hope to see each other at graduate school interviews. I have a feeling that I’ll be seeing these 23 friends again as we all progress in our scientific careers. In my first entry, I said I would be immersing in the culture of science and learning the language of Perl programming. Now I feel at home with both the culture and the language, and I believe that I am well-equipped to pursue the next stage of my scientific training. I cannot imagine a more worthwhile – and fun! – summer than the one I just had.

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Cold Spring Harbor, New York — Tonight we had a barbeque with the CSHL President Dr. Bruce Stillman and his family at their lovely home. He gave us very insightful advice about how to succeed in graduate school and throughout our scientific careers. It was very inspiring to hear such encouraging words from someone who is himself extremely successful!

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Cold Spring Harbor, New York — Every week, we attend at least one Faculty Talk and one Bioinformatics Workshop. This week, our speaker showed us her cutting-edge 3D projector! We got to see 3D structures of nucleic acids and proteins up-close and personal. Here we are sporting our fashionable 3D glasses.

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Cold Spring Harbor, New York — The URPs placed third in the world-famous Plate Race! This is an intense relay in which one runs with a stack of 40 used Petri dishes. It is really difficult to prevent the plates from falling! Here we are laughing before we are rained on by a bunch of plates.

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Cold Spring Harbor, New York — This afternoon we had lunch with the Watson School of Biological Sciences Dean, Dr. Lilian Gann, in her home. She is an excellent cook! I had informative discussions with a few faculty and graduate students about applying to graduate schools, something I definitely need to start preparing for!

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Cold Spring Harbor, New York — In the past few weeks, I have really started to feel integrated into the CSHL scientific community. Last week, there was a four-day meeting on Glia in Heath and Disease. A large meeting means better food (like seafood buffets!), but it also means a lot more scientists eat in the dining hall. I’ve sat next to scientists from all around the world and have had interesting conversations with them about what life is like as a scientist and where they get ideas for their research. Recently, I’ve also been attending seminars that are part of the Eukaryotic Gene Expression course. Although the course is geared towards graduate students and postdocs, I am really proud that I have enough background knowledge to follow the talks. It’s interesting that much of the research they present dispute the models I’ve learned from textbooks.

Lately my project has been moving very quickly. I integrated my worm drawings with the WormBase database! Now I am working on enhancing it by making the code extendible and adding more organs. In other words, I get to add on the bells and whistles!

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Cold Spring Harbor, New York — Today us URPs got to see the Broadway musical "Avenue Q." I absolutely loved it! The songs have catchy tunes and blunt, yet hilarious, lyrics. It’s a coming-of-age story about finding one’s purpose in life, so it really struck a chord with me since I have also been exploring my future plans during my time here at CSHL.

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Cold Spring Harbor, New York — I can’t believe that I am already halfway through my research internship! I feel that I have grown so much from working on my project, having fun with the other URPs, interacting with the scientists here and exploring NYC.

Let me explain my project, which is called “Visualization of C. elegans Gene Expression Data in WormBase.” C. elegans is a worm that is a very popular model organism, which means that many biologists study its systems and apply their findings to other organisms, even humans. It was the first multi-cellular organism with a completely sequenced genome, and all of the information that has been collected about it is available online at WormBase. I am working on improving the user interface of WormBase. Currently, WormBase contains the gene expression patterns for about 5,000 genes, but these are displayed only as text tables. My job is to visualize this data by creating a “coloring book” interface that shows a black-and-white outline of the worm and highlights where a selected gene is expressed. If successful, this will become a new feature of WormBase!

To complete my project, I need to know programming and C. elegans anatomy and expression patterns. As someone with no practical programming experience beforehand, this was quite a challenge! So far, I have learned the basics of Perl, CGI.pm (a module to create dynamic web pages), and GD.pm (a library of image generation software). If this sounds like gibberish to you, that’s how I felt at the beginning, too! Luckily, everyone in Dr. Stein’s lab has been extremely patient and helpful, especially Dr. Sheldon McKay, the postdoc who is guiding me through this. I have also been learning about C. elegans and drawing drafts of its tissues. I am really proud that I just finished drawing my worm and its major organs, and posted it on the WormBase development site! Now I will be working on interacting with the database, which means that I need to digest some more advanced programming.

The other URPs and I have bonded very closely over the past five weeks. We have done so much together! The program has activities for us nearly every day, including weekly bioinformatics workshops, weekly faculty talks, graduate student buddy events, a scavenger hunt and a pool party. We have also come up with many exciting things to do ourselves, such as dancing in our cabins, barbequing at the beach, bowling in the local town, fishing at Jones Beach, and laughing at a NYC comedy club (not to mention all the other places we’ve explored in NYC!). We have celebrated two birthdays and one half-birthday — we will make up any excuse to have fun.

I have also met many graduate students, postdocs and PIs by attending talks, practicing volleyball, going sailing, attending a banquet, and visiting the beautiful harbor-side house for first-year grad students. It is always interesting to hear about how they got to where they are today, especially since I hope to be in their shoes in the future. Needless to say, I have been very busy, but I am enjoying every minute of my experience!

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Cold Spring Harbor, New York — We were invited to dinner at Dr. and Mrs. Watson’s home! After enjoying a lovely meal on his porch (which has a gorgeous view of the harbor), we had a discussion with Dr. Watson about his beginnings as a scientist, hot topics in biology today and his vision of the future.

We also got a tour of his home, which has numerous paintings and artifacts from his life as a scientist, including his Nobel Prize. While we were there, Dr. Watson signed my copy of his book, DNA: The Secret of Life. I also got a photo with him and his wife. At CSHL, they are known as Jim and Liz.

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Cold Spring Harbor, New York — I was chosen to give my Preliminary Talk to representatives from the National Science Foundation and the Department of Defense, which sponsors our program. After my talk, one of the questions for me was whether I had an agreement with WormBase to do my project, after which all the faculty pointed to my PI (principal investigator) and exclaimed, “He is WormBase!” I feel so lucky and inspired to be working here.

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Cold Spring Harbor, New York — After seeing a bird’s-eye view of NYC from the top of the Rockefeller Center, I visited Radio City Music Hall. The highlight was meeting a Rockette! Afterward, I toured the United Nations. It feels so empowering to be in the middle of such great cultural, political and scientific centers.

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Cold Spring Harbor, New York — I went sailing for the first time! I got to sail in the “Double Helix” (the name of our sailboat) with Nandita (my fellow URP), two postdocs and a professor. We had an interesting conversation discussing all the famous scientists and entrepreneurs whose homes we passed by down the harbor. In addition to all the programming terms I have absorbed in the past weeks, I also got a full dose of sailing vocabulary.

The CSHL campus is filled with interesting biology-related sculptures – it is a playground for scientists! One of my other favorites is the “Waltz of the Polypeptides,” a sculpture of a ribosome translating protein, complete with mRNA, the large and small ribosomal subunits and finished product!

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Cold Spring Harbor, New York — Exploring NYC has been absolutely thrilling! I especially enjoy the dance venues at Lincoln Center. We watched a performance of the New York City Ballet in the afternoon, and went swing dancing outdoors at night. Here we are standing in the middle of Times Square – I can’t take my eyes off all the bright lights!

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Cold Spring Harbor, New York — This week, we each gave “preliminary talks,” 10-minute presentations introducing our project for the summer. Luckily, I have some experience with giving presentations from participating in the Undergraduate Research Opportunities Program at UCI. It was interesting to hear about what all the other URPs were working on. In this photo, you can see that Katie and I coincidentally wore matching outfits.

When we’re not working, lately we’ve been practicing volleyball a lot to prepare for our game against the graduate students, and our game against the faculty at the end of the summer. Unfortunately, we lost all three games against the grad students, so I guess we really need to practice more!

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Cold Spring Harbor, New York — We get free access to CSHL’s kayaks, canoes and Atlantic sailboats, so I walked down to the beach and went kayaking in the harbor. It was so refreshing! It was also fun to spot the wildlife, including horseshoe crabs, jellyfish, geese and swans. Unfortunately, there are also lots of mosquitoes.

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Cold Spring Harbor, New York — I am having so much fun getting to know the other Undergraduate Research Program participants, or “URPs.” We explored Huntington, the town next to Cold Spring Harbor. We all have a strong interest in biology, and most of us are pursuing research careers, but we come from all across the U.S. and around the world. There are even students from Puerto Rico, Canada, Israel and Ukraine!

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Cold Spring Harbor, New York — CSHL has a very dynamic scientific community. In addition to all the labs here, there are always scientists visiting for lectures, meetings or courses. I went to a lecture by Matt Ridley, the author of Genome: The Autobiography of a Species in 23 Chapters. (I wish I had brought my copy from home!) The lecture was on the life and achievements of Dr. Francis Crick, who helped discover the double-helix structure of DNA. What made this lecture special was that Dr. James Watson, Crick’s collaborator during their groundbreaking discovery, was sitting in the audience and verifying what Ridley said. Afterward, I got a photo with Dr. Watson!

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Cold Spring Harbor, New York – Here I am standing in the doorway of Glass Cabin, my home for the next 10 weeks. Although it looks like a quaint little cabin in the woods, it’s really more like a hotel. We get our beds made, fresh towels, and miniature shampoo bottles every day – it really is VIP treatment!





Dr. Lincoln Stein’s lab is in Williams House, which overlooks the beautiful harbor. Since we work on bioinformatics, it’s more like an office than the typical “wet lab,” so it is a completely different environment for me. My project will be to create a new interface for WormBase, the model organism database for Caenorhabditis elegans, a free-living soil nematode – basically, a ringworm. But before I get started, I first need to learn how to program in Perl and study C. elegans anatomy in detail.

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En route to New York — With my pillow behind me, laptop before me, headphones plugged in, drink on tray and two carry-ons safely stowed, I am finally on my way to New York! Flying always gives me the thrill of starting anew, as if a few hours at an altitude of 37,000 feet can be a sort of initiation to a new experience. Last summer, I was off to study abroad in Europe, to taste new cultures and new languages. This time, the destination is the Cold Spring Harbor Laboratory on Long Island, N.Y., and once again, I will immerse myself in a new culture and a new language.

This culture does not belong to any city or country; rather, it is the universal culture of scientific collaboration and discovery. I will spend the next ten weeks doing research in bioinformatics alongside scientists at CSHL, working, living, dining and playing with this time-honored community (one which includes Dr. James Watson!). I’ll be joined by 24 other students from around the world who have been selected as “URPs,” or Undergraduate Research Program participants. I’m excited that this truly will be an international community, but one that’s united in the culture of science. I can’t wait to meet everyone!

The new language I’ll be learning is Perl, a programming language that I‘m far from fluent in, though I did take a freshman seminar in it two years ago. I’m a little anxious about how I’ll manage to complete a project using Perl programming without being fluent in it – or any programming language for that matter – but I hope that like any foreign language, I will absorb it more quickly by being immersed in it. Luckily, I will also get to attend a series of bioinformatics seminars throughout the summer.

It’s quite coincidental that I stumbled upon this program and this research area. Before I even started at UCI, I became interested in biology after hearing about the Human Genome Project. This summer, I’ll be working very closely with genomes and using Perl programs to organize and analyze them. In fact, one of the projects in Dr. Lincoln Stein’s lab (which I will be working in) deals directly with the human genome! Needless to say, I am very fortunate to have this opportunity.

For the past two years, I have worked on independent research projects under the guidance of UCI faculty. Currently, I have a project making mutant proteins of the vaccinia virus polyadenylate polymerase, and there have been many cases when I felt that a computer program could speed up the process immensely. For this reason, and because of my own interest in the relatively new and rapidly growing field of bioinformatics, I applied for and decided to participate in this program at CSHL. I hope I’ll improve my Perl programming, learn a lot about bioinformatics, and experience the culture of scientific research firsthand. I also hope this experience will help me decide whether I want to go to graduate school in this area. Finally, I’m excited about visiting New York – as a double-major in biology and dance, I would absolutely love to watch the New York City Ballet, American Ballet Theatre and Broadway shows! I believe this will be a summer to remember.

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