The 2022 cohort of students arrived in San Diego on June 6^th to begin the pre-departure symposium. Similar to last year, this whole week was spent preparing students for their summer projects. Throughout the week, I spent time going over various professional skills that would be useful for the summer as well as the students’ careers moving forward. Specifically, I discussed how to: make and present scientific posters, give an effective elevator pitch, present at lab meetings, write a conference abstract, and effectively present complex scientific data and graphs. During these professional development sessions, the students practiced each skill using data from a paper written by their host labs. In addition to these professional development workshops, I discussed graduate school and students had the opportunity to learn about different career possibilities following graduate school from a panel of experts. Panelists had experience spanning careers in academia, government, consulting and industry. At the end of the week, we all traveled to Stockholm and arrived in Sweden on Saturday morning. On Sunday, we went to lunch in the city and the students got ready for their first day of work. They all seem very excited for the summer and I’m sure they will all have a productive summer full of adventure (inside and outside of the lab!).

Please check back for new blog posts every Friday to hear directly from the IRES students about their experiences working in the lab and exploring Stockholm and beyond!

~Mark Chapman, NSF-IRES Program Director

Occam

After we arrived on Saturday, I tried adjusting my sleep schedule before work on Monday. At work, I have been analyzing protein expression levels in lung adenocarcinoma cells to determine which genes are significant for the cancer. So far, I have determined which genes are significantly correlated with better or worse survival of cancer patients, summarized what the major functions of these genes are, and constructed gene networks to determine modules of genes that function closely together. There's also been a lot to do around Stockholm. One of the first things we did here was go to the grocery store and try to decipher the Swedish labels to make sure we were getting what we wanted which was fun. The next day, we explored Djurgården where we had lunch at Rosendals Trädgård and had a blast at the ABBA museum. We also saw My Chemical Romance perform at Gröna Lund which was a fun experience for me since I'd never been to a live concert before. I was excited to get a bicycle from Sollentuna since bicycles are so useful in Stockholm, and I was a little less excited to bike the 16km (10mi) back with breaks that needed tuning. I also got a wonderful rental cello to play during my time here which has been a great activity for the rainy days.

One of the most striking differences I've experienced since being here is how long the daylight is. There is usually light in the sky until about midnight and I've never been up early enough to see when it starts getting light again. It's also been interesting to see how people act differently because of this daylight: I often see people strolling around at 22:00 or even 23:00 and it seems a lot more lively whereas most are indoors or in cars that late in the US. As someone who likes to be up later at night, this cultural difference has been really nice to experience, but it makes me curious of what it is like here in the winter.

Claire

Hej! This first week has been a whirlwind. We arrived in Stockholm on Saturday and started work in our labs on Monday. Most of my lab is on a lab retreat in Italy this week so it has been pretty quiet. My time has been spent reading papers and working through tutorials for some of the analyses I will be doing (and doing a lot of debugging along the way!). I am excited to get to meet everyone in my lab and dive into my project next week! I have also had the chance to explore some of Stockholm with the other interns. On Sunday, we went to the island of Djurgården, where we got a yummy lunch at Rosendals Garden. Then went to the ABBA museum, where we learned more about the band's history and did some fun karaoke. On Tuesday, we went to see My Chemical Romance at Gröna Lund, an amusement park that puts on concerts throughout the summer. There were a ton of people there so it was a bit difficult to see, but definitely a fun experience! I have also gone on a few runs around our dorm and in the nearby park of Hagaparken, which has been a great way to explore the area. One of the biggest differences between here and Claremont is the large amount of infrastructure for running/walking, biking and public transportation. All the pedestrian paths have made my runs really great, and it is very easy to get anywhere is Stockholm with the public transportation!

Molly

Hej! I arrived in Stockholm about two weeks ago, and have been working and exploring the city. In the lab, I have been researching breast cancer and spatial transcriptomics (a new RNA-sequencing technique). This week, I put together a plan for the summer and got started on the coding aspect of the project. I am working with students from all over the world, and we are quickly becoming friends. It is cool that everyone has different backgrounds, as we are all learning about each other’s cultures. In these first couple of weeks in Stockholm, I have been to a concert at Gröna Lund, had lunch in Rosendals Garden, kayaked at a local beach, went to Ikea, and have tried some different restaurants. Today (Friday, June 24), I went to a midsummer celebration at Skansen. The celebration involved lots of flowers, raising of the maypole, food, music, and dancing.

One difference I’ve noticed between Sweden and America is the cleanliness and quietness. All of the public transportation I have used so far in Sweden has been very clean and exceptionally quiet, often people will talk in a hushed voice if they are talking on the bus or subway. This is different from public transportation in New York, as subway stations are usually quite loud and you can find people playing music, arguing, talking on the phone, etc. Also, the streets and public places have been very clean, I have not seen any garbage littering the streets or sidewalks. It is interesting to see the difference in cultures through something as simple as public transportation etiquette.

I am having a great time so far, and am excited for everything to come. Hejdå!

Sean

Greetings from Stockholm! It has been about two weeks since we've gotten to Stockholm and it has been an amazing experience, to say the least. I've had a great time working in the research lab and getting to know everyone (there is even another student researcher from Florida working in my lab, which is a great reminder of home). Most of my work in the lab has been focused on preparing myself and bettering my understanding of the adipose tissue transcriptome. Last week I wrote a review on the topic as a way of familiarizing myself with current literature, and this week I've been honing my coding skills by practicing on a previous data set before the new one arrives. Everyone in the lab has been so welcoming and helpful these past two weeks and I am so excited to get to work with them all this summer. Outside of the lab, I've had a chance to explore a bit of Stockholm by going to see My Chemical Romance at Gröna Lund, visiting the Stockholm Public Library, kayaking the local waters, going to the ABBA Museum to live out my Mamma Mia dreams, and attending a Midsummer celebration at Skansen (thankfully it wasn't like the movie). I've had an amazing time exploring the city by bike and trying as many different foods as possible these last two weeks.

During my first two weeks, I have noticed a striking difference in the types of food available here in Sweden compared to back home. While I have tried to be adventurous as possible in trying new things, I will say having familiar foods from home does make the transition better and a little easier overall. When shopping for groceries on my first day here, after spending about 10 minutes attempting to buy milk, I was shocked the next morning to discover I had purchased yogurt in a carton instead. I was also pretty surprised when I ordered pickles off the menu at a local restaurant and was given what looked like a salad with pickled items. Although this was all a bit overwhelming at first, I have grown more confident and adventurous with every new item I've encountered, and I look forward to trying more.

Ismael

Stockholm is possibly the most comfiest city ever. The daily unpredictable rain and never setting sun consistently keeps the many parks lush green and flourished, rich with history, there is a wide variety of architecture ranging from traditional to modern in such close proximity, events occur everyday and the people are the kindest; there is not much of anything to dislike about Stockholm, given that everyone I’ve spoken to thus far have all expressed their dismay for only the Winter season, described as being an ever long night with a small break of sunlight for a handful of hours; nonetheless, Summer on the other hand is the complete opposite with the sun barely setting but never fully vanishing, be as it may, living without blackout curtains would have made sleeping in Stockholm difficult. With that in mind, a great tool to have in hand is a watch, because it is truly the only way to be aware of the time of day. There have been times when I think it is earlier than it actually is and only to find out to my surprise that it is 9 P.M., but I love that as I never have to travel in complete darkness. The most surprising fact to me about this season is that many Swedish people usually leave for the Summer, despite it being the best time to be in Sweden.

I’ve done many things in Sweden from my three weeks of having been here already, but my absolutely favorite thing so far has been riding my bike. Biking in Sweden is such a wonderful activity to do in Sweden and it offers so much utility, be it biking for fun, to exercise, or just trying to get around, of which it is practically the fastest mode of transportation in Stockholm. The main streets are designed with three roads: one for cars, one for bikes, and the last for pedestrians, and, there are also three separate light signals for each, so riding the bike is integrated into the very city. While it is absolutely possible to live in Stockholm without a bike, not having one is like disregarding a big part of the experience of living in Sweden. Oh, the places you’ll go (with a bike)

Besides riding my bike, I have also gotten the opportunity to experience many delicious meals from fica to traditional Swedish dishes, explored museums such as the Abba museum, go to the theme park Grona Lund, attend multiple events, and meet wonderful people.

The one place I have been meaning to explore the most is Old Town, which hopefully I will finally get the chance to acquaint myself with the location this upcoming weekend.

Trenton

It has been 3 weeks so far, and I am loving it here. I was initially worried about how rough the transition would be from my home life to living in Sweden. However, I have yet to feel homesick and really like the city and surrounding area. They even have my favorite Louisiana hot sauce here through some miracle. The weather was also lovely for the first few weeks. Having said that, one thing that really confused me about Sweden was the complete absence of bottled water. I used to drink multiple water bottles daily in America, but everyone drinks from the tap here. Apparently, Sweden has some of the cleanest tap water in the world. Also, it would appear that I'm a terrible person who hates the Earth for using so many plastic water bottles all these years. For the past 3 weeks, I have been trying to make up for my sins by conducting research on cancer data collected by my lab. I have been working on creating a data pipeline to take the data collected and run them through various variant caller methods. The goal is to analyze the prevalence of structural variants in primary lung cancer compared to those seen in the genome of metastatic brain cancer. I've been enjoying the work and have learned so much already!

During these first 3 weeks, I spent some time kayaking, biking, and dancing at various locations. However, the Midsommar Eve celebration at Skansen would have to be my favorite event so far. Loved frog dancing with everyone and discovered my newfound love of jam and waffles. Speaking of which, another cultural difference in Sweden is the fact that no one puts syrup on their pancakes. As one of the few people in the world who hates syrup, I'm delighted to know that waffles here are typically served with jam instead. This week, I went to a 3-day music festival in Stockholm. There were many fascinating Swedish artists I had never heard from before, like Alesso and Veronica Maggio. But, alas, my legs are sore from standing and jumping, so I think I will be taking a break from physical activities this next week.

Occam

Hallå, a lot has happened in the four weeks we've been here. For my work here, I used the gene networks I created to determine which genes were central to the problematic parts of the lung cancer I'm studying. After determining these target genes, I found which drugs resulted in similar effects to knocking down the targets. Once I determined the optimal drugs for each gene, I started testing some of these drugs on lung cancer cells to verify their effects on the cancer. During this processes, however, there have been a few difficulties. The most time-consuming one was when I was trying to calculate the correlation between gene expression after each gene knockdown and each drug treatment. The issue was that it was comparing transcription levels in twelve thousand genes across more than fifty thousand drugs and trying to store all the information in memory which well-exceeded my 24 GB of memory. I tried a lot of different approaches from trying to find a more optimized correlation function to looking up remote computing platforms, but eventually realized I just needed to break up my data into more manageable chunks and clear the memory after computing the correlations for each chunk. This helped me learn a lot about memory management and its importance as well as different techniques I can use to optimize for memory. Since bioinformatics datasets are notorious for being massive, these memory management techniques will definitely be handy if I choose to pursue bioinformatics in the future. Even if I choose to follow any other computing path, I will likely need to use these memory optimizing strategies, so I'm glad I am becoming familiar with them now.

I've also had a lot of fun adventures in the area since being here. I went kayaking and managed to capsize within the first few seconds, but still loved it so much that I went kayaking a second time. I enjoyed the midsommar celebration in Skansen and getting to see all the animals they had there. The next day, the exhilarating rides at Gröna Lund followed by a relaxing day at the beach really showed me the range of activities this place offers all in such close proximity. Most recently, I have been exploring outdoor places from the verdant Norra Djurgården and calm waterways around the city to biking the streets where I've been "hunting deer". Running through Hagaparken is one of my favorite parts of the day where I can hear and see wildlife (the rabbits are massive compared to the ones in the US!) and clear my head for a while. In general, Sweden's monumental "freedom to roam" law is a wonderful cultural quirk that I know I will miss when returning to the US.

Claire

Hej igen! It’s crazy that we have already been in Sweden for a month. It feels like it has flown by, but also that so much has happened! In lab, I have been making progress on my project. The first few weeks have been spent searching for data (specifically ChIP-data) to use, as well as finding a pipeline to analyze this data. This week, I began running the pipeline for the data I collected. These past few weeks have also presented a few challenges. One big challenge I faced was finding ChIP-Seq data for my project. Specifically, I was looking for data for specific transcription factors in specific cell types, which was really hard for me to find at first. After talking to the post-grad who is helping me, however, I was able to get some tips on specific databases to search through and cells to look at, and I was able to find a lot more data. This showed me how useful it can be to ask for help when struggling with something, even if you feel like the thing you are struggling with shouldn’t be that difficult. Often a few words is all it takes to get on the right track again! Outside of the lab, I have gotten to explore Stockholm, as well as venture outside of the city. Most recently, my family came to Sweden to visit, and we took a three hour ferry to Gotland Island where explored their old town and swam in the baltic sea. We also went into the archipelago to visit Birka, an archeological site that was previously a viking trading village. These first few weeks have flown by, and I can’t wait to continue to explore Sweden in the next six weeks!

Molly

Hej! I have been in Stockholm for about 5 weeks now and have spent that time exploring the city and doing breast cancer research. In the last few weeks, I have spent the weekends exploring the city and trying new restaurants. Stockholm is beautiful and I enjoy walking around the city and taking it all in. So far, Gamla Stan (old town) has been my favorite place, as there is a lot of history and intriguing shops. Some other things I’ve done are swimming at the lake, an escape room, and some museums. The Paradox museum provided endless photo opportunities and was a lot of fun. This week, my parents are visiting, and we plan to check out some museums and see the Royal Palace.

At work, I have been making progress on my breast cancer project. I’ve attended meetings and seminars that have been very interesting. My coworkers and I are getting to know each other more and are even spending time together outside of work. The project I am working on is very interesting to me and I am happy with how it is going. There was a minor setback with the timing of the project due to unforeseen challenges. I am working with 3 other people on this project and we all help each other. Each of us was sick for a couple of days in the last two weeks causing us too to push our timeline back. Once we were all healthy again, we met and went over our results from the previous weeks and created a plan to move forward. The time loss was not ideal, but will not have a lasting impact as we all worked hard together to ensure we are on the right track. This has taught me to be flexible and how to work with other people in all circumstances. We all stayed in communication to know what was going on with each other and offered support when possible. I learned that it is important to have timelines and goals but it is okay if they are not done when you thought they would be and that it is important to not get too stressed about a strict schedule as research often takes longer than you think it will. This experience also taught me that it is important to support your coworkers as you are all working towards the same goal. Ensuring everyone is on the same page, healthy, and in the right mind space to get working is key to success. The meeting to catch up with everyone and discuss our work projects and how we were doing personally really helped us all connect and get excited about the project and figure out how to complete it on time. Having this foundation between colleagues makes work more fun and productive because we are all happy to help each other out. This experience will help me in future endeavors, as I have learned about time management and colleague relationships. For future projects, I will make a timeline but be sure to leave some room for unexpected challenges and not get too bogged down with exact dates. I also have learned about colleague relationships and what to look for in new team members. I will make an effort to connect with my colleagues and ensure we have a solid working relationship so that we all feel comfortable enough to ask questions and for anything else, we might need to succeed in the workplace. I have been very fortunate to have great team members, and I am excited for the remaining weeks.

Sean

Hej! I can’t believe it’s been 5 weeks since we first arrived, and we’ve reached the halfway point of the program. Although the lab has been relatively quiet ever since most people have been away for their summer vacation, I’ve still been working hard on my project. Interestingly, after some complications with the adipose tissue transcriptomics data, I started working on a new project for the summer comparing skeletal muscle proteomics data across different datasets to get a better understanding of the health benefits of long-term exercise. Most of my time is allocated towards analyzing each dataset to see which proteins are differentially regulated, and then comparing each set of proteins to datasets from outside papers that help understand the directionality and specifics of exercise-induced protein expression. So far, I’ve been able to look at studies on proteomic changes from Type-2 Diabetes and long-term inactivity. I’m very excited to learn more and keep working on this new project while I dig deeper into each one of these datasets. Outside of the lab, the group has been taking every chance we can get to explore the area and try new things. In the past few weeks, we’ve gone to Gröna Lund for both the rides and to see John Legend perform, explore some local beaches (even though they were more grass than sand), stopped for lunch at Ikea (a real Swedish trademark), tried a few new bakeries around the city, walked around Old Town, and explored the National Museum, Medieval Museum, the Royal Palace, and the Paradox Museum.

While these last few weeks have been amazing and have truly pushed me to explore new things, since starting my research, having my project switched midway through the program has been a significant challenge. After about a month of focusing on adipose tissue and preparing for the transcriptomic data by reading extensively on the topic, writing a review on current literature, and preparing my R pipeline to analyze the data, being told I wouldn’t be able to work on the project anymore was a shock and had me worried about what my final project for the summer would look like. However, with the help of my amazingly supportive lab members, we were able to get me on a new project that would not only be beneficial to the lab, but also beneficial to myself by challenging me with a new topic that would allow me to draw connections from my previous project and learn about something new. Throughout these past few weeks, I’ve learned not only about the basics of proteomics, but the importance of cooperation. Whether asking for help from my lab members, reaching out to my supervisors, or simply learning from older codes written by myself or previous students, I’ve been able to get tips from the people around me and get back on track. This experience showed me how strong a resource the people around you can be in helping get you into the right mindset and helping you in new and somewhat scary situations. I am extremely grateful for all the support my lab has given me these past 5 weeks, both in person and over emails and zoom calls, and I know I can count on their support in the future.

Ismael

I finally got to explore Old Town, also known as Staden mellan broarna (“The Town Between Bridges”), and it was a beautiful blend of history and modernity. Old town holds buildings that have been standing there since the 15th century, gorgeous churches, and wonderful museums. One of the most interesting aspects of old town to me was how after so many years, there is still a vibrancy of life within the district that in some instances continues the tradition of being the center of the city; but also in some of streets, such as Österlånggatan (“Long street east of the wall”) and Västerlånggatan ("the Western Long Street") continue to be prosperous trade strips within the city. Unfortunately, at the time that I did arrive, the churches were already closed, so I didn’t get the opportunity to enter the buildings, but seeing them from the outside was a site to still be admired.

However, I did get to experience The Medieval Museum, The Palace, and The Paradox Museum (not in Old Town), all of which I really enjoyed. The Medieval museum held a lot more historical knowledge regarding the common life that once existed in Stockholm, including some information about geography, culture, and artifacts were displayed throughout it; of which, my favorite part was a segment on nature which explored the connection people had with it and how they interpreted the significance of certain animals. The museum is built as though it is an underground cave, and it houses a little village inside that displays a concept of what the city would have looked like centuries ago.

The Palace had multiple segments, the armory, the rooms, the history of the structure, and lastly a collection of statues. The armory was filled with glorious apparel and items of royalty; what stood out to me besides the crowns and lavish cloths were the scepters and large keys that were part of the sets, I never knew that was a real part of royalty. The rooms were incredible to say the least, the most pronounced room was this hallway with statues at the ceiling corners, but the entire exhibit held sumptuous decorated rooms that I thought only existed in France. The history segment was nice too, but it was pretty dark in terms of lighting, but it was interesting to learn about how the structure had been continuously growing throughout the ages. The Statue segment was fun, especially since my peers strongly encouraged me to pose with each one.

The Paradox Museum was essentially an unadulterated fun experience, something everyone can enjoy and felt more like a theme park filled with exhibits consisting of illusory phenomena, overall being very engaging, interactive, and encouraging to take pictures. My favorite illusion was this large spinning black and white polka dot tube you walk through, which was unexpectedly difficult to accomplish due to the paradoxical effect it has on the mind; it also reminded me of the scene of when David walk through the bridge in 2001 A Space Odyssey.

One challenge that impacted my research work was an error I received on my cloud based IDE I am working on, in which the IDE would be stuck in an infinite load trying to reestablish what I had written. My supervisor, Sabina, said that this situation had occurred to her once as well and the only way to fix it was to tell the PI, Dr. Daub, that this has happened; but, to extend the problem, the PI was on vacation so I would have to email him and wait for him to read it, which took a week. Within that time, I decided to try to set up a local environment, so I installed Linux, R, all the necessary packages and programs necessary to run everything, and with all my effort, my local environment ended up being unsuccessful because my system couldn’t complete certain execution because it lacked the necessary RAM to do so. Overall, after that, I decided to spend my time just reading documentation and learning more about R. These kinds of situations are bound to happen, and the circumstances definitely were not in my favor, but even when something like this ever happens, there is always something else to spend your time on that is related to your project.

Biking has been a lot of fun too :)

Trenton

Hey guys! It's been a few weeks. Since my last post, I have explored new areas of Sweden, increased my intake of jam and waffles, and found new ways of messing up my sleep schedule. I visited a few museums these past few weekends, like the Vasa Museum and the Royal Palace. I also visited Sandhamn, a lovely island east of Stockholm. Finally, as an avid fan of escape rooms, I forced everyone in the program to attempt an escape room in Stockholm, and we beat the previous escape time record for that month by 6 minutes!

This past weekend, I took a trip to Copenhagen, Denmark! The city was aesthetically pleasing. I went to a couple of museums and a nice amusement park called the Trivoli Gardens. In addition, there is this lovely bridge that connects Sweden to Denmark that I took an overnight train on to get to the city. Unfortunately, I slept away the opportunity to take a picture out the window while I was crossing it (twice). Apparently, there is also a Netflix series about it called The Bridge. I will definitely be watching it and maybe even finishing a series for once.

For the past few weeks, I have been working on creating a data pipeline that takes the genomics data collected from the lab and gets back data files detailing the alterations in the tumor cells' DNA. I have recently started running the data through the pipeline and analyzing the collected data. Surprisingly, the creation of the data pipeline came with many problems. Most notably, I struggled to figure out the best ways to distribute the various processes efficiently and adequately. Many of the programs I run in my pipeline used up a certain amount of computation power and couldn't be run together with other programs. It took a lot of time to figure out a decent way of running the programs in conjunction. I learned quite a bit about multithreading, heap storage, and swap space between the times I banged my head on my keyboard. However, most importantly, I learned the importance of asking for help. I reached out to other researchers inside the building my lab was in who were working on similar things to me. They helped me figure out my problem and how to fix it. In the future, I'll try to be more transparent to people about the issues I am facing instead of pretending that everything is going perfectly fine.

Occam

Hej hej, it's been an exciting few weeks since my last post. In my lab, I have been able to test a few of the drugs I identified as potential lung cancer suppressors and have found that they do indeed prevent cancer growth as predicted and even suppress the correct gene targets with varying levels of effectiveness! I have also been working on creating final figures and writing a paper for publishing what I've been working on. There have, however, been a few roadblocks along the way. One such unfortunate event was when I was requesting the drugs to order for the validation of my experiment, and I asked the researcher running my experiment if they could look at what was available from my list and pick the top few. I unfortunately didn't realize until it was too late that I hadn't communicated properly, and they had tried to order the entire list, so the order got shut down leaving only the three drugs available in the lab for testing. Despite this setback, I have learned some important skills like how to pivot a project based on resource limitations and how to work with others to get to the root of miscommunications and find useful directions going forward. To avoid these types of problems in the future, I hope to make sure I am communicating more clearly and follow up on my communications to make sure that whoever I'm communicating with understands what I'm saying in the way I intend.

Outside of work, some of my favorite things I've done since my last post include exploring and relaxing in Sandhamn island, hiking around some of the wooded areas on the island of Lidingö, and visiting the luxurious Drottningholm Palace. This past weekend, however, I traveled to London which was a great adventure. I visited many of the obligatory tourist spots including Buckingham Palace, Hyde Park, Westminster Abbey, Big Ben, the London Eye, Tower Bridge, etc. and learned a lot in the detailed museums in the area. I also enjoyed seeing the nightlife there, eating some hearty meals, and being able to take any of the large selection of efficient transportation options they had to get back to where I was staying for the night.

Claire

It's crazy to think that we only have three weeks left in Stockholm! Since my last blog post, I have continued to explore Stockholm and the surrounding area. Some fun things I've done around Stockholm include going to a John Legend concert, doing an escape room with the other interns, going bouldering, and visiting Drottningholm palace where the royal family currently lives. I was also able to travel to Iceland a few weekends ago when my family was visiting, which was amazing. It was pretty rainy and cold, but the natural landscape was still incredibly beautiful. We got to see waterfalls, walk between tectonic plates, and swim in the blue lagoon. I also really enjoyed taking a weekend day trip to Sandhamn, an island in the archipelago where many Swedish people have summer cottages. We took a boat there and then walked around the island, looked at some cute shops, and hung out on the beach.

I have also been enjoying working in the lab, although there have also been some frustrating moments. One thing that has been frustrating is that the experimental data does not follow the same trend as the predicted data. Although I wish the data showed the dramatic trend that was predicted, I've had to accept that science will (often) not give you the results you want or expect. In the unexpected results, however, there are some interesting (albeit less dramatic trends) that I have been able to explore, which have helped me to stay in engaged and excited about my project, despite the originally disappointing results.

Molly

Hej! The last few weeks have been a whirlwind inside and outside the lab. I spent my time outside the lab with my family and saw some of Stockholm’s most popular attractions such as the Vasa Museum, Nordic Museum, and Nobel Prize Museum. The Vasa museum was my favorite, seeing the Vasa still in one piece today after being underwater for hundreds of years was really amazing. I also took a boat tour of the archipelago and learned some more about Swedish history. The boat tour is a great way to see many of Stockholm’s islands and it was very scenic. I also tried some new restaurants and found an Italian place that was very good. This past weekend, I traveled to Ireland to visit my grandmother. Ireland was beautiful and I enjoyed catching up with my grandmother and some cousins.

For the last few weeks in the lab, I worked on researching the best methods to use on my data and wrote scripts to analyze the data. I went to lab meetings and worked with three other colleagues to brainstorm the best ways to work with the data we have. Throughout this process, I redefined my project to a smaller scale due to time constraints. One of the main challenges with this project is the amount of data that I am working with. For this project, I had planned to analyze tissue samples collected from two breast cancer patients, which are 9 different tissue samples. My advisor and I talked and decided that I would focus on one patient for the final steps, then if time permits I will finish the analysis of the second patient. The goal of the project is to determine if collecting healthy tissue and breast cancer tissue is beneficial, or if only collecting breast cancer tissue is sufficient. For this, I have to analyze the healthy tissue, the cancer tissue, and the “normal” part of the breast cancer tissue. A problem I am facing is that not all breast cancer tissue samples have high-quality reads with a mixture of both cancerous and “normal” tissue. At this point in the project, there is nothing that can be done, as the samples were taken and sequenced a while ago. I am working with the samples I have, and will still be able to finish the project, but not having similar quality across the samples has been a challenge. From this, I have learned that no experiments go perfectly, and part of doing science is working with the data how it is. You can not expect all of the data to be high quality and easy to read. For this project, I treated all samples the same, which worked great until I had to choose one patient to work with and determine which samples had the best mix of both “normal” and cancerous tissue. I had to ensure there was “normal” tissue, as comparing the “normal” tissue to healthy tissue was a main part of the project. It would not be beneficial to analyze a sample without “normal” tissue. In the future, I would take more time to determine which samples have the highest quality and features that would be most useful to my project.

Sean

Hej! I can’t believe we’ve been in Stockholm for two months now, and I’m not ready for to go home in two weeks. For the last few weeks, I’ve been working on analyzing our skeletal muscle proteomics data and comparing it to several external datasets. After a few complications with some of the data, I’ve completed my directional analysis on the regulation of key proteins shared among the datasets. I’ve also been using my time in lab to prepare my presentation for the end of the summer, along with an abstract submission of the study for a poster presentation I hope to share my findings at. Outside of lab, I’ve been trying to cross off as many Stockholm stops off my list as possible before we head home. In the past few weeks, I’ve explored the Nobel Prize Museum in Old Town, the island of Sandhamn, the photography museum, a farmers’ market, the Modern Museum, the waters of Haga Park on a paddle board, and as many bakeries as possible. I was also lucky enough to take a weekend trip to Sorrento, Italy where I spent time with my mom and sister exploring the area and having some amazing pizza, pasta, and wine.

Although everyone in my lab has been extremely supportive while I’ve been working on my project, I have run into a few setbacks involving both the data and interpreting my results. One major issue I’ve been having is when the data doesn’t provide me with strong or clear results, and I am unable to understand if there was an issue in my process or if they shouldn’t be any strong correlations between the datasets. Although I want my data to follow a clear and strong trend, I have come to learn, more through this experience than hearing about it before, that not all data will be “pretty”. While some data may provide strong and clear results, I’ve learned that many times, even after all the work you put in, some results don’t show you anything. However, I’ve also learned that these cases are still important in science, and have taught me to review my work closely and reevaluate my thinking to find other perspectives and paths to answering my questions.

Ismael

These past three weeks since my last report have possibly been the worst. I got sick. It started with a sore throat, which I probably caught since I would go to the gym at 10 P.M. to Friskis Solna via bike, and would ride back home at 11:30 P.M.. The first couple of times I did this, it was completely fine in terms of the temperature; but, towards the last days before I got sick, the change of temperature was definitely noticeable. The morning I woke up with the cold, I didn’t think much of it, but as I layed in bed I could feel the symptoms rising, and while I really didn’t want to miss work, especially since Dr. Daub had just returned from his Summer vacation and we were going to have a meeting that day, so I decided to message Rasha, a great peer I was working with in the office, that I am feeling sick, and I sent that with a lot of uncertainty; but, after not having received a response in an hour, I rose from my bed, and I went to the train; and quite possibly the worst thing could have happened, happened.. I encountered someone who coughed out openly as soon as the door of the train opened. It was at this point that I knew that my condition was definitely not going to get better. I reached Alvsjo on the pink line, and finally received a response from Rasha, which said it was okay that I stay home, so I decided to head back home. In which case, I immediately lied in bed, and went back to sleep in a condition which was worse than when I had awakened.

My symptoms would continue to rise for about five days, and gradually diminish from then. The unfortunate reality is that my sickness would persist up to essentially the final week of my internship. Sickness is an unfortunate reality of life; nobody ever asks to become sick. I remember having an interesting conversation when a dear friend of mine, Isaiah, in which he also caught a cold, and I told him he should stay home, tucked in blankets and enjoying a nice hot coffee or chocolate milk, because something as miniscule as a cold can rupture into something much more serious and deadly, as the cold makes one much more susceptible to catching secondary diseases (please don’t quote me on this, this is a rumor I heard). I would end up spending 10 days, roughly 14% of my time in Sweden, inside my room sick. I would not step anywhere besides the grocery store during that time. It felt like forever.

I was also planning on visiting Berlin and London, but I had to cancel all my flights.

Before I got sick, the one week which is part of my three week journal entry, I got to see the Pixies, the first band I ever got to see perform in my life, which was 13 years ago; seeing them in Grona Lund was fun. I also got to visit the Modern Art Museum, which I adored; and so far, it has been my favorite museum I have visited, especially because of how interesting and engaging a lot of the exhibits were. I also got to hangout with everybody one more time at a little pub which had a pool table, darts, and pinball machines, which was a lot of fun.

Also within that week, Sabina guided me and provided some direction in my assignment. I manage to accomplish the majority of it except the analysis of the wolf genome to the human genome, or even the wolf genome, i.e. gene ontology analysis.

Trenton

Hey guys! We are close to the end of our journey in Sweden, with one week left. With only so much time left, at the beginning of week 7, I started running my data pipeline on all 62 tumor data files that my lab had developed, using one of my lab's workstation computers. I found it surprisingly tricky to ensure that all processes ran adequately in parallel to one another. Specific tasks took a lot of memory, and other tasks could not be run together simultaneously without failing.

However, the most challenging aspect of this research has been time management. Properly managing my time has been one thing I have not been able to solve this summer. It is hard to know how long something will take in advance, and I spent too much time on certain ideas that went nowhere. For example, I wasn't fully aware of how much time it would take to run the various algorithms on all the data files. As a result, I waited too long to start running my data pipeline on my lab's data. In the future, I should plan and start things earlier than I might think I need to.

Currently, about half of the data has been processed. However, I have analyzed and visualized the data using R and have enough data to present my findings for the last week of the program. My data and analysis give an overview of the structural variants detected in the genome of primary lung cancer and developed brain metastases in the cancer patients we collected the data from.

Other than research, I visited a few more places in these three weeks. I went to a skate park, a Gorillaz concert, and a photography museum, among other things. With a few weeks left, I wanted to visit another European country before returning to America. So this weekend I went to London for two days. I visited the Buckingham Palace and rode on the London Eye. This visit was probably my favorite trip of the summer. The weather was excellent, and the people I met were really friendly.

Occam

This summer has been an incredible experience. I learned so much, tried so much, failed so much, felt so much, and experienced so much that I hadn't before, so it's difficult to describe. But I'll try.

During work, I learned significantly more about how laboratory work functions than I had at any of my previous jobs. Learning how the flow of information can go from one researcher to another and from another to a principal investigator has been really interesting. Also, seeing how different large projects are divided in to tangible tasks that individual people can work on has helped me think about how I manage workflows in my personal life. From talking to others in my lab, I started better understanding the steps involved in becoming a researcher from graduate school to post doctoral research to running a whole lab. The biggest process I learned about during this summer, however, was the process of writing a scientific paper. I had written a few papers in school that were similar in format to scientific papers, but that was the extent of my knowledge before. Throughout this summer, I have worked on refining my figures to a publishable state, looking at journal guidelines for specific information I need to consider and include, and revising my writing first from my own critiques and then from my supervisors' critiques. And then revising some more. I know I still have a lot to learn about the process and hope to learn some of it these next few months.

Personally, there were so many new and wonderful things that I experienced here in Stockholm that it's a bit bittersweet knowing it's coming to an end. Some of my favorite things here include the large number of adorable dogs that seem to be everywhere, the late nights that are still in sunlight, the range of weather from the sunny days ideal for swimming to the cozy rainy days that dampen the sound, and the effortless efficiency of the word "tack". My favorite part, however, has been being able to roam freely around the abundant nature areas that are here. They offer beautiful views of forests, lakes, and seas and provide a place of escape and privacy that can be vary difficult to find in the cities of the US.

One of the hardest parts of the summer, however, was being in a lab where everyone was speaking a language I didn't know half the time. Sometimes it was the lunches that drifted into Mandarin, and other times it was the meetings that drifted into Turkish (surprisingly no one in the lab spoke Swedish). I often felt awkward not knowing what was going on, but eventually learned to enjoy it and observe the various timbres of these different unintelligible languages like listening to a unique form of music.

Overall, I can safely say this experience has been the most fulfilling part of my life so far, and it has encouraged me to get out of my comfort zone and try similar things in the future. At this point, all I can say to this beautiful country and the people who made this experience possible and wonderful is: tack så mycket och hejdå.

Claire

It’s weird writing this final blog post. In some ways, it feels like the summer has flown by, and in other ways, it seems like we’ve been here forever. Although I am excited to go home, I will also miss the city and all the people I met here. One reason I applied for this program was because I wanted to challenge myself and get out of my comfort zone. And it was a challenge at times. There were so many new things to adjust to. A new culture. A new city. Living on my own far away from friends and family. A full time job. A new lab and coworkers. But adjusting to all these new things also served as an amazing catalyst for personal and professional growth.

Professionally, I think my biggest take away from this experience is that I really enjoy bioinformatic research. Even though working full time in a new environment was a bit of an adjustment, I genuinely loved going in to lab each day. I loved writing and debugging code, learning to use different bioinformatics software, and thinking of new analyses or directions for my project. There were definitely things I didn’t enjoy (i.e. commenting my code) and days where it was more difficult to motivate, but overall, I really enjoyed the research experience, and am really excited to pursue bioinformatics in the future.

Personally, this experience has also been very impactful. My favorite part of Stockholm has definitely been exploring the outdoors. I really like running, and exploring Stockholm by running has been an amazing way to get to know the city. I also really enjoyed doing other outdoor activities like kayaking, stand-up paddle boarding, going to the “beach,” and hiking. Another favorite part of Stockholm was the coffee. Not only did the lab have free coffee, there were also many cute cafes with delicious lattes that I visited. One of the hardest parts of this experience was being so far away from my family and friends. This did, however, allow me to form some amazing connections and memories with the other interns in the program.

Although this experience had its challenges, it was also amazing, and I am so grateful for this summer!

Molly

The last ten weeks have taught me a lot both professionally and personally. Before this experience, I had never worked in a lab setting. Learning about the way lab groups run and are organized was very interesting. My lab group had weekly meetings to inform everyone about their status in the project and we also did journal clubs. The journal clubs were a way to learn about an interesting topic and enhance one’s presentation skills. The small group size made presenting less stressful which in turn allowed me to gain more confidence with public speaking and answering technical questions. I also learned how to work as a team in a professional environment, this improved my communication skills and highlighted the importance of teamwork. The research aspect of the project was challenging as there were many unexpected challenges. Throughout the ten weeks, I learned that doing research takes a long time and is not a linear process. There are many options one may try before settling on a method or other choice. Other challenges included data taking a long time to process, systems crashing, and having an error that takes a while to fix. With the help of my team, I learned how to overcome these challenges and finish my project. One of the main lessons I learned is that you can not predict the timeline or outcome of data analysis. The lab experience was enlightening and ??

Outside of the lab, I explored Stockholm and became friends with the other members of the cohort. During the first couple of weeks living in Stockholm, I experienced some culture shock but grew to love Stockholm. One of my favorite things about Stockholm is the public transportation and architecture. The public transportation system is easy to navigate, quiet, and clean. This is quite different than what I am used to in the states. The architecture here is amazing, there are many buildings with intricate designs that make the city more beautiful. Through the architecture, you can see the history and culture of Sweden. Stockholm is surrounded by water which makes the city eye-catching as well as a great place to be in the summer, I was able to go swimming and kayaking frequently.

Moving to a new country for ten weeks was both exciting and challenging. Immersing myself in a new culture was fun but came with some challenges. Some of the challenges I faced were not knowing Swedish and homesickness. Many people in Sweden speak English but there were times when I met someone who did not and then we would find a way to communicate with our hands. Also, many of the menus and signs are in Swedish which made them more difficult to understand, this was especially true in the grocery store. The first couple of trips to the grocery store took me a long time because I had to translate most of the items to ensure I was not buying the wrong thing. As the summer progressed I started to miss food and air conditioning from home. Although I did eat many delicious foods here in Stockholm, I missed some restaurants and home-cooked meals from home(syrup is not used here). All in all these last ten weeks were amazing and I can confidently say that I grew as a person and am better for it. In the future, I hope to be able to travel to new places and continue to learn about different cultures.

Sean

Hej! I can’t believe it’s been 10 weeks since we started this program and now it’s time to head home. This summer has been an incredible experience full of exploring both life throughout Stockholm and life inside a research lab. On a professional level, I learned so much about what it takes to work in a research lab, what dynamics exist in the lab setting, and how I fit within the lab based on my role, interests, and personality as a researcher. The most surface-level thing I learned throughout my time in the lab this summer was proteomic analysis, specifically how to do it using R and other tools that were introduced to me (many for the first time). On a deeper level, I learned about the multitude of processes involved in research. From project planning all the way to publication and presentation, I was able to get an up close and personal look at what each step was like. In addition, I was able to able to learn how each member of a lab works together (both in and out of the lab), by building a strong and supportive community that strives on helping each other grow and change as researchers, because at the end of the day nobody knows everything. At the end of the day, I learned that, although my specific interests lie in other applications, I am passionate about bioinformatics, and I feel strongly about my future endeavors in the field thanks to my time this summer.

Outside of the lab, I can’t put into words how amazing it was to explore the city of Stockholm, immerse myself in a new culture, and meet so many amazing people. Due to the healthy work-life balance I came across in my Swedish research lab, I was free to explore the area as much as I wanted, while still growing as a researcher. My favorite memories from this summer have to be exploring the Archipelago with both my lab and my cohort, going to every café I could find (and never experiencing a bad one), visiting as many museums as possible (the ABBA museum is definitely my favorite), and experiencing a real Swedish Midsommar celebration. While the nightlife was minimal due to the sun being in the sky for about 21 hours a day, going out to explore Stockholm’s nightlife was a great experience and allowed me to meet more people and bond with the cohort. And although the only Swedish phrase I picked up was “Kan jag klappa din hund?” I know I’ll use it everywhere I go. While the summer was full of amazing and exciting experiences, the most challenging part of living abroad for the summer was keeping in touch with everyone back home and maintaining relationships while also trying to go out exploring and experiencing new things. Therefore, whenever I wasn’t in the lab, exploring Stockholm, or sleeping, I was making sure to check in with both my family and friends back home, and check in with myself to make sure I was ok while living on my own in a new place.

Overall, this summer has been one of the most amazing experiences of my life, and while I know I did a lot during my time in Stockholm, I am dying to go back and explore more of Sweden, both in and out of a lab. I can now say Stockholm is my new home away from home. Tack så mycket.

Ismael

Getting the opportunity to visit Stockholm, Sweden, was such a wonderful experience. I left one life only to have created another one here. I go to experience so many beautiful things here, the culture, the nature, and so much more. I am going to miss all the friends I made here, all the places I visited, and practically everything; with all the time I spent here, I feel like I became part of Sweden.

In my last week, I tried to do everything I wanted to do in Sweden. I managed to visit the Natural History Museum, the Nobel Prize Museum, and the National Museum; I got to bike to work and back; and, I gave my presentation for the work I did at the Daub Lab.

The Natural History Museum was lovely. It felt like a compromise between a zoo and a collection, which I think is better than outright housing a zoo, since running a zoo is expensive and requires a lot of space, but this museum was capable of enriching the viewer with a lot of information regarding history, animals, and the process that scientists go through in terms of documentation. My favorite exhibit was the polar one, in which it held information about natural life in the poles. The models of the animals were really good, especially the detail in the environments. The best part of it all were the 4 gigantic whale skeletons they had, they were remarkable, to say the least.

The Nobel Prize Museum was short, small, and very informative. I expected it to have more props, instead there was a lot of information about the history and previous prize winners. This was also the first museum to have cool stuff at the gift store.

The last museum I got to visit was the National Museum, an incredible museum to end my museum adventure with. It is composed of a large selection of incredible works of arts from Swedish people, spanning a large portion of time. I also got to visit a temporary exhibit here, Women Sculptures of Sweden were the main subject, which explored their history, influence, and works in great detail. It was the best place to end my museums adventures, as it was best one among them all.

I got to bike to all the final destinations I wanted to on my bike. I even got to bike to work one day; which I had been wanting to since beginning, as while on the bus trip, I could see all the bike lanes that span the country side that also had lamps to light all the paths throughout the area, it looked so awesome; so, I did it, and it was as much fun as I had envisioned, I can only wish I would have biked to work more. I eventually had to say goodbye to my dear bike. I really wanted to take it back with me, but I lacked the proper packaging to accomplish the task, so I ended up leaving the bike with the person who repaired my bike and made it possible for me to have such a wonderful time.

My presentation was given on Tuesday morning. I was incredibly nervous. There were going to be professionals, peers, and my fellow colleagues all watching. All of my dear friends gave some of the best speeches I had ever seen. My own presentation was okay. After having been sick for so long, I barely had that much time to review most of my work, but I made the most of the little time I had, and I think I gave the best speech I could have made.

Overall, my time in Sweden has been dreamlike, and I wish I didn't have to leave it behind. Its a place I want to revisit in the future, and I can't wait for the future.

Trenton

Hey everyone! This is my final blog post. This trip has become one of the most memorable experiences in my life. I truly am grateful that I had the chance to do research abroad in the beautiful city of Stockholm. I've met many interesting people from different parts of the world and have learned a ton.

At the beginning of the summer, I was leaning towards going to graduate school sometime after graduating. However, I wasn't sure what I wanted to specialize in and was planning to enter the industry first. However, after spending time conducting research in a university lab with master's and Ph.D. students, I am now much more confident in entering a Ph.D. program right after graduating, and I plan to.

Outside of gaining a clearer idea of what I want to do, I developed crucial job skills. For example, I had a lot of responsibility for my project and had to set clear deadlines to get things done on time for my final presentation. In addition, as much as I hate searching for related research papers, I had to do a lot of research for my research project. As a result, I am now much better at skimming and reading research papers in-depth. Also, with this program being abroad, I interacted and learned a great deal from people within the lab from different cultures.

Lastly, from a personal level, I just really loved being away from home over the summer. I love my family, but years of virtual internships and school will make you want to branch out a bit, and this program branched me out pretty far. I loved being in Europe. I tried my best to visit as many cities as possible and enjoyed every second of it. Stockholm, in particular, is a lovely area with one of the best science fiction bookstores I have seen with nice Harry Potter and Star Wars-themed sections. I bought a Swedish board game from the science fiction bookstore in Gamla Stan. I can't read any of it, but as a collector, it was worth it.