The first cohort of NSF-IRES students arrived in San Diego on June 7th for the pre-departure symposium. Throughout this week, Taylor, Zubair, Eleanor, David, Nick and Lauren prepared for their summer research projects in Sweden. During the first day of the symposium, I went over our travel logistics, program expectations, introduced the students to Bioconductor (a software project used for bioinformatics analyses), and we had a guest speaker from the international center at USD to prepare the students for travel to Sweden. The students then spent the afternoon working on coding exercises in the R programming language. The first day of the symposium closed with dinner and a beach fire in La Jolla Shores. On the second day, I went over how to create a scientific poster for research conferences. Following this, the IRES students created and presented posters based on a paper from their soon-to-be host labs. During the afternoon, the students learned a bit about RNAseq analysis and then practiced analyzing RNAseq data using R. Continuing on with building scientific communication skills, the morning of the third day focused on perfecting their elevator pitches. Specifically, students researched their host lab websites and gave the audience two different elevator pitches - one aimed at a scientific audience and one aimed at the general public. After lunch, students learned about how to prepare presentations for lab meetings and then they practiced presenting scientific figures to the other students. Similar to the first two days, our third day closed with students working on bioinformatics coding exercises. Our final day of the symposium was primarily focused on graduate school. Specifically, we discussed why it would be beneficial to go to graduate school, how to apply to graduate school and graduate research fellowships. We closed out the pre-departure symposium with a career panel focusing on different careers that are possible with a graduate degree. Specifically, we heard from Dr. Anita Burgos, senior health policy advisor in the U.S. House of Representatives, Dr. Anna Blakney, assistant professor at the University of British Columbia, and Margie Mathewson, Vice President of Business Operations at Ossium Health. Drs. Burgos, Blakney and Mathewson all shared their experiences in graduate school and shed some light on their careers.

On June 11th, we all headed to Stockholm together and the students started working in their host labs on Monday, June 14th.

Nick

Hej! First week done in Stockholm. Following my Saturday night arrival, I have started work. Given that my lab is about 40 minutes away from the dorms, I learned how to navigate the metro, Tunnelbana or Tbana for short, and bus systems. So far, I have started contributing to the lab’s insulin response project by analyzing SNPs inside of previously identified enhancers. As Stockholm is so far north, the sun does not set until 10:00pm (22:00), so there is plenty of time to go out and explore the city after work. On Tuesday evening, the other IRES students and myself went out to dinner in Gamla Stan, which is Stockholm’s “old town” where the city was founded in 1252. As a California native, it is an amazing experience to walk the streets and see buildings that were built in the 17th and 18th centuries.

One cultural difference that I have noticed in my first week that is very different than in the U.S. is the attitude towards the workday lunchtime. While in the U.S., one may choose to eat at their desk or possibly take a working lunch, this does not happen in Sweden. Lunchtime is an opportunity to step aways from the day’s work and enjoy some social time with peers and colleagues. Even after the actual eating is done, it is common to spend some additional time on conversation. This was a pleasant surprise, especially as a new person in the lab. This lunch hour allowed me to meet and interact with some of the other people in the lab, in a social setting and to start to feel like one of the group even if just a temporary member.

Lauren

This week I was fortunate to be able to attend the Campus Solna SciLifeLab Science talks from Monday until Wednesday. In these talks different people from across different labs and departments in the the Science for Life Laboratory presented on the projects they were currently working on and the findings from them. It is really cool to be a part of Dr. Claudia’s Kutter’s lab because it’s composed of international students from Greece, Spain, Germany, and China. We met with our PI and a PhD student who will be overseeing the project and guiding me throughout the project. I spent the rest of my time this week in the lab reading scientific literature to help provide me with a full picture of the background of the project.

We haven’t travelled outside of Stockholm yet, but from what we’ve seen so far, it’s really interesting to see the balance between large city vibes and nature, scenic environment. There were a bunch of people having picnics and hanging out with their friends and families in the many parks in the city. In San Diego, I feel like we neglect our local parks and don’t normalize having lunch or picnics with our friends and coworkers as much as they do out here.

Taylor

I have been in Stockholm for almost two weeks now and I have been enjoying every minute of it. I work in the new hospital by the Karolinska Institute. My lab team has been the most welcoming and I definitely enjoy our daily Fika breaks in the lunchroom. Thus far, I have been practicing my coding skills with sample data sets and observing some wet-lab experiments. I will be presenting in a lab meeting next week so I have been preparing for that as well. My project is centered around abdominal aortic aneurysms so I will be analyzing data from patient samples with bioinformatics this summer.

Sweden is a beautiful country with lots of nature, cool architecture, and food. My daily walk to work is filled with pretty flowers and trees. The apartment buildings downtown is a mix of modern and classic architecture. Interestingly enough, I have taken quite a liking to the pizza here. I have had it about three times already. The Thai food is also pretty great. Swedish people are very friendly once you get to know them. One major cultural difference I have seen is people’s transportation of choice. There are so many bikers, walkers, people who ride scooters, and subway riders here. Basically everything except a car. Sweden has a lot more pedestrian-friendly infrastructure than we do in the States. For that, I am jealous. I enjoy walking, biking, and riding the subway so this city is right up my alley. I also learned about the Swedish phrase “Lagom” which means “just the right amount”. I like this phrase because it reminds me to make sure there is a balance in my life. To do everything in moderation and to not stress over small things that won’t matter by tomorrow. To make sure I have a productive day at work but be sure to sit back and take a break when wanted.

Moving forward, I look forward to celebrating Midsommar this weekend and getting to know the Swedish culture a bit more. I would like to travel outside the city but that takes a bit more planning. I heard there is a nice amusement park in Gothenburg so I might try to make it over there one day. I have time :)

Vi ses!

Zubair

During my first two weeks of the program, I was able to explore certain parts of Sweden, and learn more about the people in my labs. Some of the highlights and my favorite places included Gamla Stan(Old Town), Skeppsholmen, and Skinnarviksberget(the highest point in central Stockholm). Getting used to the public transport has been a bit of a challenge, but I’m hoping it’ll get better over time. The food here is exquisite and delectable, and I’ve thoroughly enjoyed almost every dish I’ve eaten. Some of these foods include smoked salmon with dil potatoes, creamy curries, spicy deer, and other Swedish delicacies. This upcoming weekend is Midsommar, a historic Swedish festival incorporating picnics, large gatherings and other culturally specific events. In the future I hope to learn some Swedish, so I’ll be able eavesdrop on conversations ;)

My project here is focusing on reversing/slowing the processes of conditions such as aging, mitochondrial myopathy and type 2 diabetes with exercise proteomics data. Proteomic data from these conditions will be compared to a baseline proteomics study to identify what types of training can possibly be used to reverse the aging process or damages caused by the diseases at the proteomic level. As of now, I have started refining and modifying a limma pipeline in R to prepare myself for future bioinformatics analysis.

I’ve noticed that Swedes don’t have paper seat covers in the bathroom, and they also have very fancy stalls for handicapped individuals. I was a little surprised, but then again it is always possible to just use toilet paper as a lining.

DAVID

The first few weeks here in Stockholm have been amazing. The many islands around Stockholm make it the perfect place to go out for a late walk, as it never gets too dark and you can see the beautiful architecture everywhere you go. So far, I’ve visited Gamla Stan, Skeppsholmen, Skinnarviksberget and I plan to visit many more since public transportation is very accessible. Currently, I am doing research at the ScilifeLab on uncovering key adaptations for physiology remodeling in mammals. As of now, I am working with a software named Evolver, which simulates the evolution of the nucleotide sequence of a whole genome. It will provide us with the long-term effects of mutation and selection over an entire species.

One cultural difference that stood out in Sweden, is going to college. In the US, that is considered the top priority in high school and usually, it is a must for everyone. Everything is built to prepare you for college and they expect you to start college as soon as you finish high school. Here in Sweden, it is not as common to go to college once you are done with high school. Many take a gap year or a few, depending on their situation. During this break, they work to save money or explore their interest before they make a final decision in applying to their desired program. I was surprised when I found out about this because I thought college had the same priority around the world. I hope to continue to learn more about Sweden throughout my stay here.

Eleanor

I've just finished my 3rd week at the SciLife Lab in Stockholm and I now feel like I've got my feet under me. This week I graduated from numerous coding tutorials and practice exercises and began new work on my specific project. The lab that I am working in is interested in looking at the 3D genome architecture within the nucleus. Basically they want to know where certain chromosomes are in relation to each other as well as to the periphery of the nucleus. They are also curious as to where certain epigenetic modifications to the genome are located within the nucleus. They are currently using mice genomic DNA to create these maps. My job this past week has been to search databases that have files that hold the DNA sequences of known functional elements (such as these epigenetic factors) and compile them into a list which will be used later in linear regression models to observe the differences between stem cells that have undergone different treatments. I've also started to perform some image analysis with immunofluorescence images that have been collected from a new stem cell treatment group. I've made lots of plots using R!

Outside of work I've explored areas of Stockholm by foot and by metro. I even visited Skogskyrkogården (The Woodland Cemetery) which is a UNESCO World Heritage Site. I also keep finding myself going back to Gamla Stan. Most recently I returned with Lauren and Taylor where we spent Midsommar Eve. We went to an amazing restaurant called The Hairy Pig that has amazing sausage! We then wandered around for a while, walking past the Royal Palace and eventually making our way to a little ice cream shop. In the coming weeks I hope to visit some of the museums that are located all over Stockholm. At the top of my list are the Vasa Museum, the ABBA Museum, and the National Museum.

As Taylor mentioned, Stockholm has a very pedestrian friendly layout and you can see how the city was really built around public transportation like metro stations. However, I have been surprised to see mopeds and other motorized vehicles, other than electric bikes and scooters, take up space on the sidewalks. Also, Swedes have a very advanced "helmet" (though you can't really call it a helmet since it doesn't go on your head). While walking to work I constantly see bikers with what looks like a cross between a neck brace and neck travel pillow around their necks. Apparently it's called Hövding and it is the safest head protection for cyclists in the world. You wear it around your neck as a collar and it monitors the movements of your head. If you are in an accident, an airbag inflates and protects your head!

Nick

Hej! Since my last post, I have continued work in the lab, fully settling into a 40-hour work week. I am working on a project to automate the extraction of data for analysis of genomic variants based on CAGE data. Before beginning the analysis, we had to build a program capable of analyzing the CAGE data utilizing a mix of SAMtools and Python. As with starting any new project, they are bound to be challenges. One such challenge was initially conceptualizing a solution for a problem in a discipline I am not immediately familiar with. My degree is in Computer Science and while I have familiarity with bioinformatics concepts, actually putting this knowledge into practice is a new experience. However, working together in a team, I am able to accomplish more than I could alone. In my lab, I am working with another student from Portugal whose background is in genomics. It’s a great experience to work as a part of a multidisciplinary and multicultural team. Our differences complement each other as we need both my lab partner’s strength in biology/genomics and my strength in programming/computer science. We have also put our physical strengths to work with some indoor rock climbing. It was a nice opportunity to connect outside of the lab. Next week we will transition from developing the program/pipeline to actually putting it to work.

During the weekends when there is no work, there is still plenty to do! While Stockholm may not have the immediately recognizable sites such as London’s Big Ben or Paris’s Eiffel Tower, there is still a wealth of culture and icons inside of the city. One such icon I have visited so far is the Vasa Museum, home to the warship Vasa, which sank on its maiden voyage in Stockholm in 1628. Today it has been excavated from the seabed and holds the distinction of being the world’s best preserved 17th century ship, being over 95% original. Additionally, Stockholm is home to three UNESCO World Heritage sites and I have so far visited one: The Woodland Cemetery. Known as Skogskyrkogården to the locals, the cemetery earned its designation as a World Heritage Site for “its qualities as an early 20th century landscape and architectural design adapted to a cemetery.”(whc.unesco.org). Stockholm is a beautiful city.

Lauren

Over the last few weeks, I have worked on compiling information about mammals from different databases to compare and identify genes that allow mammals to hibernate. I have recently begun coding using R to create graphs and figures to assist us in interpreting the data collected. I don’t have a lot of experience coding in R, but I’m excited to get the opportunity to get hands-on experience and look forward to seeing my coding abilities at the end of this program. Once I make a little bit more progress with the graphs I will begin analyzing the results from the graphs and identifying interesting outliers to further investigate.

Additionally, during this week’s lab meeting, I was assigned the responsibility to ask hard, detailed specific questions to the group presenting an update on their research to ensure they’re prepared for similar questions in the future. I was pretty nervous about it, but I was able to ask a few questions that led to a large discussion. During a lunch that David and I had with the lab, we were discussing the different cultural norms in the places that we’ve lived and visited. We introduced the lab to Tajin, a mexican spice that can be put on a variety of different things. This upcoming week, David and I are planning on getting fruit and Tajin and sharing it with the lab!

Outside of the lab, a group of us went to this food place called Bun Meat Bun after work on Friday and had burgers and milkshakes. We then went to the Ice Bar in the Stockholm Hotel and got to have fun and dance in very cold temperatures. I’ve really enjoyed wandering the city and taking pictures of the interesting architecture and places that we’ve visited.

Zubair

In my lab over the past couple weeks, I have almost completed the pipeline that I will be using to compare exercise and aging related proteomics data. I have noticed some pretty interesting correlations and relationships between the differentially expressed proteins throughout different age groups and exercise training, but I have to understand what the functions of these proteins are. Once this pipeline is complete, it will be much easier to understand other relationships in human pathological conditions like Type 2 diabetes and Mitochondrial Myopathy. I have noticed that strength training seems to oppositely regulate many of the differentially expressed proteins in older age groups. In addition to working on my project, I have also began preparing my abstract for the 2021 BMES meeting.

One challenge that I have faced during my time here is creating efficient and reproducible code that can be applied in multiple scenarios. Performing simple data cleaning and data analysis is not too difficult, but understanding how to simplify that code, make it more efficient and use it for other situations is challenging. However, I believe that this comes with practice, and there is no better way to become a better programmer than to keep working on projects like these :D

Outside the lab, I was able to visit Sweden’s technology museum,( Tekniska Museet), visit the Mall of Scandinavia, and even go to an Ice Bar! I’ve met a ton of students that live in our student dormitory from all around the world, and since most of them are international, they all have a completely different story to tell. I’ve also been playing a ton of badminton and ping pong!

Taylor

Hej hej! A lot has happened since my last blog post. Once I got comfortable with my coding skills, I finally moved on to the main purpose of my summer project...analyzing real human abdominal aortic aneurysm data! First, I completed bulk RNA-Sequencing analysis meaning that I analyzed the gene expression of a tissue sample. Then, I began to analyze the AAA data through the lens of single cell RNA-Sequencing analysis. Single cell sequencing is an extension of bulk RNA sequencing. However, instead of looking at an entire tissue sample, I am looking at each individual cell type within that tissue sample. By doing this, I am able to determine if there is a difference in gene expression within the tissue sample amongst the different cell types. Without this step, it would be easy for researchers to overlook the cell to cell variability due to the assumption that all cells within a tissue sample are the same. With single cell sequencing, we are able to conclude that this is not always the case and that vital information can come from this type of analysis. So, with this step in my project, I have mainly been reading scientific articles and creating cluster plots. One major challenge I had while creating the cluster plots is that it can be quite difficult to determine the correct cell type. What you have to do is create “feature plots” which show you where in the cluster a certain gene is expressed. This expression can vary across the entire plot. The challenge comes when the gene is expressed in multiple areas of the body. So, oftentimes I will find a gene, look up to see which cell type it typically belongs to, and I will get a confusing answer. For instance, a gene can be a marker for liver cells, but the data set I am analyzing is for the aorta. I overcame this challenge by speaking with Wu, another bioinformatician in my lab. He gave me some good pointers and advice on how to overcome this problem because he too had this issue when analyzing the data. I basically simplified the analysis by decreasing the amount of clusters on my plot. This way, I have a broader view and a lot less noise when it comes to figuring out the cell type. This challenge will help me in the future because it helped me get comfortable with not knowing the answer and asking for help. It also helped increase my understanding of how to tackle larger problems that may come up. If it is too complicated in the beginning, stepping back and simplifying it will probably help.

Along with my progression in my summer project, I have not forgotten to have fun as well. Since my last post, I have sunbathed by the water, eaten more delicious Swedish pizza, shivered at an ice bar in central Stockholm, danced my way through the ABBA museum, and went back in time to see the viking way of life. My lab manager, Alex, hosted a small dinner party at her home. Her family treated our lab to a three course meal. It was a nice blend of traditional Swedish cuisine and classic American BBQ. Most significantly, I went on a weekend trip to Göteborg, Sweden. Göteborg is the second largest city in Sweden with lots of charm and things to do. The main difference I noticed is that since the city is not as big as Stockholm, everything seems to be within walking distance and life moves at a slower pace. There is no metro system, only trams which are a nice convenience but definitely not necessary to get around. While I was there, I went to Haga which is their version of an Old Town. There were many cute Fika cafes, antique shops, and cool boutiques. I also went to the art museum which had lots of cool paintings and sculptures. Of course, the food was amazing as well. Overall, I really enjoyed Göteborg for its charm and ease of getting around. I highly recommend it to anyone thinking about going.

David

Since my last post, I’ve continued working on with Evolver, trying to understand how the software works and how we can use it to simulate evolution. It will stimulate events within a chromosome like substitution, insertions, deletions, and copies. Evolver comes with a sample test that we can use, but it is not ideal. It’s a medium file size so it’s not efficient if we want to run multiple times on a local computer. Therefore I wrote scripts in Java to generate my own gene sequences and annotations that will make the process of simulation much faster. This will not only allow me to run it on my computer but I can scale it if I want to run it on a cluster. With each simulation, we can then use gene alignment tools to compare the sequences and see how each gene changed with time. Now that I have Evolver running, I am working on another software, EvolverSimControl. It can simulate multi-chromosome genome evolution on an arbitrary phylogeny. It will also be able to create summaries at each node of the simulation so we can extract fasta files and compare.

Outside of work, I’ve enjoyed what Stockholm has to offer. I visited the Royal Palace that was built in the 1600’s and saw the amazing art inside the palace. I also went to the Tekniska Museet which is the technology museum. It was fascinating to see the amazing exhibitions, especially “Moving to Mars” and “Hyper Human”. They really make you think about the potential humanity has to offer in the future. One fun activity that I wanted to do in Stockholm was go kayaking and I finally did it. We went kayaking around Vaxholm and it was an experience I won't forget.

Since starting my research work, one significant challenge that I have successfully overcome is getting Evolver to work with my scripts. Once I started to work with Evolver, I had to create my own scripts to customize file input size. But after weeks of writing code, I couldn’t make it run without errors. Once I fixed one error, another would appear. I had to spend more time than I initially planned, reading the manual over and over and talking to my PI trying to figure out why my scripts were not working. Fortunately, in the end, I got it to work properly and in the process, I understood how Evolver worked. By constantly looking over the software and trying to figure out why my code wasn’t working, I learned more about Evolver. In the end, I was able to navigate through evolver and understand what the output files were and how to use them. In the future, this experience might help me on a personal level and not feel like a failure when something does not go my way. There will always be a roadblock when working with new software but by constantly thinking and setting time aside, a solution will arise.

Eleanor

Hello again! It's crazy to think that I'm finishing week 6 out of 10 here in Sweden. Reflecting back on what I've done for the past few weeks in the lab I see moments of struggle and challenge that have (almost always) lead to feelings of accomplishment and satisfaction. Going into this program and internship I knew that I didn't have the strongest background in coding and that the job was going to consist of a lot of me learning as I go. It was going to be a lot of trying and failing, then trying again... and failing again and that's been really challenging at times. I've learned/ been reminded of two things during the times of frustration where I can't seem to get a line of code to work or I don't even know where to begin. The first is that google is your friend. There are so many resources that you have access to online that can help you understand the R package you are trying to use or what the error message that keeps popping up means. Often times there is someone else out there who has struggled with the same thing or very similar thing before you and they have posted a possible solution to the problem. The second thing, which ties in really well with the first, it that nobody expects everyone to know everything. There have been moments when I'm meeting with the Post-doc that I'm working with and he'll have to look up commands and error messages on google. I'm constantly grateful for my Post-doc's patience and availability to help me when I'm stuck and also to be reminded that people at all skill and knowledge levels sometimes still need to google how to do stuff sometimes.

I think what I've taken away from that experience is that we shouldn't be afraid or ashamed of using the resources that are available to us whether it's a professor, mentor, co-worker, or google. It's important to remember that there are things that even people at the top of their craft are still learning and might need to ask for help on. In addition, I think this experience has reminded me that we shouldn't judge or criticize people that ask for help, especially if they are less experienced than you.

These past few weeks I've been building scatter plots that measure the correlation between certain genetic and epigenetic features and the GPSeq score that we've calculated to see how well these features predict centrality (the chromosome's location along the radius of the nucleus). So far I've only looked at some of the epigenetic factors like histone modifications through acetylation or methylation. I've also looked at the correlation between GPSeq score and the presence of some transcription factors. We hypothesize that the features that we are looking at somehow influence the organization of DNA within the nucleus.

More recently my time has been spent preparing a presentation to present to my lab about the progress that I've made and the results that I've found. I've also been working on the abstract that I will be submitting to the Biomedical Engineering Society (BMES) for their annual meeting conference in the fall. The timing of the when the abstract is due and when I'm presenting to my lab is really nice because making the presentation has really helped me write the abstract and condense everything that I've done for the past 1.5 months down into something much shorter.

Outside of work I have continued to explore Stockholm. This past weekend I toured the one of the ten (yeah ten!) Royal Palaces. I went to the one actually called the Royal Palace in Gamla Stan. The amount of history that the building holds and shows through both the architecture and interior design is amazing. They also currently have an exhibit at the Royal Palace called 'Daisy. Crown Princess Margareta'. The exhibit is all about Crown Princess Margareta (who was known as Daisy to family and friends) and how she was a women ahead of her time and changed the image of the Royal Family. Her influence and impact can still be seen today. She was actively involved in many of the major social issues of her time including humanitarian initiatives for children's wellbeing, disability rights, and the survival of prisoners of war during WWI.

This past week I also took one of the ferries to Nacka Strand to visit God our Father on the Rainbow which is a famous sculpture made by American sculptor Marshall Fredericks but whose origins came from the sketches made by Swedish sculpture Carls Milles. The sculpture is a 12 meter high arch where half of the arch consists of an arch of water. Unfortunately when I went the fountain part of the sculpture wasn't on but it was magnificent nonetheless. I plan on visiting Millesgården Museum which is where Carls Milles lived with his wife and it has since been turned into a museum with a sculpture garden showcasing some of his work.

Nick

Hej! Since my last post, I have finished work on the python program. With the program complete, we were able to use it to interrogate our dataset for over 6000 identified enhancer SNPs. We focused on just the loci where the obese subcohort dominantly expressed the alternative allele, while the never-obese expressed the reference allele. From this set, we found some interesting loci including several “novel variants”, SNPs that lack any associated publications. Excited with our findings, we submitted an abstract to present at the Biomedical Engineering Society Annual Meeting in Orlando. Now, we are starting a new project, using the same cohort of individuals, but studying chromatin structure, with some previously obtained Hi-C data.

Studying Enhancer RNA is an interesting project to be a part of especially since there is a lack of understanding on eRNAs. For instance, genetic variants need to be assessed for statistical significance, especially in the light of linkage disequilibrium, genetic associations, pathway analysis, and functional predictions, but this is difficult to study due to this gap in knowledge. While this may be a challenge with no apparent answer, missing this analysis does not necessarily mean the project is a failure. What we do have now is a groundwork for exploring putative disease related enhancer loci variants. Coming from a purely academic background, there is always a “right” answer to a project/test/etc. When in the lab, this isn’t necessarily the case. There isn’t always going to be a “right” answer. While this is neither good nor bad, it has been a good insight into the realities of lab work.

Outside of the lab, I have continued to explore the city. Stockholm is very different from other cities I have lived in, as while in other cities there is a clear distinction between, say, a municipality and suburbia, Stockholm is different from this in that parks and nature are blended nicely with skyscrapers and municipal buildings. I took advantage of this these past few weeks by visiting both the Tekniska museet (Museum of Technology) and Drottningholm Palace Park. The Tekniska museet provided a family-friendly look at Sweden's contribution to the world’s technology. I found the exhibit detailing Sweden’s contribution to video games to be particularly interesting, as they are Sweden’s biggest cultural export. For instance, famous games such as Minecraft, Candy Crush, and the Battlefield series came from Swedish game studios. Video games have become so profitable they have begun to rival the country’s traditional exports such as paper.

Drottningholm Palace Park is the home of Drottningholm Palace, the private residence of the Swedish royal family. Not only is the palace itself impressive, the scenic views in and around the surrounding park are also remarkable. Stockholm may not be as “sectioned” as other cities, but it blends both suburbia and metropolitan areas beautifully.

Lauren

Hello! Since my last post I have made a lot of progress on my project! My project is looking at understanding the functions of genes that can enable hibernation in mammals. I have curated a list of genes that are believed to be related to hibernation and have analyzed whether they are being conserved in hibernating mammals compared to non-hibernating mammals. I am currently working on expanding the number of species that are being compared to help validate the results that we initially found. This week, I had the opportunity to present an update of my work to our entire lab, where I was given feedback and tips on ways to further improve my research.

A challenge that I’ve faced is coding and being able to generate graphs that can reveal significance in the data. I have basic experience with a variety of languages, but I don’t excel in one specific coding language. It’s been challenging for me to have to debug and edit my code to do certain additional functions. One thing that I’ve learned to really respect and admire about people who code is the patience and commitment they have to work through their code and the errors. There are plenty of times when I receive an error and instead of immediately asking for help, I’ve practiced working through it myself and trying to exhaust all of my options before resorting to help. When I am given help, I try to ask questions to fully understand where I went wrong and the functions of the correct code. This research has helped strengthen my tenacity, patience, and problem solving skills that can be applied to any situation.

Outside of the lab, I’ve had the opportunity to go to meet and interact with so many great people. I’ve been able to grow closer to the people in my lab and learn about where they come from, their aspirations, and the things they're passionate about. I’ve really learned a lot from the members in my lab and they’ve become an inspiration to me. I also recently got to do glassblowing! I was able to create a water pitcher and a wine glass! It was such a once in a lifetime experience and I’m so grateful for the people who worked there for their hospitality, patience and guidance! Additionally, Zubair, Eleanor and I got to go sailing with one of Zubair’s coworkers and it was such a cool experience to sail around the Archipelago and see Sweden from a different perspective! More recently, Zubair and I went to one of the best brunch spots in Stockholm and tried some great food! I look forward to trying new food places, taking pictures around the city, and meeting up with some of our new friends that we’ve made here!

Taylor

Hej Hej! Since my last blog post I’ve continued to explore the city and move towards the final deliverables of this research program. In the lab, I have continued with the single cell analysis. Now that the cluster plots have been completed, I can create complimentary plots to show my findings in new ways. I made volcano plots, stacked bar graphs, dot plots, etc. The plot that made the best addition to my cluster plot was my stacked bar graph. With this graph, I am able to show the cell type proportion amongst the entire sample. It is just an easier way for the audience to visualize what is being shown in the cluster plot. With the stacked bar graph and cluster plot, I was able to submit my abstract to the BMES conference.

During my time conducting research, one challenge that I have not been able to overcome is staying focused on my task or even just keeping interest in the topic at hand. Research can move slowly. A lot of things become repetitive, and sometimes I just don’t have anything new to work on. I often have trouble staying focused when I just sit at a desk all day. It honestly makes me nervous because this aspect of the job can be common across all fields unfortunately. From this challenge, I have learned that I value a fast-paced environment that will present multiple challenges to me often. I will keep this in mind when conducting my job search in the near future.

After my trip to Göteborg, I visited Skansen which is an open air zoo/museum. They have animals and real buildings from different time periods in Sweden. They also have volunteers there who are wearing the traditional clothing of their particular time period and they will speak to you as if we are all in that time period. I saw bears, reindeer, seals, and some monkeys. I also went to see Drottingholm Palace which is the current residence of the Swedish Royal Family. The palace was beautiful and I definitely felt like I was fulfilling an 8-year old me’s dream of visiting a palace with real royals in it. Next, I also went to Vaxholm which is the capital of Stockholm’s Archipelago. The boat ride there was about 90 minutes long. We sat and ate a good lunch, visited Vaxholm Castle/Fortress, and got a pastry from a local bakery. I am starting to feel a little homesick, so to help with that, I went to a cafe that served traditional American pancakes. They were pretty tasty and it felt good to get some time to relax a bit. I finally was able to see the Vasa Museum which showcases a 17th century warship that sank but was then restored to nearly perfect condition. It was quite a sight to see. Finally, I was also able to see a movie in the theatres which is something I have not done in over a year! I saw “Old” which was quite interesting to say the most. I did enjoy my popcorn and slushie however. Vi ses!

Zubair

Hello! As the weeks continue to fly by, I am beginning to wrap up my project and prepare for the final deliverables. The bioinformatics limma pipeline is complete, and I have been able to understand and depict the proteomic comparisons between exercise, aging, type 2 diabetes and obesity, specifically related to muscle degradation. This pipeline can be used to understand many different types of complex diseases with the correct datasets. In the past couple weeks, I have been using excel and R to filter out significantly differentially expressed proteins that are both oppositely regulated and regulated in the same direction. I’ve noticed that endurance training mainly has the biggest impact and the most oppositely regulated proteins compared to strength training. Once these proteins were found, I used a website based tool called enrichr to examine the functionality of these proteins and see how they relate to muscle wasting and muscle degradation. I have found some pretty interesting correlations and proteins throughout the three datasets. There has been a little bit of overlap, but over the course of next week, I will focus mainly on the functionality of proteins separately, rather than making comparisons to each one, see if there are any interesting finds. Our presentations and final deliverables are due in the upcoming two weeks, so the majority of my work from now on will be creating presentations and posters.

In addition to working on my project, I’ve also continued to explore the city, participate in various activities and meet a ton of new people. I usually alternate between working at SciLifeLab and working at Biomedicum, and whenever I go to SciLife, we always end the day with some competitive table tennis. This past weekend I visited Gröna Lund, Stockholm’s amusement park, took pictures at a garden near Vasastan, and also got some great views of Stockholm from Mariaberget. I also traveled to Gröndal with some friends that I met at KI for a cheese tasting night. On Wednesday I had the opportunity to visit the Huddinge Hospital once again to see how our lab group collects and performs biopsies on our research volunteers. I ended the week with a lab dinner at Minh Mat, where I was able to try frog legs for the first time!

In the creation of my bioinformatics pipeline, I’ve noticed that the code always needs to be modified and changed from time to time. Currently the pipeline is not efficient, as it can only handle certain types of data. Since the program is coming to an end, I have been doing some of the work manually and, I havent really been able to focus on making the pipeline reusable for other datasets. Fixing this issue takes time, patience and a little bit of trial and error, and it’s a great way to work on your coding/problem solving skills. If I am stuck on a line of code or have an error that I can’t fix, I approach the lab members with a heavier computational background, and it’s always fascinating to see their thought process about how they would go around solving the problem

Eleanor

Hello everyone! These last few weeks seem to have flown by. It's crazy to think that I've finished my penultimate week here in Sweden! As my time here is starting to come to close, I've been working towards wrapping up my research project. This last week specifically I spent most of my time preparing a comprehensive overview of my results from my project to present in front of Dr. Chapman, the other NSF IRES interns, as well as PIs and mentors from all of our respective labs. The other interns and I actually presented our overviews of our projects today. I was able to take a lot of the data and results from my presentation that I had presented to my lab a couple weeks ago.

In terms of an update for you guys, I have finished building the scatter plots to measure the correlation between certain epigenetic features like histone markers and transcription factors and have been able to identify certain markers that seem to hav an impact on centrality. I've also been able to build these same scatter plots to look at genomic features like GC content, exons, and gene-coverage. In terms of genomic features it seems that GC content plays the biggest role in chromosomal organization which isn't surprising because the same thing is in true in humans. From the scatter plots I've been able to build a multivariable model that uses a combination of histone markers, transcription factors, and genomic features that accurately predict GPSeq score. I confirmed this by calculating a predictive GPSeq score from the tracks and comparing to the observed GPSeq score that we calculated from our data.

Hopefully in my last week I will be able to focus on local changes in the genome rather than the global changes that I've been looking at for the past 9 weeks. Our thoughts are that while we don't really see a big global change (genome-wide) in organization, we hope that by looking at genes that are known to interact with the complex that our inhibitor is affecting, we will see more drastic organizational changes.

In the past 2 months I've learned a lot about myself and one challenge that I find myself facing week after week is my patience and ability to stay focused while sitting behind a computer for most of the day. One thing that I've come to realize about bioinformatics research (and all research) is that it does't always progress linearly. There have been periods of time where I've got a lot of stuff that I can do to help me move forward in my project and then all of a sudden I hit a roadblock or need to wait before continuing and everything seems to slow, even time. It's at these moments that I struggle. When things are moving at a slower pace than I'd like them to, it makes hard for me to focus, especially when I'm sitting at the computer. This has been educational and helped me realize that in the future I would ideally like to find a job that has a balance between the sedentary tasks at the computer, analyzing the data, as well as doing part of the job that is a little bit more active and physical (like being a part of the earlier processes such as the wet lab).

In addition to working, I've been trying to complete the checklist of things to do in Stockholm I made at the beginning of the trip. Most recently I've been able to go to the Vaxholm, the Vasa Museum, the National Museum, Millesgården, and Haga Park. The National Museum is Sweden's museum of art and design and the different collections include paintings, sculptures, drawings, and prints goin all the way back to the Middle Ages up until the present day. The building itself is gorgeous and you could last hours inside the museum with all of the different styles and artists.

Millesgården has been at the top of my list for a while so I was really glad to go visit. Millesgården is a sculpture garden at the home of the sculptor of Carl Milles and his wife painter Olga Milles which was built in 1908. The home has since been turned into a museum that includes an antique collection, an art gallery, and a restaurant in addition to the sculpture garden. Carl Milles actually spent a lot of time in the United States where he is best known for his fountains. Some states that have his work include Delaware, Missouri, Michigan, Virginia, Illinois, Minnesota, Pennsylvania, Massachusetts, New York, and Wisconsin (Wall reliefs on the Racine County Courthouse).

David

Since my last post, I’ve begun to expand on Evolver. Previously I figured how to make it all work together with my Program to create a random genome and evolve it. Now I made a script that will not only create one genome but multiple genomes according to a Phylogeny tree. I thought I was going to run out of memory but the files were still in the kB range making it possible to create 4 new genomes. Using these genomes I then was able to use online tools like NCBI Blast to compare the alignments. This gave me blast files that I can then use for GenoPlotR which will graph the alignments and use synteny bands to show the similarities and possible changes within the genome. Now that I had genomes, I downloaded the tools that I was going to compare. I started with Forward Genomics and RERConverge. I was worried at first since from past experience, I run into many issues when trying to download them. Fortunately, I was able to download them without any problem and successfully ran their sample code.

Now in order to get it to work with Evolver files, I created a program to convert the files to the proper input files. This made it automatic and easier to use Forward Genomics. Once I had my program working I ran Forward Genomics and I got no errors. I felt accomplished at last! At a second glance, I realized something was wrong. When running the sample test, it was doing an extra step that my test did not do. With only one week left for the presentation, I felt hopeless. I read the documentation over and couldn’t realize why. It wasn’t until I started digging into their code I realized why. I started printing every line of code and seeing where they were getting the extra step. It turns out, their sample test had missing data, which made it take an extra step. Due to time, I had no other choice, I had to stop and work on my presentation. Fortunately, the presentation went great and everyone seemed to enjoy it.

Outside of work, I enjoyed going around Stockholm and exploring what the city had to offer. One thing that I wanted to do from the beginning was to visit Grona Lund. In terms of the distance, it was quite small but very entertaining. I managed to get on the majority of the rides and experience the beautiful view of Stockholm at a high altitude. One thing I have left to do is go kayaking around the inner city of Stockholm which will secure the end of my trip as a success.

Since starting my research work, one significant challenge that I have not been able to resolve is working with the tool SimControl. SimControl was going to make a lot of the work faster and more efficient but after downloading it, I couldn’t get it to work. I downloaded everything exactly as they suggested. After a week of just trying to get this running, I ran out of ideas since I kept getting error after error. It made my experience frustrating but made me realize that in research, not everything may go your way. There will be roadblocks and this is where you are tested. You can either give up or keep trying. This is a learning experience and the more I learn now, the better I can handle these types of situations in the future. If I ever create documentation for a program, I will make it possible for a 5 year old to understand how to install it.

Nick

Since arriving 10 weeks ago in Stockholm I have grown both professionally and personally. Coming from a Computer Science background, my experience in Bioinformatics was limited to one, introductory class. So, after spending time in the lab, I have learned alot about not only biology, but also how research is done, how to formulate a question that can be answered by data, and how to determine which results to include in a final report. What was most impactful professionally was the opportunity to see how my expertise in computer science could partner with science experts and together we could collaborate on a project, with each of us contributing our unique skills.

Personally, Stockholm is the farthest I have ever been away from home and even though I am not here alone, it was still mentally challenging to pack a suitcase, fly across an ocean, and live and work in a completely new place in the midst of the global pandemic. I came over prepared for some homesickness about the “big” things (missing friends, family, etc.), but I didn’t realize how much home sickness there can be about small cultural differences. For instance, some grocery items may be in different packaging than in the US (i.e. box vs. can). Since the accommodations came with a kitchen I did a lot of cooking and finding spices the first time around also proved to be challenging. In those moments, these minor differences seemed more difficult than they were, contributing the most to any homesickness I felt. So while the big things I was prepared for, these smaller, in reality inconsequential things were the hardest. Looking back, one now-funny moment is when at the beginning of the trip I arrived back to my dorm room from shopping thinking I had purchased toilet paper only to learn they were paper towels! Shopping in the beginning was a challenge simply because it was harder, even with the help of iPhone translations. Another unique challenge was laundry. Unlike home where you can access the laundry room any day, any time, here you must schedule a reservation for a particular day/time. On the one hand it's a nice system as you know a washer/dryer will be available for you, but on the other, once scheduled the rest of your activities revolve around your laundry date. So it’s not unusual if you are trying to make plans with someone that they decline with the reason that they have to do laundry.

Stockholm is a beautiful city with a deep history that blends both municipality and nature beautifully. I am very thankful to have had the opportunity to experience the beauty of Skogskyrkogården and marvel at the age of the Vasa. The public transit system is much more robust than it is in San Diego, which makes travel around, and even out of, the city easy and extremely affordable, especially when compared to the cost of services like Uber. In my experience, the public transit was easy to use, and as my mom was glad to hear, was clean and I felt safe. It was a neat experience to see how quickly the season moved from the height of the Summer to even now I can feel the Fall approaching as the days have gotten much shorter. When I arrived in early June, the dark of night only lasted about 5 hours and even then never seemed truly dark. Now the days are shorter with sunset coming at 20:30 compared to 22:30. The sunsets over the water are beautiful and the long summer days are perfect for late night walks along the water. My favorite thing about living in Stockholm was getting to meet so many people from such diverse academic and cultural backgrounds. It was a unique experience to work in a Swedish lab where none of the members were from Sweden.

Overall, these past 10 weeks have been an excellent learning experience and I leave having learned a lot about both enhancers and SNPs as well as life in Stockholm, with several new friends and mentors as well. I am very grateful for this opportunity and hope to return to Stockholm, for business or pleasure, very soon.

Hejdå för nu Stockholm!

DAVID

During my time in the research lab, I learned that failure is more common than usual. We always see the end results of the research but we never get to see the process. In our lab meetings, I realized I wasn’t the only one who had setbacks. I saw firsthand how they reacted to the unexpected results but they kept trying. Being part of this lab, made me more perseverant. There were times where I wanted to give up because I could not get anything done due to technical issues, but I kept pushing and trying new methods. I also learned how to ask for help. Throughout my entire academic life, I have always kept to myself and tried to find a solution. After this experience, I realized asking for help is more beneficial, especially when I am surrounded by experts. By interacting with others, ideas are thrown around which I might have never thought of.

My favorite thing about living in Stockholm is seeing the beautiful architecture mix with the surrounding water. Everywhere I would go, there would be a different style of architecture which made the experience new every time. Attached to these, there was always a story behind every building. Stockholm also has a diverse culture so we were able to meet different people from all around the world. Luckily everyone spoke English, making our time here easy. The most challenging part about living abroad is the food. From eating fresh meals everyday to meal prepping to save money and time is very difficult. Part of the challenge was learning how to cook and what to cook. Also since all the food was labeled in Swedish, it was difficult to navigate the grocery store and look for items. Without google translate, it would be almost impossible to get the right item.

Zubair

The past 10 weeks here in Stockholm have been extremely rewarding. Staying abroad while doing research is an experience many students do not get to experience. Being away from friends and family is difficult, but it is something that you can get used too after settling in. This research experience has taught me to be more independent, and has provided me with a glimpse of what the real world would be like. Most of my days here included working form 9-5, then going to the gym, and finishing the day off with dinner and a shower. The weekends were saved for exploring the city, and learning more about the history of Stockholm. Due to working in both Biomedicum and SciLifeLab, I have been able to meet two different lab groups, both with highly motivated individuals who are mostly pursuing their PhD or masters. Working with people that were so much older was intimidating at first, but this became second nature to me after a couple weeks. The research here has confirmed my interest in data science, computational biology and systems biology, and will most likely lead me into pursuing future graduate studies. I have learned many bioinformatics tools and how to incorporate them in R, as well as becoming a better programmer and learned how international research collaborations work. One of my favorite things about living here was being so independent and having a certain subject area to focus on. I enjoy working on projects more than taking classes in school because they allow you to test your creativity and imagination and expand your knowledge. One of the most challenging parts about living abroad for the summer was not being able to see my friends back home. The time difference between the two places did not make it any easier. My parents were able to visit me during my final week here, and it was great to see them after such a long period of time. Regardless of any challenges and obstacles, my summer spent here in Stockholm has significantly improved my knowledge in bioinformatics, allowed me to network with some of the worlds leading scientists, and has provided me with the opportunity to visit and explore one of Sweden’s most beautiful cities.

Taylor

Hej Hej! I seriously cannot believe that it is time to write my final blog post for this research program. I knew that the 10 weeks would fly by and they definitely lived up to that expectation. Research has been a completely new and eye opening experience for me. I decided to join this program because I wanted to see if going into higher education and/or biomedical engineering could be something that I am interested in. I came in feeling a little nervous about my skill set. I wanted to impress my new lab, but I was not sure if I could meet their expectations. Well I had nothing to worry about because I think I had the most supportive lab in the world! My coding skills and the little biology I know got me through the entire summer. For the parts of my research I did not know, I either asked for help from my supervisor or tried to troubleshoot it myself. I gained a lot more confidence in my problem solving skills through this research experience. I got to accomplish some really cool research deliverables. I am most proud of my single cell cluster plot because it was the most challenging part of my summer and I finished it! Overall, this program has taught me that while research is not for me, it is still good to get outside your comfort zone and try new things. There’s nothing to lose!

My favorite part about living in Stockholm has definitely been the modes of transportation. I really enjoyed walking to work pretty much every day with Eleanor and taking the metro. I don’t get to do this when I am in San Diego so I am glad I took advantage of it. The only thing that could have made it better is if I had a bike. The most challenging part about living abroad is changing your routine and having to adapt to the local way of life. There were times when I wished I could just stop at a Target or go to Trader Joe’s for my favorite snack. Those stores do not exist over here obviously so I had to find new favorites. It is also hard to see your friends and family do exciting things while you are gone. You wish that you were there with them but you also want to appreciate that you are here. This program is an extreme privilege and I feel very fortunate to have been a part of it. Ten weeks is a long time however, and I am ready to go home. I have seen and done everything that I wanted to so I feel complete and good about how I spent my time here.

I have made a lot of good friends during this time whom I will miss immensely. I hope to return to Sweden some time in the future.

Hej då!

Lauren

Hello! This experience has been such a life changing experience! This research experience has confirmed my desire to go to graduate school. I think I had the best lab and they were all so welcoming. Our lunches were priceless because I could learn from their life experiences, while strengthening my bond with them. I like how collaborative research is and I look forward to incorporating that into more aspects of my life. Because of this experience, I think I’ve gained more patience and tenacity when faced with an obstacle. I also gained more security in doing things by myself and taking myself on adventures everyday. What I enjoyed the most about being in Sweden is the ability to be present in the moment of everything that I was doing. It felt like a way for me to disconnect from everything that was happening back in the states and having a fast paced lifestyle. It was nice to be able to slow down and enjoy the scenery. Simultaneously, it was pretty difficult being away from my family. Prior to this trip, the longest that I have ever been away from my family was 3 weeks, so this trip was an adjustment and I’m fortunate to have been able to talk to my family everyday. I’m grateful for the great memories and relationships that I gained from this experience.

Eleanor

Ahh hello again! Today (I guess more like yesterday) marks the end of my 10 week internship here in Sweden and I will be heading home on Sunday. I feel so grateful to be have given the opportunity to participate in this program, during my time here I have gotten to experience and learn so much. Walking in I had no expectations for what the internship was going to consists of and I was ready to learn whatever I could and take on challenge my mentors gave me. This opportunity was my first real research experience and one of my personal goals for the program was to learn more about what doing research full-time could be like and use it to help me make a decision about what I wanted to pursue after graduation.

I would say there were 2 big things that I've learned about bioinformatics research and research in general:

1. Research isn't a linear process, not everything you do will move you forward in your project... it could even set you back sometimes

2. Research doesn't progress at a constant pace. There are moments when a lot of things may be happening at once and you have a full schedule, but at other times things might be a lot slower.

The past 2.5 months have really tested my patience and problem-solving skills at times because of those two things. During those times of struggle I was glad that I had coworkers and mentors surrounding me that were there to support and help me. I especially appreciate everything that my mentor has done to help guide me through my research project. I really couldn't have done anything this summer without him.

Non-work related I've really enjoyed my time exploring Stockholm and I believe the summer had a good balance of professional work and education as well as fun tourist activities. As a final hurrah before finishing up our last week of work Taylor and I ventured out of Stockholm to go visit Uppsala which is home to Uppsala University and lives up to the description from my coworkers as a mini-Boston. It had such a different vibe than Stockholm, letting it have its own unique charm.

I think my favorite thing about living in Stockholm has been how much culture and history I've been surrounded by. I think Stockholm (an all of Sweden... as well as Europe) has done a great job at integrating the deep and long history it has with modern day life. All of the old, historic buildings that have been repurposed or turned in to museums allow Stockholm to grow and keep up with life now while also never forgetting where they came from. The number of museums seem never-ending and everything is just gorgeous.

I think the most challenging part about being abroad for so long has been missing some of the little things back home and always being a little uncomfortable. Being in Sweden I've had to change some of my normal habits and kind of create a new routine, which is always hard to get into. I'm looking forward to being able to get back on track when I get back home and surround myself with the comfort of friends and family and my favorite things that I haven't been able to find/do here in Sweden.

Overall I'm glad that this program was able to run and allow me to explore and experience what it's like to live and work abroad and I could definitely see myself doing it again in the future!