BE 20.109(S20) Class blog

As the rest of my fellow 109 peers breathe a sigh of hopefully relief, not despair, at the passage of the deadline for the research article, now would be a better-late-than-never entry for the blog. I have spent much of the last week and weekend writing, agonizing, finalizing, sometimes bitterly cursing(shhh) and anxiously editing my research article. I think the research article was hyped to me as the toughest assignment in 109 by friends who have taken the class before leading me to enter the writing process with lots of apprehension. For what it’s worth and perhaps prematurely, I will tentatively claim that it didn’t go as bad as I expected. Perhaps I went in with extremely low expectations for the easiness or perhaps I am highly mistaken about my writing quality, but I think the article went as well as I could’ve asked. The change to having a defined list and orders of figures definitely eliminated a lot of the choosing dilemmas I would otherwise have. Although sometimes this led...

Hello, We are done with the research article! Over the past few weeks, I have discovered that I need to start reading more research articles. Not about anything in particular, but to just expose myself to things. It would have been useful practice for the journal club. It also would have been nice to know about more things going on in the bioE field so that I could come up with better ideas for the project proposal. I feel bad relying on Desmond so much but he really is out here suggesting things that I have never heard of before that all seem genuinely interesting. Lastly, it would have been nice to have read a bunch of papers because I would have a better idea of how people write them and actually have things flow together. Writing this research article was HARD. It took so much longer than I thought it would. I really struggled with the discussion section. I feel like I don't really know enough to suggest good future works. I also have no clue what is going on in the field rel...

Last week, my class received an email from one of the professors moving the next day's 9:30 AM lecture to 8 PM due to a family health emergency. Two days and three emails later, that lecture had been entirely cancelled, and the next class' paper discussion had been replaced with a lecture from another professor pertaining to COVID-19. So it was with great excitement tempered by worry that I joined the Zoom lecture that day. Hearing from a professor who was actively working on COVID with an international consortium would promise to be interesting if nothing else. Listening to the professor speak about the fascinating biology of the virus, it was too easy to forget that this was the same virus that was wreaking havoc on people all over the world while causing entire countries to shut down. For example, the virus' transcription mechanism was quite fascinating, with transcription initiated from successively later points in the cDNA, so that it produces more copies of the vira...

That 12 mins of rewatching my journal club presentation was my longest and cringiest 10 minutes of my life. However, I learned lots of thing about presenting and preparing powerpoint despite the latest submission (probably same for research article).  It's really hard to keep the motivation of doing assignments without the help of panic monster while ignoring the greatest attraction of "Youth with you" idol producer that's airing right now.  At least my sleep schedule is fine and and I'm exercising a lot (glad that I got my splits back)

Writing this scientific research article was quite difficult for me, and on many terms that I did not initially expect. I guess some of the most troubling roadblocks that I ran into was how to actually interpret and explain my data. Although we did learn a lot of new statistical analysis methods that I do believe are very helpful and I will sure be encountering them again in the future, I still found my unfamiliarity with what they were actually analyzing and what conclusions I could draw from them to be a source of struggle for me. Therefore, the results did take me much more time than I had anticipated, as most of my time was spent on digging through old notes and the R code, and researching what certain plots meant.  In addition, I feel like the open narrative of the study was another point that I got stuck up on. I’m generally someone who likes having a guide or structure to follow and I generally tend to panic when such structure is taken away. Therefore, this did allo...

Looking over our assignments at the beginning of the year, the research article was definitely what I felt most stressed/nervous about.  As aspiring scientists, we read countless research papers a year.  However, typically (as we've discussed in class) I just read the abstract and scan the figures to get a general sense of what is going on.  The nitty gritty of the methods and results often seem quite technical and go right over my head.  Really thoroughly reading a research paper from start to finish is a hefty task.  Therefore, the thought of writing one was daunting. I was getting very stressed as the deadline started to creep closer.  However, when I sat down to start piecing everything together I did find we had already done a decent amount of the work.  The pieces that we turned in and got feedback on as homework assignments were ultimately very helpful to me.  I feel like without realizing it we were forced to be proactive in writing and ...

Surprisingly, I actually really enjoyed writing my research article.  I definitely did not expect to have any fun with it, and at first I didn't.  It's always really hard for me to start writing anything.  After I established a rough outline of what needed to be done, I found myself bouncing around a lot between sections, just trying to get something done.  However, once I felt the pressure of the very quickly approaching deadline, it was much easier to focus.  As I was writing, I think I finally felt the "story" I was supposed to be telling come together, and it was a very satisfying feeling.  Having said that, I am relieved to have completed it.  My cat was definitely ready for me to be done so I could pay attention to him instead.

At times, I found the size of this project to be overwhelming, but looking back I think it was a good challenge. I found it difficult to weave all of the figures together, and the thing I struggled with most was organizing the discussion and results section. Looking back, I believe I should have spent more time planning out my discussion and my results section. Creating a more detailed outline of the discussion and results would have ensured important information was highlighted.   I found the homework assignments we did throughout module 2 very helpful while putting together my research article (starting the intro, working on the methods, outlining the figures, etc.). One homework assignment I would have found helpful would be to briefly outline the subsections for the results or roughly outline the discussion section. Beginning to think about these outlines earlier on would have helped me when it came to writing the research article.   Dana

Writing a scientific article the second time around was definitely easier, but not exactly easy. Because we weren’t in the classroom to do the experiments ourselves, I felt separated from the data and purpose of our experiment. I tried to use office hours to ask questions, but in the beginning of the module, I felt like I didn’t even have enough base knowledge to craft a coherent question.  One thing I really appreciated with this research article is that very little background information was given on the biological systems, so we could craft our own story of how the data fit in with the general public and published scientific literature. Instead, during lectures and labs, we learned about how to work with the vast amounts of data that we were collecting from RNAseq and qPCR. I also appreciated the help organizing the paper, because that was something I was most worried and confused about before I thoroughly read the instructions for this assignment.  Even though I w...

The Research Article was on my to-do list, unchecked, every day haunting me. I had to start adding the unproductive things I did just for the satisfaction of checking something off (i.e browsing Airbnb for 2 hours dreaming of living in a ranch in Arkansas with my friends this summer). I doubted myself and tried to create accountability milestones with people, even meeting with Maxine from the Comm Lab twice. I accidentally called her Justine and I feel horrible. People made it easier. Shoutout to Diana my lab partner for checking in on me as I attempted to work on the Research Article, and even more for pointing out which side of the heatmap significance scale was what. We scheduled a "productivity call" Saturday to work on the research article where she was productive and I'm not sure what I was. I am currently on a call with my Course 20 junior friends who are "bullying" me into finishing this article. It doesn't seem like its that hard to write yet it ...

Throughout Module 2, I often felt lost in the data and had trouble seeing the significance of the results. Instead of the usual workflow of doing an experiment, analyzing the results, and interpreting them to guide the next steps, we had to follow a pre-determined path that made me feel disconnected from the research. Going through the process of writing the Research Article was eye-opening. Looking up past papers and learning about specific findings finally put our results in context and sharpened the motivation behind this module. My favorite part of the Research Article to write was the discussion section, though it was easy to get carried away with possible future directions. When I looked up one paper, their references would carry me to another, and another, and so on. Seeing the extensiveness of published data in niche topics and the endless set of unanswered questions they generate reminds me why I enjoy research so much. I definitely miss being in lab! Having completed th...

The Research Article is done, and I feel like I have mostly caught up from break. I am looking forward to the next few weeks of 109 where I can learn about something new without the stress of a major writing assignment. The topics I looked up for homework were all very interesting, and I feel even more eager to learn because I felt such a deep personal connection to each topic. My goal as a scientist in the future is to help people in any way I can, and this assignment reminded me of how far research has come and how much work there is still to be done.  Anyways - the Research Article. While writing this and doing more research for the background/discussion, I realized how many scientific papers I have been reading lately, between this class and my UROP. In the past few months alone I have gone from barely being able to get through an article to becoming fairly proficient in understanding the main points and extracting important data from articles. Writing my own on the other ...

It was such a relief to finally turn in my research article. I have to say that I have so much respect for my UROP supervisor that is publishing a research paper. After struggling to read countless for UROP and journal club, writing one myself was not any easier. I do not have much experience with writing research papers, but I imagined that experience reading them and the data summary would make the experience easier. However, I soon discovered how difficult it was to put together a cohesive story with all of our data and be able to understand everything well enough to write so much about it. Maybe I was hindered by my overall lack of understanding of the purpose or the module itself, but I also found it difficult to grasp the main point and goal of this module with everything that went on. I initially thought the genes of interest were the main points, but then changed it to the general RNAseq findings and GO analysis. After more thought, I then changed it to comparing two cell lin...

Having finished the capstone of Mod 2, the research article, I think I should thank the 20.109 teaching team for ensuring putting it all together went so smoothly. Much like the data summary, I felt like the individual homework assignments retroactively felt like I had been slowly writing the article throughout the module, with the big help of having had edits to make it better (the methods section especially comes to mind here). It really helped having already basically drafted a plan for the results section, as having already considered what would go in/I would write about the figures made it much easier. I find that once I’ve put an idea down/given myself a rough roadmap, I can write pretty easily because I’m just following the story, and that was easily the case here. Really, the only part I felt that I really had to think/come up with concrete new ideas I hadn’t thought about before in the homework was when I was fleshing out the discussion section. I would say that this module d...

Wow, that research article was really something. I think one part I found challenging about module 2 was being able to follow the R exercises and really understand the plots and heat maps as I made them. I actually kind of like coding and maybe would have liked a better understanding of R, but I know the focus in 109 isn't to learn all the fundamentals of   coding in R. I often just felt like I was copying and pasting commands, which made it harder for me to see what data was actually being used to generate certain values or produce certain graphs. Also, the fact that we were unable to do many experiments ourselves made it harder for me to feel as engaged in the module. In writing the results section, I found it hard to see an overall, cohesive story line , but I do feel like I was able to gain a lot from analyzing all the data we gathered. I also thought that writing the methods section was going to be easiest since I had already written most of them, but I found it more d...

It's one day after we submitted the research article, and I feel quite exhausted. It's crazy to think that I've written 13 pages of scientific material (greatly guided, of course, by the awesome 20.109 teaching staff). I've definitely never written anything of this scale before, and though it could be significantly improved, I'm still kinda proud of it. This shouldn't be shocking, but the advice that was given somewhere about giving yourself enough time to be able to put certain ideas aside, chew on them, and then come back to it was very true. When I started trying to draft the research article, I was really confused about the purpose of the scatterplots. My first attempt to make the transition from the GO terms to the scatterplots was cringeworthy. It took a few days of looking at them and visiting office hours and then thinking about it some more before I finally was able to make a (hopefully) logical connection between the two. Even if my transition isn...

Crazy to think that this past weekend was supposed to be one of the highlights of our sophomore year, with ring delivery, CPW, and the exciting marathon gatherings on our day off. Also crazy to think that we would have had so much to do this past weekend with our research article due on Monday and a 7.05 exam on Wednesday. Writing this research article took a lot more time than expected. I think understanding what the takeaways or the big picture of our findings was the hardest part for me. It was also hard to put together an interesting, cohesive story without rambling on. Now that I have it turned in, I feel like I have a big weight lifted off my shoulders. These past few weeks of 109 have honestly been a lot, and now that we only have one more big project due (and it's supposed to be a more creative and fun one) I feel a lot better. I'm also really excited about this research proposal because the things I was researching were SUPER cool. For example, one paper used ML to i...

These written messages were donated to the museum by a survivor of the HMS Prometheus Submarine incident.  Day 1 of the Expedition Dear Anne, As we all prepare for this expedition, I feel a great apprehension wash over me. The ocean is a great and terrifying place to sail upon, but we have chosen to submerge ourselves beneath its awesome might. Our mission is one of discovery, and although we shall soon dive to depths unknown, I trust that upon our return we will bring knowledge far beyond what man has discovered today.  To be truly honest, I know not of what we are seeking. We have traveled along the surface of the water to a point in the middle of the Etopo Sea, and using our unique navigational tool, the Doldrum-1, the captain has chosen a point for us to begin our careful descent.  I will continue to regale our experiences to you as we journey downwards. I know you love stories of the ocean. Yours truly, Michael Day 4 of the Expedition Dear Anne, ...

Since today would have been the Boston Marathon, it seems fitting that I feel like I just ran one. This research article was definitely not an easy task and my procrastination didn't help. After writing the data summary, I felt I had a better understanding of how to write about data and interpretations, but actually sitting down and letting those words come out required great activation energy. One part I did enjoy was creating the figures which was the part I started with, although I probably spent too much time trying to make them look prettier. I think I particularly struggled with figuring out how to take all these analysis results from different experiments to create a cohesive, compelling story. Re-reading through prelab slides and googling helped me understand what we gathered from each component of this module. The comments on homework assignments also really helped to guide my writing in the right direction. I found i...

After submitting my research article, it truly felt like there was a massive weight lifted off my shoulders. After working on the article everyday for a good week and a half, I feel like I can finally catch my breath for a good day or two. Through my research article writing journey, I really learned a lot about myself and the things I love and hate to write.  With this mammoth paper, I felt like I needed a plan of execution and an order to write all the components of the assignment. I decided my order would be figures and captions, results, wrap up methods, discussion, introduction, abstract, and then title. Below are my opinions on the writing process: Figures and Captions: I definitely spent most of the weekdays working on this component. I honestly really enjoyed combining my figures and arranging the panels perfectly and redoing elements to make them more clear. In some ways, I felt like an artist working on this project. There was no procrastination to work on this part....