BE 20.109(S19) Class blog

How I felt after turning in the research article ^^ Sleep deprivation is a thing. I had no idea why it would take so long to write everything but it did. Like 5 entire days dedicated only to it with very few hours sleep (& 2 late days!!). To be honest though I think I messed up a lot because my results took the longest and I realized it was because I was mixing interpretation in there which is a NO NO. Once I started writing my discussion and had a better idea of what the big picture is, things came a lot easier and I actually felt like I somewhat knew what I was talking about. I think next time I'll start writing the discussion or intro before the actual results. Im pretty glad there's no lab tomorrow so I can catch up on some sleep :)))

You don’t realize the size of a task it is until you’re about a tenth of the way through it. And then when you reach the halfway point, you realize yet again that you completely underestimated the amount of work and now, you actually have 80% of it left to do. That was my experience with the Research Article. I knew it was going to be hard. I knew it was going to be a long, grueling journey. But I didn’t realize quite how much. It seemed straightforward. Write the methods. Go redo all the transcriptomic analyses we did in class to really understand what’s going on. Regenerate figures and make further analysis if necessary. Write up the results. Interpret the results. Scour the internet for references. Try to find the one interesting finding that ties up the whole experiment, and then go back and write the introduction and abstract and the title. Breaking it down step by step made this colossal task seem more manageable. But what I learned while going through this process is t

Words, words, words, We use them everyday, every second, everywhere, yet when it comes to using them to explain RNA-seq data they just vanish. I struggled hard to explain my RNA-seq data, but I think in the end most of my sentences were coherent thoughts. I think the RNA-seq data was the most difficult part of the research article because of how dense the outputs of the analyses were.  The one real comment I have about the research involves revision. I feel like the quality of this assignment would be significantly higher had there been a revision step.  Until next time, Pedro La Rotta

Honestly, everything came crashing down this past weekend. There were so many different things that I needed to do that the Research Article, intimidating as it was, was only another thing on my list of things to get done. It wasn't until Friday that I was able to sit down and think about this assignment. So as a result of my procrastination, I had to submit the article a few days late. In general, I feel that throughout this semester in particular, it's been a constant race of catching up with everything and whenever I think that I've caught up and can start to get ahead of the next thing, the next day I end up in the same catch up routine. I really enjoy this class and everything we learn and do in it but I really hope I find a way to be more on top of my work.

I really should have started the research article earlier. Starting about a week and a half before it was due was not the move, even if it seemed like there was still plenty of time left in the moment. Not the move. Regrets on past decisions aside, I think writing the research article was a good experience. Even if it was long winded, arduous, and challenging, I can say I really put a lot of effort into slaying the beast. I got more practice with generating figures, trying to write critically about science such that I could try and piece together some sort of narrative, and I got more practice with writing the methods section. Things I wish I had done differently? Probably listen to all the instructors and try to start earlier. When they said you should start drafting sections of the research article throughout the module, they weren't kidding. I would have definitely benefited from doing so rather than dabbling on the research article throughout the week before it was due a

One day has passed since submitting the research article, and yet I am still paralyzed with fatigue from typing up the whole article. How much time did I spend, I wonder, sitting in front of my computer making figures, writing up the article, rewriting them again and again. Every time I try to count the hours spent on it, the haze in my memory hinders me from giving the exact duration; I am simply left with the fact that it was way over 20 hours. Sure, I knew that the research article would take longer than the data summary in the Module 1. It is no longer a group project and every section has to be written in full sentences. But the increase in the work load cannot be explained by those trivial factors. The cruelty of the workload stemmed from the data that we were handling, a completely different kind from Module 1. Module 1 had a simple story in the experiments we conducted. You want to find a new binder for FKBP12, and you test it. What is great about this story is that you are

asdfljwearajweroqh Just needed to get that out there. Anyways, the 20.109 Research Article was one of the most difficult assignments I have ever completed. I've helped write two manuscripts at my UROP, and they involved a team of researchers coming together to fabricate the article. It's usually a very lengthy and protracted process where you continually receive feedback. It's also written for a project that everyone has a vested interest in, not an assignment. The assignment is crammed into a short timeframe. This required a huge amount of discipline to pull off and created a lot of mental angst. These are the drawbacks of making an assignment like this within the artificial and imperfect environment of a research class. Having said all of that, it was really satisfying to look back on my paper and be proud of the work I had done. However, this assignment wouldn't have been completed without the help of some very important resources. Office hours were really import

These past 3 days have been the most stressful days of my entire life. I spent the entirety of last week organizing a huge event for a student group I'm President of, PaksMIT. When I finally got done with it on Friday night, I realized something: I had to write MY ENTIRE RESEARCH ARTICLE IN ONE DAY! I realize now that in the last week, some priorities were misplaced and some regrettable choices were made, but I, (yet again) underestimating how much time it takes me to communicate science and not word-vomit, thought (naively) that I could probably do it within 10-12 hours. I'm pretty sure I have permanent eye-damage from staring at my laptop screen for 10 hours straight. But despite the focus and commitment with which I had started, I realized by 7 PM the next day that there was no way I would be able to submit it by 10. It wasn't just time, I just had a lot of questions and I somehow managed to not go to any office hours in the past week so I suffered in silence for a wh

The phrase, "beauty in the struggle" has never meant so much or been so true. The most significant struggle was overcoming the fear of a research article. Simply sitting down and trying to plan the order or the layout of figures seemed like an enormous hurdle. When writing, I felt like every word had to be in the perfect place, otherwise it would cause an avalanche of other problems that would negate any positive points of the paper. It wasn't until late in the writing process that I reflected on my work and my worries and realized, "My professors do not want me to stress about finding a life-altering phenomenon. They want to test my ability to gather, analyze and efficiently communicate the data." From that point on, I was able to take a much more objective and effective approach to writing. Then, out of the blue, I found myself enjoying my role as a biological engineer/data scientist. On that more technical note, I really appreciated this module for the rob

My brass rat got me through this assignment. I spent a good chunk of this unit fairly confused, typing code aimlessly into R and praying that I get a result that makes some amount of sense. I started actively working on the research article about two weeks before it was due. But with 5 days left, I still felt like I was not in a good place and barely had a story. I also was feeling pretty unconfident and unable, as this unit was pretty confusing, and I honestly did not follow what was going on in lecture or why we were doing so much R analysis in lab. AND THEN I GOT MY BRASS RAT. And she is so beautiful. The next day, when I was still doing my R coding and trying to find a story, I would look down at my hands, typing as fast as they could, and was reminded that I can, in fact, do this. My attitude towards the assignment shifted from “ugh, I can’t do this and I hate it” to “wow this is actually really interesting and I am an engineer ”. By the time I finished on Saturday at 9:50PM, I

remember when the Jocelyn of the data summary ages told herself she would fix her homework as soon as she got it to save time later on? well, obviously she didn't do that, or else the title of this blog post would've been something more positive... but it's okay! third time's the charm, the Jocelyn of the post-research article cram is trying to stay optimistic!! Something I hate about myself is that I'm terrified of asking for help, even when there's no reason to be and plenty of resources available (I also hate my schedule, which is 9:30 am to 5pm nonstop class/UROP every single day, courtesy of my love for suffering and poor judgment in the spring). I will admit that I still don't quite understand what the RNA-seq data analysis we did on day 5 and day 6 meant. Because of this, writing the results section was incredibly incrediblyyyyy hard. I've never spent so much time writing before than this weekend and am so glad that module three is collaborative

This journal paper was really a struggle, but thankfully we made it through! From talking to my 20.109 predecessors, I knew that the research article was going to be one of the most time intensive and difficult things I had to do at MIT so far. With this in mind, I tried to start as early as possible, however I quickly realized that I couldn't really start if I didn't completely understand what was going on (lol). Because of my lack of previous knowledge in R, I took me a really long time to understand everything. It was also hard to figure out what the data was saying because of the lack of significance in results. I wish we had slightly more instruction in R and knew more about the actual data sets, because there were so many simple things that I would have known how to do in python that I spent a lot of time trying to figure out the syntax for in R. Going to almost every office hours available really helped me build a more cohesive story in the end, because as soon as

I still can't believe I wrote over 3000 words for that research article...shaken to my core. I was so stressed about writing enough, I didn't believe it when I had somehow written 14 full pages. I know this article felt so, so long to me, but it just made me that much more aware of how long Real research articles are. Some of them are like twenty pages! And sure, they're written by a bunch of people working together. But that's actually insane. Writing the paper definitely helped me understand this module as a whole much better. I have to admit, I was really confused about the coding we did in R. I don't think I really understood the data analysis from the exercises until I was trying to write about it in the results section, so that was definitely interesting. Looking back, I'd say that I wish I had made a draft of my outline for the paper before and after creating my figures. And I also wish that I'd taken longer breaks in between writing some of t

Overall, I found this assignment to be one of the most difficult I've completed while at MIT. Every time I sat down to craft a figure or write part of the article, I questioned every choice I was making. I found it difficult to synthesize a narrative from the data I had, as some of it appeared disjointed and it was my job to weave it together. Additionally, I was not exactly sure what the conclusion of my research was, as it felt a bit incomplete.  I found the M2D6 and M2D9 homework assignments most helpful for the completion of the research article. They both gave me some context as to what data would be relevant and how it should be interpreted in the results versus in the discussion. I found it challenging to create certain figures such as the GO term tables, or the conceptual A549 figure, in such a way that expressed the important information in a concise, easy-to-view manner. Ultimately, I felt a little dissatisfied with the over aesthetic of my figures compared to some of

After an accumulation of probably over one hundred hours of drafting, editing, and revising of my research paper, I finally submitted my research paper at 9:35 pm of Saturday night. I had never felt as relieved and joyous as I closed 20+ tabs on my laptop. In the weeks leading up to when the research paper was due, I felt a roller coaster of emotions - most of which was stress and confusion. However, with the help of the BE Comm Lab and feedback from Leslie and Noreen I can happily say that I am proud of my final research paper.  Over the span of the last week before the research paper was due I met with the BE Comm lab two times. In the first meeting, I came prepared with my introduction and methods complete. The fellow I met with helped me identify ways to concise my methods and create a flow throughout my introduction. In the second meeting, I came prepared with an outline and the beginnings of my figures. The fellow I met with helped me walk through the process of coming up w

After submitting my research article yesterday, I can say with full confidence that I have zero desire to do anything right now. I honestly don't think I've ever worked harder on or put more time into an assignment then I did this research article. That being said, I was proud of the work that I did but it's safe to say that it took a lot out of me. Everyone always says that everything is on the wiki and they're right. Almost every question I had could be answered by finding a resource on the wiki. When I was writing the abstract or results or introduction, I just had to look to the Comm Lab slides and I knew exactly what kind of information I needed to put in each section. So my biggest tip would be to use the wiki. I'm also really happy that I started working on the assignment well ahead of time, so as I went through the process I was able to talk with my peers or with Leslie to ask any questions that I had about the data or what exactly I should be showing in m

I have got to say, there is nothing more satisfying in this world than closing 30 (maybe even 40!) open tabs on your laptop. I had so many tabs open spanned over 3 open windows. It got to the point where none of the apps on my laptop was working properly. But I was so scared to restart my computer... What if I had lost the link to that one paper that didn't really help me but was too important to lose!?!? I must say, my logic was not the best, but man, did it feel good to delete all those tabs. Something interesting to note is that 20.109 so far, not just the research article but the class itself, has allowed me to realize how much I like working in coffee shops! I really needed to work on my journal club presentation, and I was getting too distracted in my dorm room. I was getting hungry, so I thought, let's venture to Flour and eat while I read my paper some more. And I don't know if its just from a change of scenery, or the aesthetic vibes I got sipping on my chai as I

I just submitted my research article, and I have to say, I'm feeling all. of. the. emotions. Of course, I've been working on this-- and only this-- for the past week and a half, putting in 60+ hours, so it's logical that I would feel all the things over the course of writing this article. Some of my feelings include: dread, excitement, worry, stress, apprehension, fear, anger, frustration, despair, helplessness, confidence, tiredness, sad, overwhelmed, triumphant, proud, relieved, and nervous. This paper was mentally and physically demanding. I sacrificed a lot of things for this paper: sleep, a normal eating schedule, marathon Monday, my tendency to avoid caffeine if I can help it, my sanity (I'm kidding), and, most recently, spending time with my family. However, I'm incredibly proud of the product I turned in. Every word of the 5,073 I submitted was chosen carefully. I wrote, rewrote, criticized, got feedback on, rewrote, and revised sections and figures until

I don’t think my computer has ever had to handle more tabs open on chrome or excel than it did for the week leading up to the research article deadline. I don’t think I’ve ever written a piece of scientific communication as extensive as this one or spent this much time on a single assignment before. I also don’t think I’ve been as satisfied with any other assignment as I am now, looking back at what I learned through this process and at the final product that I created. The RNA-seq data felt like a gigantic maze. There were so many different paths you could take, and so many storylines that could result depending on the path you took. Sometimes the genes I was looking at or the GO terms I decided to investigate felt almost random. I found myself continuously getting distracted by different threads in the data, investigating them, either finding some interesting conclusion, deciding the thread was no longer interesting or getting pulled into some different thread. I wished

This journal paper has by far taken the most amount of time to complete than any other assignment I have ever been given. I found it a struggle to create a cohesive storyline with the our minimal data. For instance, my cell viability assay was not optimal and  I found myself not being able to gather the data I wanted in R studio simply because I did not have the knowledge to do so. Having such nonspecific results in R made it hard to deduce anything significant or interesting. I constantly re-routed my data portion of the paper to try to make sense of it all. With that being said, I have finally gotten past what I consider the hardest part of formulating the paper: coming up with a storyline and figures to support it. I figured out how to use R for simple application and I am proud of that! Now having almost completed the paper, I am thankful for all of our homework assignments. The feedback greatly sped up the drafting process for the introduction and methods portion of this paper.

Justin Liu Finishing this research article was a huge personal victory for me. As a whole, it was by far the longest paper I've ever written, and the content was so different from other things I've written about too. The resources I found most helpful were the homework assignments. The homework assignments primarily served as a way for me to stay on track. It got me writing, and it got me writing early. There's something about being able to be writing my main research article and then just going back to previous homework assignments and pasting in my work that made me feel so productive, watching that page counter jump by 1 or 2 pages. The M2D9 homework specifically also got me thinking about the whole "story" my paper would try to tell. In order to make good data and form a results/discussion section based on it, a hypothesis (at least a rough idea) was necessary. This homework not only served its purpose of making me feel good about myself when pasting in

Despite my presentation feeling like a dumpster fire, speaking to others about anything, especially when you should technically know more about the subject than the audience, can be pretty fun. Journal club was no exception. However, as fun as the act of presenting is, writing it can be a bit more unappealing and definitely takes a lot more motivation. Reading a paper and being tasked with presenting its most important contents in only a few minutes really forced me to look at what the audience could best take away from the paper, rather than what the authors might have specifically thought to be most important. Seeing shortcomings in the paper, like poorly organized figures or unexplained jargon, now affected me and my future audience and only made me angrier than usual. But as much as a pain as that can be, it's pretty fun to be able to say a paper written by people with far better credentials than yourself isn't the best.  Finally, I thought I had learned from my mistakes

This whole assignment was a lot of work, but I really enjoyed it from start to finish. I think I gained confidence in my abilities to 1) read and understand a journal article on my own 2) effectively communicate the journal article to others. In high school, I was part of my science research program and we always had to give either poster presentations or powerpoints. I loved the nervous  rush of presenting and also just getting to share my knowledge (even if it was limited) to others who were equally interested. This assignment was the first time since high school I had to present to others, and it reminded me how much I enjoy the process. The hardest part for me was making sure I thoroughly understood my paper. I spent a ton of time re-reading sections and annotating. It then also took me a while to come up with a clear, simplified presentation storyline to get the message of the paper across. Now looking back, journal articles do not intimidate me anymore!

So I just had my journal club presentation and to be honest it didn't go as well as I was hoping for personally. I felt like I got everything important said and I made all of my points really clear. The powerpoint presentation was pretty good in my opinion and I felt that I got my story across. However, the actual delivery of the presentation did not go as smooth. I felt like I talked a bit too fast and had some stutters here and there and I know for a fact that I went a bit over the time limit which is a small problem but still a bit of an oof since I had practiced so much for it. However  the worst part was when I clicked the wrong button on the clicker thing and looked up to see my presentation screen just completely black. Of course I fixed it pretty quickly but it was still so embarrassing. That being said, I still feel like I learned a lot from this journal club assignment regarding how to make professional presentations and how to read papers. I just wish I hadn't

Prior to 20.109, I had not read a research article before. Since then, and largely due to this Journal Club assignment, I am not only able to read them, but I am able to understand most-ish of the material. This is very encouraging! I have very little biology coursework/background, so being in classes or spending time with people who have involved UROP positions and other experience is awesome – and slightly intimidating. Because this assignment required me to communicate the details of a scientific paper, it forced me to understand. It was painful and frustrating, but I feel like I have a strong grasp on the material in the paper, and I am incredibly encouraged! Journal Club itself seems like a great idea for those who want to conduct their own research, keep with the latest news/progress in the scientific community and socialize with like-minded individuals. I personally enjoyed listening and thinking critically about other research papers. I feel like I am much more equipped t

^^When you have absolutely no idea what you just said in your presentation but at least its over ((: So something I definitely don't recommend is reading your paper the night before (may or may not be from experience)... Journal clubs ended up being held during a really heavy exam week and I wasn't able to actually start reading the paper/making the slides the night before. Definitely don't recommend because I don't think I gave myself enough time to fully understand the paper and all the nitty gritty details of the methods and all that, which I think is super important with the questions especially. Also, it meant I stayed up all night to work on it and that's probably why my brain wasn't entirely with it while giving the presentation itself. That's why my advice is get a good night's sleep kids!! :) Another reflection I have is about practice. In the hour before my presentation I wrote a script and I was actually start to feel confident abo

During my time in high school and even a little bit here in some HASS classes, I had to give a few oral presentations. However, I was completely unaware of what presenting actually meant until JC. The fact that for JC we had to immerse ourselves in our paper and become THE expert in it gave me a whole new perspective on presenting. This skill will definitely be super useful in the future. So once again, thank you 20.109!

According to the National Institute of Mental Health, 73% of US adults are estimated to have a fear of public speaking. Every time I get up to speak in front of a group I am reminded that I am part of the 73%.  I really like designing the visual aesthetic for figures and schematics so that was definitely my favorite part of preparing for this assignment. I was most surprised by how easy my paper was to understand. I'm not sure if that's because it was just a straightforward paper or if I'm getting better at reading scientific articles.   I was expecting that including figures from the paper in my presentation would be easy but I had to ]remake some of my figures because they were so low resolution! You'd think if you went through the trouble of producing high-quality data you'd be bothered to make it look nice. I tried my best to replicate their graphs and make them more visually engaging. I was surprised and thankful of the fact that I didn't have too

Honestly, I was so dreading journal club. I was so afraid that someone would ask me why the researchers used TopHat software or why they chose to represent gene length by minimizing the binomial probability of it occurring. I googled every little thing from the difference between isoforms and variants to the specific reagents needed to do FISH. Out of fear and paranoia, I learned everything with my limited 7.05 knowledge. And then journal club happened. The ten minutes went by in a flash (and trust me, I was definitely RUSHING to get all the information across and used a lot of "ums," 'and, like," "so yeah") and then people asked super reasonable questions. Afterwards, after my epinephrine and adrenaline levels went down, I was surprisingly mad. I was mad that I prepared all this obscure esoteric material and people asked questions about things I rushed through. After I got over my ridiculous anger, I was kind of sad (wow, it's almost as if I'm goin

There it was, the #1 spot to present today was still open despite me being the 4th person to choose. Do I present first? Do I step out of my comfort zone and present first? Only those close to me know this, but I am terrible at presenting. I get nervous easily, causing me to become flustered and lose my train of thought. There have been times I get so paralyzed about presenting that I spent days, sometimes even weeks, dwelling on what could have gone better. And while I always feel as if I did horrible, I always lose the sense that we are all human. We all make mistakes. While I may interpret something as the worst presentation of my life, it probably just seemed average to anybody else. Going into journal club presentations, I really tried to focus on that type of mindset. I acknowledged that everyone is human and everything will be fine. As I was called to choose my spot to present, my heart rate was surprisingly calm, and I said, eh, why not, and snagged that first spot.

Every time I reread my article, I became more confused. I would think I understood, but then find that I couldn’t follow the steps that I thought I knew and understood. I felt like despite defining and understanding the “vocabulary” I was clueless to the actual happenings of the article. Luckily, I received a white board for FREE from SDS (10/10, would recommend). I carried this mini-white board (and the beautiful colored markers) around with me for 5 days and mapped my article out. I mapped each section, then how the sections flowed together, then how different topics in the article I still didn’t understand was happening, and lastly which information I was going to actually present (because this article really had SO much). This was so critical for my ability to understand the information and present it in a digestible way. Unfortunately, I was incredibly nervous about this presentation. And I am already kind of a spazzy person so when I got up to give my presentation I cou

Edit 4/18 (Forgot to put my name): Justin Liu Originally published 4/8 The Journal Club assignment marked my first time truly understanding a published journal article. Sure, previous UROP positions had required me to get some background information on the project by scanning a few papers. However, all I really did for those was scan the introduction and figures and then have my supervisor actually explain it to me. Thus, I was very unsure of what to expect for this presentation. Will other people care about my presentation? Will I be interested in the material? Will I even be able to understand it? It turns out that the answer to the second and third questions was yes, but I can't exactly speak for the first question. While working on creating the presentation, the most surprising thing was how much of the authors' data that I had to cut out. I felt very reluctant to leave out charts and data that I understood, and it took a lot of mental gymnastics to convince myself tha

I don't care to read journal articles. Whenever assigned to do so by a supervisor or professor, I usually put it off until the last minute, or read the abstract and nothing else. When I read articles, I read the text, because it's impossible to understand the figures. Of course, it's just as difficult to understand the text, but at least they're familiar letters and sounds. Reading one page with two columns can easily take me fifteen minutes, and even then, I still won't understand anything. I felt that way about the paper the first time I read it. And the second. And the third. By the time I got to the fourth or fifth time, I began to feel more comfortable. I understood what the authors intended to say. I realized the meaning of the figures. I was even able to criticize their work. To get there, it took a LOT of googling. It also took quite a bit of note taking. However, when it was all said and done, I believe I was able to coherently present. The most challen

Sounds strange but I've gotten infinitely more better at reading research papers because of this class. Now that I know what the usual lay-out of a paper is, I know exactly where I need to scroll to for specific information. I understand what kind of information I'll find in figure captions and usually what a graph is trying to show. The other day I helped a friend of mine do her p-set in some random course 7 class by just skimming through the paper she had to read for her p-set and finding answers based on where I would expect them to be. She complimented me generously (a rarity indeed) so I know this tangible skill-set I've obtained is very real and very useful. Even in terms of reading and understanding protocols, I've found myself able to digest information a lot faster (or maybe Mod2 just has a lesser amount of experimental protocols?). I'm looking forward to seeing myself translate the things I'm learning in this class to real life and surprise myself

Public speaking has always been something I struggle with, despite my gradual progression to a social extrovert over the years, so when I heard that the Journal Club Presentation is one of the major assignments for Mod 2 (and that it was worth a whopping 15% of my grade!), I couldn't help but balk a little. Reading scientific papers has always been an intimidating task for me. They always seem too dense, too confusing, or too try-hard, resulting in a very confused Nathan as he tries to decipher said scientific papers. However, being forced to actually sit down and decipher the paper I chose ended up being not nearly as daunting a task as I thought it would be (though it did cost me the latter half of my Spring Break). Some of the figures were either unnecessarily complicated or overburdened with data, and the author's point about PR-DUB only took me an hour of staring to understand, but overall, I think I got the general grasp of my paper, which is good.. pretty sure. Now t

When the Journal Club Assignment was first mentioned in class, I was excited because I love teaching. This was a chance for me to teach my audience about an interesting paper - that's how I framed it in my mind, and it did make the assignment easier. However, in order to teach something, one must know it very well. And to me, that was the most difficult part. Scientific papers are never easy to read, and I find the best way to digest all the information is to take notes and sketch flow diagrams while reading. It’s very easy to lose track of the function of a certain protein, or how it relates to the other components of a pathway, especially if 20 other proteins are involved. But I was set on understanding the paper thoroughly, and this meant extensive note-taking. I ended up reading a lot about assays that were used in the paper to understand how they worked. I also discovered that the more you understand your paper, the more interesting it gets. Ultimately, the schematics I dr

This wasn't the first time I was tasked with presenting on someone else's research paper. For our final project in AP Chemistry, we picked a research paper (on anything) and presented it to the class. It was an extremely easy assignment for me; I don't think I spent more than 3 hours on it in total. I basically just gave the definitions of some relevant terms, plastered a mass spec image from the paper onto a slide, and explained in very simple terms what the experiment found. I only put one figure from the paper in my presentation, and I didn't edit it or bother to explain the actual data in the graph. No one questioned it. (20.109 me now questions it very much). Facing what I thought was the same task 3 years later, I didn't expect this presentation to be too much more than copy-pasting figures from the paper and explaining the results. I picked my paper based on the one that seemed the most similar to the one we will have to write. I was a bit nervous about the

Module 2 has definitely been the steepest learning curve yet. When 20.109 req’s said we had to have taken 6.00, I didn’t really understand what we’d do with a programming background. And then they unleashed R. When I check and recheck the instructions for how to program something, I really wish I’d paid more attention to and retained more 6.00. I still have the monsters of this module - the journal presentation and the research article - to come. With regards to the journal presentation, I selected my paper by reading the abstracts of papers whose titles sounded cool. What I really should’ve have done, though, was taken a peek at the length of the paper I chose: a whopping 40 pages. Thankfully, I had time over spring break to get through it (it literally took me a whole day to read and begin to process). I think the toughest part of reading this paper was remembering what the point of the whole article was - by page 25 and on supplemental figure 5.12 (hehe like 5.12 but not) my

***(journal) club going up on a tuesday(/wednesday)!!!!(???)*** (just kidding, I don't understand that song lyric reference but thought it could work) (Instead, I relate to this meme more: ) Module 2 has been really fun so far, I love tissue-culture (especially spraying my gloves/things down with 70% EtOH). However, I am absolutely dreading journal club presentation. I'm incredibly self-conscious and introverted, and growing up, would barely talk to non-family members. Just imagining presenting in front of people increases my heartbeat and makes my hands tremble/sweat (which is making typing this a lil' harder). I know that messing up won't be the end of the world and that I might even forget this one day after the 10923810923 (I can't math) more days I'll live, but public speaking and death will always be my greatest fears. My inner self realizes that this is a good opportunity to grow as not only a student but also a scientific communicator and that I c

I haven't presented my journal club presentation, but even in the midst of prep I can't help but feel a certain dread in presenting for Journal Club. I've spent countless hours rifling through my paper and googling every single thing that sounds remotely important in fear of the questions that may come. My biggest fear is veering away from the game plan. Ten minutes is not much given the density of information in these research papers, and the it's a bit different presenting in front of everyone compared to shouting at your window in your room. However, I'm kinda excited. Excited to get it over with. On the real though, I am kind of excited. I presented my research to my lab (50+ people including my PI) over the summer and admittedly....it didn't go as well as I wanted it to be. I spoke way too fast and went under the allotted 7 minutes (which isn't as big as a deal, as no one in my lab like these group meetings). My PI asked me a question, and I kind of

I'm very, very relieved to be done with my Journal Club presentation. Cannot stress how relieved I am. I'm actually surprised that I didn't freak out more during the presentation, but I think I practiced enough that it became sort of muscle memory at times. I practiced with notecards and I looked at them every time, but when I was doing it for real, I stopped using them about halfway through. That was crazy! I didn't expect to do that at all.  I think the hardest part of the Journal Club assignment was figuring out how to create a coherent storyline from the paper. My paper ended up with a lot of results, so I had to figure out which were important and which were not as integral to the paper's main message. Making the actual presentation and running through it helped me understand the paper a lot more, because I had to consider it from the perspective of someone who had never read it. I think this also gave me more confidence in my presenting skills, which I&

First major assignment of 20.109 is done, locked in the books. Looking back at it, the entire process from the initial draft to the revisions that were made couldn't have been possible without the availability of the staff and the time spent in office hours.  To the Comm Lab Fellows, thank you for meeting with us at a day's notice. For sitting down and break our abstract apart. For showing us what worked well and what didn't. For helping our abstract go from needs improvement to significantly improved. To Leslie, thank you for bearing with the hundreds of emails we sent your way. For patiently replying to us anytime and every time we needed tips and suggestions. For spending hours in office hours before the first draft was due. For meeting to go over last minute questions before the revision was due.  And to my lab partner, Tooba, thanks for sitting with me late into the night to tear apart our on work. For working with me to identify our weakness and create a s

My expectation that Mod2 will be a similar experience to Mod1 is now completely shattered at this point. Did I ever imagine that this class would become so computational and presentation-heavy? (Maybe I should have read the syllabus more carefully) Despite many differences, I realized that I am enjoying Mod2 more than Mod1. This is not only because I like computational work, or because we get to read many primary literature, but also because we have some power over the experiments. When thinking back for Mod1, I realized that all of the tasks completed were instructed by the instructors. Yes, I did learn a lot, but there was no space to add my personal flavor except for the final draft. And now in this current module, we have so much more freedom! The original R script is given, but we can modify it to analyze whatever way we want. We can choose a paper by ourselves for the journal club presentation. And moreover, we can design our own cell viability experiment to test our hypothes

Think logically. What's the worst that can happen? Nobody really cares about how good or bad you actually present. We are all going through this together and no matter how badly you mess up, life will go on. As long as you read the paper and make semi-decent slides, you will be fine! Worse comes to worst, make a ton of notes that you can resort to.  My urop lab does Journal Club presentations once in a while (undergrads don't have to present, phew) and there is definitely great value in them. Even though they are very boring sometimes, it is really nice to be able to obtain the key information from a paper without actually having to read them. The presenters definitely do the hard part; they have to digest the paper into useful, coherent points that make our lives easier. I found all of the papers presented so far interesting, and I am glad I didn't have to read them to get the important information. Good luck to you all that still need to present! -Pedro 

I’m not going to lie; I really dislike anything that has to do with coding. It is just so stressful to never know whether or not your code is going to work and when it doesn’t work, which is 99.9% of the time, debugging is the worst. So, when I realized we were going to have to code in R in order to make our data from the qPCR meaningful, I was pretty scared.  At first, I was right to be scared. For the first R exercise, I had no idea what was going on even after rereading and rereading the instructions provided. Thankfully, Leslie and Catherine were really patient and answered all my questions even when I was so confused that I didn’t even know what question to ask. I think it was also super helpful that for all of the exercises, we were only ever running a few lines of code for each step. Slowly, the code started to make more sense. My heat maps and dendrograms started working and once I was finally able to get my code working for the gene ontology part, it was so interesting to se

Public speaking has never been my strong suit. Even after numerous presentation experiences, I still get antsy thinking about talking in front of a large crowd and worry about things going terribly wrong. I think the best advice given by the Com Lab, though, was to just envision your talk going well. I tried to keep that in mind and head into the talk with a positive mindset, and it helped! As soon as I got in front of the room and started talking, I immediately relaxed and began to enjoy the experience of sharing some cool science with my peers. Something difficult about the experience was trying to define the scope of what I would share and what I should know. A lot of the paper presented new material, I wasn’t sure how much background reading I should be doing. We were supposed to present one paper, but reading about that one paper didn’t provide us with the necessary background information to understand and explain its every intricacy. I ended up having to do a lot more research

You know what's a terrible idea? Reading a computational biology paper for the first time while running on a treadmill. By the end of my run I wasn't exactly sure what was making my head spin: the 3 miles I paced through, the biology jargon, or the statistical models. Regardless, it was not a great time. After finally getting through my paper for the 3rd or 4th time (while stationary in my room), the puzzle pieces finally started clicking. My constant "OHHHH THAT'S WHAT THAT MEANS" could probably be heard by my neighbors two doors over. From here, it had to be easy, right? You thought. Compiling the relevant information to make a clear story for my peers and instructors is a whole other journey. Choosing figures and facts that support my presentation is a real struggle, one that I am currently working through intermittently while writing this blog post. While this presentation-making process is not my favorite, I'm really looking forward to seeing it all