BIOL368/F16:Class Journal Week 3

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Matthew K. Oki

  1. What is your comfort level when working with the bioinformatics tools during the in-class activity? What would increase your comfort level?
    • My comfort level for the bioinformatics tools that we used on the Week 3 assignment was fairly comfortable. However, I would say that without the direct guidance of the handout, I would’ve been very confused. Now, I feel as if I have a good grasp on how to use the tools.
  2. What was the easiest aspect of reading/understanding the Markham et al. (1998) article?
    • I think the easiest aspect of reading the paper was the concise formatting for sections such as the introduction, results, and discussion. These were worded well, and it was easy to follow. The fact that they could fit so much information into around 5 total pages without being confusing is a testimony to how concise the paper was.
  3. What was the most difficult aspect of reading/understanding the Markham et al. (1998) article?
    • The hardest part of the paper for me to read was the methods section of the paper. I didn't know about many of the methods when I read the paper. So, it was a very dense part of the paper with a lot of terms I didn't know.

Will Fuchs

  • What is your comfort level when working with the bioinformatics tools during the in-class activity? What would increase your comfort level?
    • I was really confused getting started and navigating through the different programs for the sake of the assignment but once I saw the big picture the different processes became much more digestible and simple to manipulate. In general, I'm not entirely comfortable yet but the rate of my improvement is comforting and ameliorates any fear of long term difficulty. What would improve my comfort level is a little more direction in regards to what the end goal is going to look like. I feel if I receive that I may learn faster.

  • What was the easiest aspect of reading/understanding the Markham et al. (1998) article?
    • I appreciated how succinct the article was. I really liked the nature of the study and terminology used. I also appreciated how the paper addressed confounding evidence found in a separate paper which broadened the scope of the study.
  • What was the most difficult aspect of reading/understanding the Markham et al. (1998) article?
    • The figures they presented in the paper were a bit difficult to comprehend. Understandably, my immediate comprehension isn't expected without participating in their field of work but even then the labeling was misleading and somewhat sparse.

William P Fuchs 20:52, 19 September 2016 (EDT)

Shivum Desai

  • What is your comfort level when working with the bioinformatics tools during the in-class activity? What would increase your comfort level?
    • I am pretty comfortable when it comes to using the bioinformatics tools that we used in class during week 3. They are slightly complicated but the directions in the handout we were given explained everything so that it was easily understandable.
  • What was the easiest aspect of reading/understanding the Markham et al. (1998) article?
    • The easiest aspect of this article for me was actually the methods section. I think the authors did a great job of breaking down each section of their experiment, while still explaining thoroughly how they performed each section.
  • What was the most difficult aspect of reading/understanding the Markham et al. (1998) article?
    • For me the most difficult part of this reading was understanding the dS/dn ratios because in the first place I had no idea what they were. Secondly, when they were discussed in the results portion of the paper I had a hard time keeping up with the acronyms dS, dN, and NS because they all sounded so similar when they were written out. Good thing it was only a small segment of the paper.

Shivum A Desai 21:04, 15 September 2016 (EDT):

User:ZacharyTGoldstein

  1. What is your comfort level when working with the bioinformatics tools during the in-class activity? What would increase your comfort level?
    • I feel pretty comfortable working with the bioinformatics tools. If we were to do tutorials before activities it might help with understanding the point of the activities so we are less focused on learning how to use the tools and better able to analyze what we are actually doing. A quick lesson on how to use the tools before we use them in an activity would go a long way.
  2. What was the easiest aspect of reading/understanding the Markham et al. (1998) article?
    • Reading the discussion of the paper before reading the actual article made it a lot easier to understand what was going on in the study. Also reviewing HIV in class before the article was assigned helped the reading process go smoother that it might otherwise have been.
  3. What was the most difficult aspect of reading/understanding the Markham et al. (1998) article?
    • The most difficult part of reading the article was analyzing the figures, especially table 1 which I have to present to the class. There is an overwhelming amount of data in this paper which shows that great research and detail was performed but I had to reread all of the figures, and the paper as a whole for that matter, many times before I began to understand anything.

Zachary T. Goldstein 17:12, 17 September 2016 (EDT)ZacharyTGoldstein


Matthew Allegretti

  1. What is your comfort level when working with the bioinformatics tools during the in-class activity? What would increase your comfort level?
    • My comfort level when working with the bioinformatics tools was moderate to low. I believe increased use of the tools would make me more comfortable. I was not comfortable because I was unaware of where to find various things, but after finding them, I believe I will have an easier time using the tools in the future.
  2. What was the easiest aspect of reading/understanding the Markham et al. (1998) article?
    • While the paper was pretty dense with information, it was still written in a concise fashion. The length of the paper made it much more approachable despite not fully understanding every aspect of it.
  3. What was the most difficult aspect of reading/understanding the Markham et al. (1998) article?
    • The paper was filled with very specific molecules and details about HIV that made it quite hard to conceptualize or comprehend what was being discussed in the paper.

Matthew R Allegretti 23:54, 17 September 2016 (EDT)

Courtney Merriam

  1. What is your comfort level when working with the bioinformatics tools during the in-class activity? What would increase your comfort level?
    • I was moderately comfortable. Learning to understand the online database and explore its nuances took a little bit of time, but once I got the hang of it, it did not present much of a challenge. It may have saved me some time if I had received prior instruction, but it’s not a significant issue. It’s almost kind of fun learning how to navigate and edit my openwetware page, it is something that I have so far not been exposed too. Prior experience with web design would’ve helped me in this area, but as I said, it’s exciting figuring things out.
  2. What was the easiest aspect of reading/understanding the Markham et al. (1998) article?
    • The easiest part of the Markham et al. (1998) article was understanding the overarching point of the article and how it relates to global HIV research and discovery. I understood in general what was going on by using context clues when various vocabulary words were grouped in conjunction to the point that it almost appeared a foreign language. But once I broke it down, I was able to picture in my head the individuals conducting the study, and it made the whole article a lot easier to get through.
  3. What was the most difficult aspect of reading/understanding the Markham et al. (1998) article?
    • What was difficult for me was getting through the methods portion of the article, where the actual weight of the scientific terminology was used. I’ve been around scientific language my whole life, but so many special terms were used that it was easy to get lost. Again, however, once I worked through it slowly and tried to understand each sentence before moving on to the next, the main points of the article revealed themselves.

Avery Vernon-Moore

  1. What is your comfort level when working with the bioinformatics tools during the in-class activity? What would increase your comfort level?
    • I was confortable. I think overtime I am using new software or generally speaking anything electronic it feels foreign for a bit. After I become a bit more familiarized I am usually fine. I think starting off some of the bigger parts of the assignment as a class in the beginning could help a little bit, but I know that could depend on what we are doing week to week.
  2. What was the easiest aspect of reading/understanding the Markham et al. (1998) article?
    • I honestly had a hard time with paper because I don't personally enjoy research. It doesn't appeal to me, I don't enjoy doing it, reading it, etc. The way it is written is hard to understand, especially when you weren't involved in the research and as a person who doesn't have much background knowledge or experience with the topic of the paper. Generally in scientific papers I seem to have the easiest time reading the methods section as it is simpler than the rest of the paper.
  3. What was the most difficult aspect of reading/understanding the Markham et al. (1998) article?
    • In general not knowing what it is talking about. I had to read it multiple times and I still feel like it is hard for me to grasp. The paper was just very in depth about HIV and I have never learned about it previously so I just couldn't fully comprehend the paper.

Avery Vernon-Moore 21:13, 19 September 2016 (EDT)

Colin Wikholm

  1. What is your comfort level when working with the bioinformatics tools during the in-class activity? What would increase your comfort level?
    • I felt comfortable working with the gene sequence analysis tools that were specified in the instructions. However, I would feel more confident if I had a better overall idea of how the entire program works. For example, I would like to know what tools other than ClustalW allow one to do with gene sequences. It might be useful to have access to more articles that use Biology Workbench for sequence analysis in order to get real-life examples of how this software might be used. On the other hand, I did appreciate that we were expected to somewhat "figure out" how to use the software independently. If feel that this is sometimes the best way to learn and retain procedural information because it often requires trial and error.
  2. What was the easiest aspect of reading/understanding the Markham et al. (1998) article?
    • The easiest aspect of reading/understanding this paper was the terminology that was used. For the most part, this paper used terms that I understood. Even for those words that I didn't understand completely (see above section), I could mostly understand the word in context. Although I don't have extensive background in microbiology, this article mostly made sense to me.
  3. What was the most difficult aspect of reading/understanding the Markham et al. (1998) article?
    • The most difficult component of understanding this article was visualizing/understanding all of the methods. Although I know what PCR is, the research group did not explain the specific types of PCR that they used. What is more, I did not recognize the software that were used, which primarily slowed the reading. Finally, some of the acronyms (ex dS, dN) did not make intuitive sense. It took some time to find what they stood for. Although most scientific words made sense, the lack of clarity made some parts of the reading more arduous or uninteresting.

Colin Wikholm 00:18, 20 September 2016 (EDT)


Anindita Varshneya

  • What is your comfort level when working with the bioinformatics tools during the in-class activity? What would increase your comfort level?
    • I was comfortable using the bioinfomatics tools during the in-class activity. I had difficulties finding the files associated with the paper and downloading that information as I didn't think it was incredibly intuitive, but after working with the NCBI website, I feel much more confident. My comfort level would increase if I had more practice maneuvering through the website. The instructions provided were fairly straight forward and were a great help in completing the activity.
  • What was the easiest aspect of reading/understanding the Markham et al. (1998) article?
    • The easiest aspect of reading/understanding the article was the methods section. For the most part, the methods section was incredibly descriptive, and aside from some PCR protocols mentioned, I was familiar with much of the methods used by the researchers.
  • What was the most difficult aspect of reading/understanding the Markham et al. (1998) article?
    • The most difficult aspect of understanding the article was putting together all of the different pieces and understanding the results of the outlier patients. In particular, it took a couple tries to understand why and how subjects 1, 9, and 15 were different from the other subjects as well as how those results affected the overall findings.

-- Anindita Varshneya 20:27, 19 September 2016 (EDT)


Mia Huddleston

  • What is your comfort level when working with the bioinformatics tools during the in-class activity? What would increase your comfort level?
    • I felt generally comfortable using the bioinformatics tools in class, as long as I am taught how to do each thing I can generally remember the steps to reproduce that result. More practice would increase m comfort level with the tools.
  • What was the easiest aspect of reading/understanding the Markham et al. (1998) article?
    • The introduction and the methods section were much easier to understand, although I had a difficult time understanding certain sections when there were terms I didn't understand, even after reading the definition of that term.
  • What was the most difficult aspect of reading/understanding the Markham et al. (1998) article?
    • Like I said above, some of the terms made it difficult to read, but I also though the discussion section was quite difficult as I did not understand when they referenced to other articles and experiments since I am still not completely familiar with this subject and only slightly familiar with what was talked about in this specific article.

Mia Huddleston 21:56, 19 September 2016 (EDT)

Jordan Detamore

  • What is your comfort level when working with the bioinformatics tools during the in-class activity? What would increase your comfort level?
    • I am starting to get my stride working with the tools. I can usually figure everything out. A list of all the notations on one succinct page could be useful.
  • What was the easiest aspect of reading/understanding the Markham et al. (1998) article?
    • I understood the flow of the experiment and what was actually going on.
  • What was the most difficult aspect of reading/understanding the Markham et al. (1998) article?
    • It was difficult to understand some of the terminology and the many processes that I had not heard of beforehand. It was easy to get lot in the words at times.
  • Jordan T. Detamore 00:26, 20 September 2016 (EDT):

Isai Lopez

  1. What is your comfort level when working with the bioinformatics tools during the in-class activity? What would increase your comfort level?
    • I feel fairly comfortable with the tools given to us in this class, the instructions seem clear on the packets. I think simply practicing and getting the syntax down would help the most to cut down on time spent trying to get comfortable with the material
  2. What was the easiest aspect of reading/understanding the Markham et al. (1998) article?
    • Having read many research articles before, the structure of the article is one that I'm very familiar and comfortable with. Therefore, engaging the material and knowing how the paper was structured was the easiest for me.
  3. What was the most difficult aspect of reading/understanding the Markham et al. (1998) article?
    • Many of the techniques and names of analysis practices were very unfamiliar to me, so when I read them I gained little from the passage. My only understanding was that the names had something to do with computing the data into figures that could be more easily interpreted.