Difference between revisions of "Class Journal Week 7"

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==Emma Tyrnauer's Response==
 
==Emma Tyrnauer's Response==
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# At this point, while I don't feel as though I am completely lost in handling data diversity (more familiar compared to how I was at the beginning of the semester), I still don't feel very confident. If I were given data in one format, I would probably be able to recognize pieces of the data from material we have gone over in class and assignments thus far. However, unless I were given a large amount of time and access to help resources, I don't know if I'd be able to convert the data to a different format.
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#I don't think that there will ever be one true data format for biological databases because there are just so many that are used and some formats allow for better representation of specific data compared to others. In other words, not all data is the same so I don't know if it would be practical to have it all in the same format.
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#I definitely feel very out of my comfort zone doing coding and coming from a biological background. While using Wiki has become routine for me every week, I still feel kind of lost using the command line and html. Nevertheless, I find it very helpful that we are assigned homework partners each week in the opposite discipline to help compensate for any discrepancy.
 
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 15:19, 16 October 2017 (PDT)
 
[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 15:19, 16 October 2017 (PDT)
 
{{Emmatyrnauer}}
 
{{Emmatyrnauer}}

Revision as of 22:59, 16 October 2017

Zachary Van Ysseldyk's Reflection

  1. Coming from a more technical background, I do feel more comfortable with data diversity. I think that if I was given a certain data format and I had to change it, I would be able to find a way to do that. I think that the implementation of "sed" is a little confusing, but the concept itself makes sense to me.
  2. I think that there should be a universal data format for biological databases. I think that at some point there will be. This is not to say that the format of the data format cannot be altered, but I do think that one universal standard would be more efficient. Almost like how HTML is the standard web page language, one can alter and change HTML to read as wiki markup, however the foundation is HTML.
  3. I think I have gone beyond my comfort zone with this class in regards to biology. I have not taken biology since sophomore year of high school, so the biology side of it is very intense for me. I think that the biology readings are a little too intense. I know that we are college student and that there is a standard that we must uphold, however these academic biological journals are extremely difficult to understand. My understanding was that we would be exposed to the basics of computer science and the basics of biology, however these biological academic journals are so foreign to me I have to look up every other word. Other than that I think that this class definitely challenges me to get outside of my academic comfort zone.

Zvanysse (talk) 11:49, 15 October 2017 (PDT) Zvanysse

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments

Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 14

Individual Assignments

Zvanysse Week 1 | Zvanysse Week 2 | Zvanysse Week 3 | Zvanysse Week 4 | Zvanysse Week 5 | Zvanysse Week 6 | Zvanysse Week 7 | Zvanysse Week 8 | Zvanysse Week 9 | Zvanysse Week 10 | Zvanysse Week 11 | Zvanysse Week 12 | Zvanysse Week 14 | Zvanysse Week 15

Shared Journals

Zvanysse Week 1 Journal | Zvanysse Week 2 Journal | Zvanysse Week 3 Journal | Zvanysse Week 4 Journal | Zvanysse Week 5 Journal | Zvanysse Week 6 Journal | Zvanysse Week 7 Journal | Zvanysse Week 8 Journal | Zvanysse Week 9 Journal | Zvanysse Week 10 Journal | Zvanysse Week 11 Journal | Zvanysse Week 12 Journal | Zvanysse Week 14 Journal

Antonio Porras's Responses

  1. How confident do you feel at this point about handling this data diversity? If you were given data in one format, do you feel that you would be able to find ways to read this format or to convert the data to a different one? At this point in the class, I do not feel confident in handling the data diversity because there hasn't been enough time to have a confident fluency in data diversity. I think I definitely could figure it out with enough time but I likely am not as efficient as a computer science major would be.
  2. Do you think there will ever be “one true data format” for biological databases? Why or why not? I don't think there will ever be one true data format in the near future, but at the same time, there may be an completely new innovative way to format data right around the corner that could standardize biological database information.
  3. Considering your emphasis coming into this class (e.g., biology, computer science, etc.), how would you evaluate your exposure beyond your comfort zone so far? Is it too much? Too little? Just right? Any specific areas that you would like to encounter? As a student of biology, I would say my exposure to computer science has been far too fast for me to understand the more complex coding. For example, I look at the code and don't understand how the basics of the language like backslashes and why it closes a set of code. So if we had gone into basics more, then I would say my exposure would be about right. I would love to encounter how hackers are able to get information, similar to what has been happening with companies like Equifax.

Aporras1 (talk) 14:48, 15 October 2017 (PDT)

User Page: Antonio Porras

Assignments

  1. Week 1 Assignment
  2. Week 2 Assignment
  3. Week 3 Assignment
  4. Week 4 Assignment
  5. Week 5 Assignment
  6. Week 6 Assignment
  7. Week 7 Assignment
  8. Week 8 Assignment
  9. Week 9 Assignment
  10. Week 10 Assignment
  11. Week 11 Assignment
  12. Week 12 Assignment
  13. Week 14 Assignment
  14. Week 15 Assignment

Individual Journal Entries

  1. Week 1
  2. Week 2
  3. Week 3
  4. Week 4
  5. Week 5
  6. Week 6
  7. Week 7
  8. Week 8
  9. Week 9
  10. Week 10
  11. Week 11
  12. Week 12
  13. Week 14
  14. Week 15

Class Journal Entries

  1. Class Journal Week 1
  2. Class Journal Week 2
  3. Class Journal Week 3
  4. Class Journal Week 4
  5. Class Journal Week 5
  6. Class Journal Week 6
  7. Class Journal Week 7
  8. Class Journal Week 8
  9. Class Journal Week 9
  10. Class Journal Week 10

Team Page

  1. JASPAR the Friendly Ghost

Individual Assessment and Reflection

  1. Individual Assessment and Reflection

Corinne Wong's Responses

  1. I’m still intimidated, but I definitely feel more confident. If I was handed some random data, I would probably just stare at it blankly at first. However, I would feel comfortable breaking it down and looking up what I don’t understand to help me interpret it.
  2. I feel like it would be very convenient, but because the coding formats are always changing and evolving, it may not be likely. There will always be a more preferred data format for certain things and processes, so having one would not necessarily be convenient for everyone.
  3. As a biology major, I have learned a lot about data and coding that I never though I would know before. There are some points where I feel way out of my expertise, but eventually it starts to make sense, so I’m still learning. I enjoy the new exposure because I have a new understanding of coding and data that I can use in my future or everyday when I use the internet.

Cwong34 (talk) 23:04, 15 October 2017 (PDT)

cwong34

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments

Journal Entries:

Shared Journals:

Group Project

QLanners Responses

  1. At this point in the course, I would say I feel relatively comfortable working with different data formats. While I would not trust myself to teach these concepts to someone else, as I am not very strong with the correct terminology and all of the nuances to it, I do feel given the tools I have learned in this class (and have previously learned) I could read and convert this data. It would probably just take me a few attempts to get it right.
  2. While one universal data format would incredibly convenient, I do not actually think it will ever happen. There are already so many different data formats out there available, and there are more being made all of the time. And since each data format comes with its own advantages and disadvantages, there is always going to be certain people that prefer certain formats. And this differing in opinions on which format is superior will always lead to people utilizing different formats.
  3. While I had a bit of background in both biology and computer science coming into this course, I still feel this course has explored areas that I was not exposed to it either. The concept of genomics and biological databases was something that I had never learned about in any of my life science courses (as I have yet to take genomics), so studying that area has definitely been new and interesting. And as for the computer science, all of my knowledge is self-taught, so I have enjoyed learning in a more structured approach that is ensuring that I understand the concepts we are working in. Plus I had never used HTML before so it was nice to get some exposure to that as well. If anything I would enjoy a bit more content on the nitty-gritty of the data formats and how to best work with data, but probably would need to take a comp sci to have enough time to devote to that.

Qlanners (talk) 12:44, 16 October 2017 (PDT)
Main Page
User Page
Assignment Pages: Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 14 | Week 15
Journal Entry Pages: Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 14 | Week 15
Shared Journal Pages: Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10
Group Project Page: JASPAR the Friendly Ghost

Edward Bachoura's Responses

  1. Yes. Not sure how much of that confidence has come from this class and how much has come from GRNsight, but in this past year or so, I have become much more confident in my understanding of the different data formats that I've been working on. And through GRNsight, I also feel comfortable enough that I would be able to convert one format to another.
  2. No. For the same reason there won't ever be one universal grocery store. There are a lot of formats out right that are competing with each other and it doesn't seem probable that one will be the others out and become the "one true data format."
  3. I feel that I am being exposed to more biology than I would've hoped. I was happy to join this class to learn about databases and such, but I was never really excited about the biology side. It feels like I am being pushed to have to learn bio just to finish some of the assignments, but I was hoping that wouldn't be the case.

Ebachour (talk) 14:40, 16 October 2017 (PDT)

Katie Wright's Response

  1. I feel relatively confident in handling the different types of data that we have encountered in class. Some of the formats are more familiar to me because I have used them in class before (such as .csv and FASTA.) I believe I could figure out how to view almost any type of data, whether that means trial and error with different software, converting the file format to something I am more comfortable with, or even doing an internet search for help.
  2. I don't think there will ever be "one true data format" for databases. This is primarily because I think restricting databases in that sense would impede the development of better file formats. I also think it would be nearly impossible to convince every scientist to agree on the same file format. I believe if a regular database user has a file type preference, she or he would cause quite an uproar if s/he were told to stop using it.
  3. As someone from more of the biology side of things, I think I have been exposed to just the right amount of computer science. I feel that I am learning a lot about coding, and while I am not comfortable with everything we are doing, I think that it's a good thing. If I weren't uncomfortable, that would probably be a sign that I wasn't being challenged enough.

Kwrigh35 (talk) 14:50, 16 October 2017 (PDT)

Simon Wroblewski's Reflections

  1. I feel confident in some ways and intimidated in others. I believe that if the format was fairly well known, I'd be able to read it and reformat it, depending on the time and research available to me.
  2. I would guess no. This is because I would guess that some data formats are better suited for some biological information than others. Due to this reason, I don't think scientist would sacrifice the quality of efficiency of their data just so that they could uniform its format.
  3. So far, I'd say its been pretty good. I'm a CMSI major and a Bio minor so this class is familiar to me. That being said, I'm still a novice in respects to both biology and computer science, especially because I just recently changed my major; which results in a lot of re-learning.

Simonwro120 (talk) 15:07, 16 October 2017 (PDT)

List of Assignments

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14 Week 15

List of Journal Entries

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14 Week 15

List of Shared Journals

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14 Week 15

Emma Tyrnauer's Response

  1. At this point, while I don't feel as though I am completely lost in handling data diversity (more familiar compared to how I was at the beginning of the semester), I still don't feel very confident. If I were given data in one format, I would probably be able to recognize pieces of the data from material we have gone over in class and assignments thus far. However, unless I were given a large amount of time and access to help resources, I don't know if I'd be able to convert the data to a different format.
  2. I don't think that there will ever be one true data format for biological databases because there are just so many that are used and some formats allow for better representation of specific data compared to others. In other words, not all data is the same so I don't know if it would be practical to have it all in the same format.
  3. I definitely feel very out of my comfort zone doing coding and coming from a biological background. While using Wiki has become routine for me every week, I still feel kind of lost using the command line and html. Nevertheless, I find it very helpful that we are assigned homework partners each week in the opposite discipline to help compensate for any discrepancy.

Emmatyrnauer (talk) 15:19, 16 October 2017 (PDT)

Links

  1. My User Page
  2. List of Assignments
  3. List of Journal Entries
  4. List of Shared Journal Entries
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