Class Journal Week 7

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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

Arash Lari's Reflection

  1. As a computer science student, I feel pretty confident with data diversity. Any commonly used format has a lot of documentation online that tell you what applications are needed to read them, and if it's the case that I'm writing a database for various different formats, it doesn't matter to me what the files themselves are, just how they're stored in the database.
  2. It would be convenient if there was a universal file format for biological databases but I don't think that can happen because although I haven't studied very much biology, I find it hard to imagine that there would be any one uniform way of representing data that would be best for all the types of data you can retrieve from biological organisms. For example, I would want information about the configuration of the molecules in an organism to be in a different file format than the DNA sequence of that organism.
  3. I think I've ventured far out of my comfort zone in terms of the biology part of class. Much of the biological information in class went over my head and I really had to read a lot to try to catch up with the class. The readings are also not the kind of articles I'm used to reading so they were hard to adjust to at first as well. The timing of the assignments has been something I've been trying to adjust better to as well.

ArashLari (talk) 23:37, 16 October 2017 (PDT) Arash Lari

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments


Journal Entries:

Shared Journals:

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 class 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

Blair Hamilton's Response

  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?
    • Although I feel more confident than at the beginning of the semester, I still feel a bit overwhelmed by data format and information. Looking at the data bases such as Ensembl or NCBI however colorful and organized, I still find the information bit daunting. I find that converting data would be much easier for me than being able to read and interpret the information.
  2. Do you think there will ever be “one true data format” for biological databases? Why or why not?
    • No unfortunately because some data looks better in certain formats that others. By this I mean if you needed a certain graph, but JSON looks better than xml you would use JSON even if xml is the standard. Also, many scientists are stubborn and would refuse to change to something they are not comfortable with.
  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?
    • This class has definitely taken me outside my comfort zone in terms of Biology. Although unfamiliar, the Biological aspect to the class has come at just the right pace. Ideally I would like to encounter more computer science elements in terms of webpages and database integration. Homework assignments like Week 4 and 7 have definitely been the most interesting to me.

Bhamilton18 (talk) 16:49, 16 October 2017 (PDT)

Category Links
User Page Blair Hamilton
Weekly Assignments Bhamilton18 Week 2   Bhamilton18 Week 3   Bhamilton18 Week 4  Animal QTL  Bhamilton18 Week 6  Bhamilton18 Week 7  Bhamilton18 Week 8  Bhamilton18 Week 9  Bhamilton18 Week 10  Bhamilton18 Week 11  Bhamilton18 Week 12  Bhamilton18 Week 14  Bhamilton18 Week 15
Weekly Assignment
Instructions		 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
Class Journals Class Journal Week 1   Class Journal Week 2   Class Journal Week 3   Class Journal Week 4   Class Journal Week 5   Class Journal Week 6   Class Journal Week 7   Class Journal Week 8   Class Journal Week 9   Class Journal Week 10
Final Project Lights, Camera, InterACTION!  Lights, Camera, InterACTION! Deliverables

John Lopez's Responses

  1. I feel relatively okay with handling data diversity simply because I have only been exposed to common formats of data, like XML and JSON. Furthermore, to my knowledge, because these are pretty much the standard formats that most people use, I know that it's possible to learn how to use them by following online documentation, resources, and perhaps forums.
  2. I do not believe that there will be just one format for biological databases because each format serves a particular use. The developers of the databases will use whatever method necessary, whether it be XML or JSON, to fulfil whatever requirements they need for the project.
  3. I would say that the exposure to biology is slightly out of my comfort zone only because my knowledge of it is so limited. I've noticed that even some biology majors do not fully understand the work we have to perform, meaning that this material is beyond what even they have learned. However, in terms of CS, I am comfortable with what we are doing because of the practical applications of it in terms of obtaining a job. I believe that the skills I learn in this class will help me obtain an internship managing data well before some of the other CS majors of my age because of what I know.

Johnllopez616 (talk) 21:34, 16 October 2017 (PDT)

Individual Journal Entries and Assignments

Class Assignments

Class Weekly Journal Entries / Project Weekly Journal Entries

My Page

Eddie Azinge's Responses

  1. I feel extremely confident about handling diverse quantities of data, If I was given data in any specific format I have full confidence that I'd be able to find a way to read it / convert it into something useful given the situation.
  2. I do not believe that there'll ever be "one true data format" for any specified system in general, let alone biological databases. The data format is tailored to the most common use cases given the data itself; with the advent of new technologies, techniques, and biological findings, we'll eventually discover more efficient formats for data, and evolve along with the respective field.
  3. I feel like I'm not really that far outside of my comfort zone. The computer science has stayed close to home and the Biology hasn't really been too difficult to grasp, I would refrain from saying that my exposure beyond my comfort zone is "just right" though. I feel like while it's good for me to have a rough understanding of the biology going on behind the scenes, the only thing that I've remained interested in has been the computer science layer surrounding it all. If I could be educated more so on Biological Databases from a predominantly Computer Science standpoint rather than a general half/half Comp Sci - Biology standpoint, I'd be more than attentive.

Cazinge (talk) 22:50, 16 October 2017 (PDT)

Mary Balducci's Responses

  1. I feel somewhat comfortable handling this data diversity. But, I still feel like I need more practice. I think if I was handed data in one format, I might be able to find ways to convert or read it, depending on the original format. I do think I'd do better at it now than at the beginning of the semester.
  2. I don't think there'll ever be one true format for biological databases. I think this because of the wide range of different formats, which all have some slight advantages. I think it would be difficult to create just one format that has all the advantages and none of the disadvantages of the current ones. i don't think it would be possible to make one that works for every possible need.
  3. I'd say that my exposure beyond my comfort level is about just right. I was worried coming into the class that I'd be overwhelmed by the computer science, but the structure of the class helps. It helps to be given walkthroughs of what we're doing and to have homework partners who are already knowledgeable. I think I'd like more practice with the command line and putting commands together.

Mbalducc (talk) 22:06, 16 October 2017 (PDT)

Hayden Hinsch's Responses

  1. I feel fairly confident in handling data diversity. I definitely need some more practice, especially when invoking commands in the terminal. I can usually troubleshoot and embark on a series of trials and errors to get the correct answer or the results I want, but still have trouble understanding why what I tried worked. I am definitely getting more comfortable and competent as time goes on.
  2. I'd really hope that there will be one "true" data format. I suppose that it is the nature of life that there will always be conflict, so I doubt there will ever be one "true" data format. It would be really nice if we could standardize the data formats, but different people like different things so I don't think it will ever happen. There are many different ways to cite things:APA, MLA, Chicago to name a few, but we still find different reasons for using different citation at different times. Maybe in the very far future data will be standardized, but due to the nature of people, I doubt it will.
  3. I just transferred to LMU this semester from a community college, so I would say that almost all of this class is pretty much foreign to me. Although it is not necessarily comfortable, I do enjoy the challenge. I do definitely need a more firm understanding of the molecular biology portion of the class; a lot of it is foreign to me and I'm afraid I might miss something altogether. I sometimes feel that it is too much, but remain determined to learn. I would definitely like to encounter more of a broad idea of what our class is working towards; I enjoyed hearing that we would be contributing to grnsight.

Hhinsch (talk) 22:30, 16 October 2017 (PDT)

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
Week 15

Hayden's Individual Journal Entries

hhinsch Week 1
hhinsch Week 2
hhinsch Week 3
hhinsch Week 4
hhinsch Week 5
hhinsch Week 6
hhinsch Week 7
hhinsch Week 8
hhinsch Week 9
hhinsch Week 10
hhinsch Week 11
hhinsch Week 12
hhinsch Week 14
hhinsch Week 15
Page Desiigner Deliverables Page

Class Journal Entries

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

Electronic Notebook

Hhinsch Electronic Notebook

Hayden's User Page

Hayden Hinsch

Dina Bashoura's Responses

  1. I feel semi-confident that I would be able to handle this. I would not say that I would know how to do so without trouble, I would definitely go through a process of trial and error and perform outside research to understand what I'm doing and what to do next, but I'm confident that I would eventually find a way.
  2. I do believe that eventually there will be one "true" data format. Just like how I believe language will eventually, over probably a few hundred years, will evolve to just one universal language because of the need for a dominant language out of ease and accessibility. Unlike language, it might not take as long for there to be one dominant data format because of the advances in technology and the demand that it calls for.
  3. I would say that I was definitely pushed beyond my comfort zone with this class. I have never taken a class anything remotely close to computer science so this class is all new information for me. I am learning a lot of coding skills that I most likely will not use in the future at all but I am a strong believer that no knowledge is wasted knowledge.

Dbashour (talk) 23:41, 16 October 2017 (PDT)


Dina Bashoura

Biological Databases Homepage

List of Assignments

List of Individual Journal Entries

List of Shared Journal Entries

List of Final Assignments

List of Team Journal Assignments

Nicole Kalcic's Responses

  1. I feel confident in the sense that I may not be able to 100% of the time know how to read or convert the data, but I would be able to quickly find the resources that would help me/guide me if I got stuck and proceed with ease from there.
  2. It would be convenient for most of the world if there was one true data format, but for those who know the ins and outs of data, one true data format wouldn't make sense. Different formats provide different advantages, and I can't see all of those advantages being combined into one form.
  3. Out of everyone in this class, I probably am the furthest from computer science/biology in terms of my major (studio arts). I think I have been pushed was outside of my comfort zone, but I usually take that as a good thing, and it has been an interesting challenge to complete the assignment each week. I like when I work with a partner on an assignment such as the one we had this week, because I get to talk extensively with someone outside of class about the work, but I am also held accountable for my half of the project. I definitely enjoy the computer science side of things more, just because I feel accomplished when I understand/complete something under that belt. I studied very basic biology in high school, but this has been my first encounter with computer science, and I am intrigued to pursue knowledge outside of the classroom.

Nicolekalcic (talk) 01:29, 17 October 2017 (PDT)

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