Class Journal Week 3

From LMU BioDB 2017
Revision as of 03:44, 20 September 2017 by Bhamilton18 (talk | contribs) (Fixed a typo)
Jump to: navigation, search

Eddie Azinge's Responses

  1. Pull out a quote from the first two sections of “What is Code?” that you think directly relates to what you experienced in the individual portion of this assignment. Explain why this quote is particularly resonant for you.
    • "Every character truly, truly matters. Every single stupid misplaced semicolon, space where you meant tab, bracket instead of a parenthesis—mistakes can leave the computer in a state of panic." - Paul Ford's "What is code?", Section 2.3
    • This quote specifically resonates with me from this homework assignment, specifically the bit about 'every single stupid [...] bracket instead of a parenthesis.' At the tail end of the assignment, when I was transforming the raw curl'd output into a neatly formatted version, I had made the mistake of using a pair of brackets instead of a pair of parenthesis in the grep regex `<(BR|PRE)>`, and vice versa in the sed regex `s/<[^>]*>//g`. This lost me a good chunk of time, as I couldn't figure out what other part of my command would have been wrong. It was only after I had thrown my regex into an evaluator that I realized that I had confused their definitions, and my code finally worked. Ford's comment about every character truly mattering resonated quite a bit with me after that.
  2. What do you think you need in order to grow more comfortable, confident, and effective with the command line and manipulating data at a “raw” level?
    • All I believe I need is more practice interfacing with the command line and with data. Until recently, I haven't needed to use the command line in order to generate and format data, but if I were to work on more projects that require the functionality of retrieving data from some remote server, then I believe that necessity would force me to become more effective with the command line and manipulating data at a “raw” level.
Cazinge (talk) 14:28, 16 September 2017 (PDT)

Corinne Wong's Response

  1. "There are 11 million professional software developers on earth, according to the research firm IDC. (An additional 7 million are hobbyists.) That's roughly the population of the greater Los Angeles metro area ... There are programmers for everything. They have different cultures, different tribal folklores, that they use to organize their working life." This quote stood out to me because I knew coding was up and coming, but it really put it into perspective for me. There are a lot of people that code in the world. Moreover, for a lot of them it's not necessarily their profession. This really allowed me to see how much coding is a part of our daily lives and how anyone is capable of doing it, whether it's for their job or to help simplify their lives. Similar to this class - a lot of us are biologists who likely had no intention of coding in our careers, but here we are. Not only are we doing it, but we can also see how code is involved in biology and how it has shaped our field and the tools we use.
  2. I think I need more practice. It seems to require a lot of knowing certain sequences and commands that I do not. Once I start practicing more, learning new commands, and frequently using them, I'll be able to remember the codes and be more comfortable and confident with my skills.

Cwong34 (talk) 18:16, 16 September 2017 (PDT)

cwong34

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments

Journal Entries:

Shared Journals:

Group Project


Mary Balducci's Responses

  1. "Thinking this way will teach you two things about computers: One, there’s no magic, no matter how much it looks like there is. There’s just work to make things look like magic. And two, it’s crazy in there." This quote resonated with me because while doing the experiment, I found myself thinking a lot about what's going on behind the scenes whenever I use a computer. By using the curl code, I could have a sequence of DNA translated just like putting it into a website and hitting the submit button would do it. This is cool because I went from having no idea how forms on websites worked, to knowing how to use a code to do the same thing. Not knowing how they worked, computers have always seemed sort of magical, like something I could never understand, but now I have a slightly better understanding of how it all works.
  2. In order to be more comfortable, I think I need a lot more practice, and more information on structuring commands and how and when to use certain codes.

Mbalducc (talk) 19:07, 17 September 2017 (PDT)

Zachary Van Ysseldyk Responses

  1. The quote "A programming language is a system for encoding, naming, and organizing algorithms for reuse and application." resonated with me because, like other languages, it is a form of communication. Furthermore, both verbal and programming languages follow a unique set of rules that must be followed in order to make sense. The part that I really thought was thought provoking was the programming languages are systems for reuse and application. It is interesting that the computer science community is very open about their work. Reuse and application is encouraged, not frowned upon. Regarding this assignment, I was thinking how all I was doing was communicating to the computer to do something. I was using a programming language, not just typing in characters.
  2. I think that more practice will help me to be more comfortable with the command line of course. I also think that knowing where to look and how I want to go about it will help. Understanding how to go about the problem I think is half the battle, and I think that I struggle with that.

Zvanysse (talk) 20:56, 17 September 2017 (PDT)

Emma Tyrnauer's Responses

"Every character truly, truly matters. Every single stupid misplaced semicolon, space where you meant tab, bracket instead of a parenthesis—mistakes can leave the computer in a state of panic."
  1. I found this quote particularly resonant with me because I found myself making a lot of mistakes in misplacing characters, or forgetting them all together. I would wonder why my code was't working and after re-checking, I would find a silly mistake.
  2. I think that I need to have a good foundation of memorized commands because I find myself having to look up a lot of things. It's in the process of using syntax for new commands that I end up making a lot of mistakes. I guess this is just all part of the process though!

Emmatyrnauer (talk) 09:11, 18 September 2017 (PDT)

Links

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

Arash Lari's Responses

  1. I think this quote resonated me the most: "Every month it becomes easier to do things that have never been done before, to create new kinds of chaos and find new kinds of order. Even though my math skills will never catch up, I love the work. Every month, code changes the world in some interesting, wonderful, or disturbing way." I've felt that on the assignment because the longer I worked towards a solution the more I felt I could do. However it really resonated with me because it's how I've felt since starting computer science about 4 years ago. I was always tech savvy but never really had any experience coding when I first started and everything seemed so daunting, and that feeling didn't stop at any point, but every class I passed and assignment I completed made me feel like I could do that much more than I used to be able to do. Now I work on tons of extracurricular coding stuff that I never thought I'd be capable of and it's all just from practice and persistence,
  2. Going off of my last response, I think the biggest thing is practice. I just need to create different types of challenges for myself and try to do new things in bash, just like how I learned every other programming language. Failing and trying again are the key to learning programming in my opinion.

Arash Lari

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments


Journal Entries:

Shared Journals:

Quinn Lanners' Responses

  1. The quote I chose from the reading was: “The reason I’m showing it to you is so you can see how every character matters. Computers usually “understand” things by going character by character, bit by bit, transforming the code into other kinds of code as they go.” (Ford, 2015, Section 2.3). This quote resonated with me, as I experienced a great amount of frustration in the process of writing my command for the retrieval of the raw data from the ExPASy website due to a typo of one small quotation mark. I was completely convinced that my code was correct and was unable to figure out why it was not functioning properly. Finally, after trying to make several other modifications to my command promt, I realized that it was a simple out of place quotation mark that was causing the problem. This speaks to the fact that every character matters when writing code. A computer has no way to assume that typos were simply mistakes, and thus is unable to perform the desired function unless the code is inputed perfectly character for character.
  2. To become more comfortable with the command line and manipulating data at a raw level, I could use knowledge of more available functions and syntax to operate these functions. Once I know the functions and syntax better I can work on learning ways in which these functions and syntax can be effectively used together. In essence, I could use much more practice with the command line. When it boils down to it, to become better at any kind of coding language, practicing with the code appears to be one of (if not the) most effective way to do so.

References: Ford, P. (2015). What is code?. Bloomberg. Retrieved from: https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/

Qlanners (talk) 10:54, 19 September 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 Response

"Many algorithms have their own pages on Wikipedia. You can spend days poking around them in wonder."
  1. This quote stood out to be because when I am coding, I find myself spending a lot of time scouring the web for the best possible algorithm to achieve the desired task. For this assignment, I found myself in a similar situation because I was using Curl, which I didn't know very well, so I spent a lot of time looking through the modifiers trying to find one that would achieve what I needed for that curl call.
  2. Time with exercises and examples. I find myself learning best when I am learning when I have time to work through exercises and examples on my own, and through this experimentation, I can better learn how that system works.

Ebachour (talk) 11:36, 19 September 2017 (PDT)

Dina Bashoura's Response

“My people are split on platform,” he continues. “Some want to use Drupal 7 and make it work with Magento—which is still PHP.”
  1. This quote perfectly explains what I thought about this weeks journal--it was a completely foreign language. This was the first time I have ever used a command line, so naturally I had a bit of trouble catching along. "sed", "grep", "bash" are all words I have never used or even heard of before this class. Doing the homework this week was like trying to take a quiz in Dutch with only the dictionary as my guide. But with the help of the instructions and my partner, I was able to complete the assignment and develop a better understanding of the command line and what the language is like.
  2. With more exposure, practice, and some research, I believe that I will become more confident in my ability to code. Going to office hours to clarify questions will also help elucidate my confusion and allow me to succeed.

Dbashour (talk) 13:14, 19 September 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

Blair Hamilton's Response

  1. Pull out a quote from the first two sections of “What is Code?” that you think directly relates to what you experienced in the individual portion of this assignment. Explain why this quote is particularly resonant for you.
    • "Which is to say I’m not a natural. I love computers, but they never made any sense to me. And yet, after two decades of jamming information into my code-resistant brain, I’ve amassed enough knowledge that the computer has revealed itself."
    • This quote perfectly describes both this assignment and how I feel about programming. I have always been fascinated by the puzzles and the secrets that programming has to offer, and like this week, it takes time to learn and explore every possibility. While looking at ways to take all the "junk" from the curling project I was fascinated by the symbols and ideas behind each stroke of the keyboard. While at first, like in high school, I am very overwhelmed and confused by programming I quickly collaborate and explore the possibilities and realize my true potential every computer project I turn in. This particular quote reminds me that although I am not a computer science major I work hard and "jam information into my code-resistant brain" and figure it out. Much like Paul Ford's experience I can now safely say I understand when another programmer/coder is talking and not sound too ignorant.
  2. What do you think you need in order to grow more comfortable, confident, and effective with the command line and manipulating data at a “raw” level?
    • Practice. Like everything the command line is just another obstacle that requires a bit of familiarity before becoming efficient and confident. My previous experience with the command line has not been as thoroughly presented as this class has allowed for, which makes this experience much better. In the past I was just typing letters and dashes hoping for the best. With practice and familiarity manipulating data will come more naturally.

Bhamilton18 (talk) 20:44, 19 September 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
Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2017/index.php?title=Class_Journal_Week_3&oldid=1520"