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Eddie Azinge's Responses

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Cazinge (talk) 00:09, 3 October 2017 (PDT)

Arash Lari's Responses

  1. I think I'm best with Data Analysis, Visualization, and curation. I feel as though I acquired those skills by being a computer science student. The visualization and understanding of how to apply your input data to get your desired output is a huge part of computer science, so I feel that the more I code the more I've strengthened those skills.
  2. I'd like to better understand the ethics, intellectual property laws, and culture of practice because I feel as though I personally haven't had to abide by these standards and practices very heavily and I should better acquaint myself with them before entering the professional field.

Arash Lari

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments


Journal Entries:

Shared Journals:

ArashLari (talk) 20:15, 7 October 2017 (PDT)

Eddie Bachoura's Responses

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Mary Balducci's Responses

  1. The core competency that I'm most familiar with/ skilled in is probably Metadata. I think that I've gained familiarity with this by doing labs at school where every detail about data collected is important. I've learned that it's important to have as much information about the data as possible in order to fully understand the data itself. When doing experiments, every detail matters to make sure that the results are as trustworthy as possible. From this, I think I have some skill in making sure all details are known about the data I'm collecting. That said, I'm sure there are definitely aspects to this which I'm not good at and would be interested in learning more.
  2. A core competency that I'd like to become more familiar with is data preservation. I know that it is important to make sure the data is well preserved, otherwise it becomes useless. I'd like to know how to do this well, so that I can be sure that my data or someone else's data that I'm viewing is safe. I'm especially unfamiliar with data preservation in the world of computers, I do not know which ways are the best to save or protect data, so if I had important data I would not feel secure that I saved it accurately right now. This is why I'd like to become better at this.
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Mbalducc (talk) 18:32, 2 October 2017 (PDT)

Dina Bashoura's Responses

Week 5:

  1. The core competency I am most familiar with is data preservation I would say. I am familiar with this information because of the lecture that Dr. Dondi gave us regarding this topic during our Biological Databases class.
  2. I want to know more about Data Conversion and Interoperability because I feel that being able to transport data and changing its format to fit a format you would like is very useful when working with data. Learning what the standard data formats is also useful when coding because if others are using a standard method of formatting than I feel like I should know that standard method and implement it into my coding abilities.

Dbashour (talk) 22:06, 2 October 2017 (PDT)

Week 4:

  1. Yes, we coded in HTML for this assignment.
    • Yes, we used a standard library.
    • Yes I understand what Paul Ford meant by coders being "angry". From what the article says, coders are praised for their quick thinking and responding abilities, probably because it correlates to quick coding abilities. This also means that coders are quick to speak their mind about issues regarding coding like new languages and which language is better. Being outspoken in a quick manner often is portrayed as being angry over a topic, so in this sense, I can understand why Paul Ford said that coders are "angry".
  2. I would imagine the original version of the web had similar fundamental aspects to what the web is today, of course. The design of the web would be different back then because it was created initially to connect people and have a space of shared knowledge and ideas, whereas today this still holds true but was taken to an extreme. Today's web can interact and do much more than just be a space to share knowledge. I would say that today's web is worse than back then because so many people are on the web and because it is designed to be an open shared space, there is room for others to steal knowledge and now there are copyright issues that need to be taken into account. Also, the issue of privacy comes into play because almost everything involves the web now so there is more private information on the web meaning that there are more chances for others to access that information because of the design of the web being an open place that everyone can access.
  3. I liked the SGD website the best because of the clear organization and flow of information. Almost all of the information I needed for this assignment was on that page. The design of the page also made it easy to follow with the tabs on the left indicating the sections that the page contained. I found this page to be the easiest to follow and the most aesthetically pleasing. I would say that the NCBI was my least favorite just because it was the least useful for this assignment.
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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

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Dbashour (talk) 23:41, 25 September 2017 (PDT)

Blair Hamilton's Responses

Template:Bhamilton18 Shared Week 0

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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
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Bhamilton18 (talk) 21:41, 25 September 2017 (PDT)

Hayden Hinsch's Responses

Week 5

  1. I am most skilled in the discovery and acquisition of data core competency. Honestly all of these core competencies are fairly foreign to me, so I will have to admit that I developed my skills regarding the discovery and acquisition of data through the Week 5 assignment and the lectures presented in class.
  2. I would like to know more about data preservation. Anything to do with the technology of the data that people use everyday is extremely interesting to me. Hhinsch (talk) 22:38, 2 October 2017 (PDT)

Week 4

  1. Yes, my partner and I coded in the language: html. Yes html had a standard library which my partner and I used to write our html favorite gene page. I understood what Paul meant by stating that coders are "angry". I believe he is referring to the lack of filler words coders use, which helps them determine solutions more quickly to technical problems.
  2. Well I think that Tim Berners' World Wide Web has changed a whole lot and very little at the same time. It was incredible to read Berners' ideas on what the World Wide Web would become, knowing what it has turned into. I feel that his initial ideas and html made a platform for which everyone and anyone could build upon to make the web an awe inspiring massive place. The best part of the current web is the amount of information that is available and accessible to anyone with internet access. I think the amount of access points makes the web better than it use to be, as well as the constant improvement from users. I do think however that the size of the web could also be a crux. It is nearly impossible to create security throughout the entire web, nor regulate what goes on; sensitive information and behavioral patterns of users that is available on the web also makes it a potential threat to the safety and wellbeing of people all over the world(equifax!).
  3. Out of the four databases we used for this assignment I preferred SGD. It was the most visually pleasing, easily navigable, and contained all of the information about our favorite gene we needed to complete the assignment. Ensembl was my least favorite. Although it had the information we needed for the week 4 assignment, it wasn't that easy to find nor was it as visually pleasing as SGD.


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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

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Hhinsch (talk) 23:13, 25 September 2017 (PDT)

Nicole Kalcic's Responses

  1. Because of the assignment this week, I would say I am most familiar with Data Curation and Re-use. I read up on everything about The Monarch Initiative in order to complete the assignment. I feel like I have a good grasp of how curation is beneficial to scientific advancements in particular. Last week, the database research we did left me thinking that databases were usually just regurgitated information sourcing back to one main database. Now I see what different, smaller databases can provide, and I understand how much work is put into them through devoted institutions and individuals.
  2. I would like to know more about Ethics, including citation of data. The database I did my assignment on was forbidden by certain sources to license their work. There was no information on that, and while I'm sure it's a simple answer to those who understand ownership around intellectual property, I would be interested to know more. This is especially relevant to me because I am constantly citing data in this class each week. If I were to curate a small database of my own, I feel as if I would violate some sort of copyright or privacy concern.

Nicolekalcic (talk) 15:42, 2 October 2017 (PDT)


1. Based on what my partner explained to me during coding the page:

  • Yes, my partner and I coded in HTML for this assignment.
  • Yes, we used a standard library for this assignment.
  • Yes, I understood what Paul Ford meant. Coding is such a fast paced world that one must learn to be quick on their feet and entirely blunt in order to be apart of it and stay on top of their skill. A blunt individual is often regarded as rude or unthoughtful when engaging with others. Also, Paul Ford mentioned that those who code will specialize in one language, cling to it, and defend it to their death to some extent. The quality of being blunt, along with the stubborn view on coding languages could definitely create some angry people and a harsh work environment.

2. Today's web is very similar to Tim Berners-Lee's original version of The World Wide Web. Like he envisioned, it is accessible and free... which is pretty awesome, considering the internet is one of the main reasons our society functions at the level it does right now. However, there is so much more information available on the web than Tim Lee could have imagined. The internet is also more capable in today's reality. You don't go online and just view a webpage. You can watch movies, play multiplayer games, pay bills, etc. The internet can be great and it can be evil, but it sure is incredibly advanced.

3. I touched on this question when I was writing out the answers to the assignment this week and I was freshly done with research. I loved UniProt. Although SGD is a close second because of it's surplus of information, UniProt was user friendly and looked up to date with its layout and great use of color. I suppose it felt fun, to some extent. I really did not like NCBI Gene Database. It reminded me of this HUGE, clunky computer I used to have on my desk when I was 10. The display just felt very out of touch, old, and dull.

Nicolekalcic (talk) 00:14, 26 September 2017 (PDT)

Nicole Kalcic's Homepage


Assignment: Week 1 Shared Journal: Class Journal Week 1 Individual Journal: User Page

Assignment: Week 2 Shared Journal: Class Journal Week 2 Individual Journal: Nicolekalcic Week 2

Assignment: Week 3 Shared Journal: Class Journal Week 3 Individual Journal: Nicolekalcic Week 3

Assignment: Week 4 Shared Journal: Class Journal Week 4 Individual Journal: Nicolekalcic Week 4

Assignment: Week 5 Shared Journal: Class Journal Week 5 Individual Journal: Nicolekalcic Week 5

Assignment: Week 6 Shared Journal: Class Journal Week 6 Individual Journal: Nicolekalcic Week 6

Assignment: Week 7 Shared Journal: Class Journal Week 7 Individual Journal: NicoleKalcic Week 7

Assignment: Week 8 Shared Journal: Class Journal Week 8 Individual Journal: NicoleKalcic Week 8

Assignment: Week 9 Shared Journal: Class Journal Week 9 Individual Journal: Nicolekalcic Week 9

Assignment: Week 10 Shared Journal: Class Journal Week 10 Individual Journal: Nicolekalcic Week 10

Assignment: Week 11 Shared Journal: Not Available Individual Journal: Nicolekalcic Week 11

Assignment: Week 12 Shared Journal: Not Available Individual Journal: Nicolekalcic Week 12

Assignment: Week 14 Shared Journal: Not Available Individual Journal: Nicolekalcic Week 14

Assignment: Week 15 Shared Journal: Not Available Individual Journal: Nicolekalcic Week 15

Quinn Lanners' Responses

  1. Of the core competencies, I would say I am most skilled and knowledgeable in Databases an Data Formats. This past summer I had a position as a "Big Data Intern" during which I learned all about this topic. In fact, for about a full month all I was doing was writing queries to access a certain database within the company in order to format that data in a report-like layout. Along with learning how to write a successful query to extract the right data out of a database, I also learned all about the concepts of primary and foreign keys and how these play an important role in the structure of a database.
  2. I definitely want to learn more about data analysis and data visualization. Being that I ultimately want to go into some sort of data analytics career, I am incredibly interested in learning about all of the ways there are to effectively present data. While we can store all the data in the world, none of it means anything if there is no way to draw conclusions from it. And being that that is the ultimate goal of data analytics and visualization I am very excited to continue to learn more about this field. However, I also understand that in order to excel in those areas, a strong knowledge on the structure of databases and data in general is crucial.

Links:
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

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Qlanners (talk) 21:53, 1 October 2017 (PDT)

Arash Lari's Responses

1.

  • Yes we coded in HTML, which is a markup language.
  • Yes we used a standard library, which was HTML syntax with bootstrap for formatting.
  • Paul Ford says coders are angry because of a bunch of reasons. The world of coding moves so fast that in 18 months you can be obsolete.They're rewarded for quick thinking, this leads to people being blunt and specializing in their own field, which people will quickly cling too and proclaim the best. The mixture of these creates a culture of "angry" coders.

2. I think the author got the internet surprisingly well defined considering how long ago it was, but one thing I don't think he touched on was the paradigm shift of how the world uses the internet that we've gone through. Internet access is being a basic human right is a topic of debate within global communities and nowadays the internet is where some people go to school, go to work, and much more. It's much more a necessary part of life than the original author foresaw (which makes sense because that's more similar to how the internet was used and accessed in 1994).

3. Because my partner was more focused on the biological research of this assignment I referred to her experience and then checked out each of the website and agreed with her after I saw what she meant. The SGD database was definitely the most intuitive and the Ensembl website felt like it was designed for someone that was trained to use it, and not just for anyone that's curious.

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Arash Lari

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments


Journal Entries:

Shared Journals:

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ArashLari (talk) 18:36, 25 September 2017 (PDT)

John Lopez's Responses

Answers to the Questions

  1. Out of the competencies for scientific data literacy, I would say I am the most familiar with #2, Discovery and Acquisition of Data. I gained the skills of locating data repositories and finding data from general curiosity about data and investigating different databases. These location skills were refined through this class, in particular the ability to find biological data.
  2. I would like to know more about competency #10, Data Analysis. I feel like understanding this competency would be the most useful for obtaining a job in the ever growing field of data management. Out of these tools, workflow management would be the best to learn how to use.

Individual Journal Entries and Assignments

Class Assignments

Class Weekly Journal Entries / Project Weekly Journal Entries

My Page

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Johnllopez616 (talk) 22:43, 2 October 2017 (PDT)

Antonio Porras' Responses

  1. Which of these core competencies are you most skilled with (or which is most familiar to you)? Where and how did you gain the skills/become familiar? I would say I am most skilled with ethics, including citation of data. I became familiar with this core competency since the beginning of high school since my teachers emphasized how serious plagiarism can be in terms of research and publishing works. That being said, especially with data and information online, everything becomes public on the internet and available.
  2. Which of these core competencies do you want to know more about? Why? I would definitely love to be competent in all of the core competencies, however, I would definitely like to learn more about data analysis because I only have heard of the tools available to analyze massive amounts of data. Ultimately, I want to be more competent in this area to use in areas in which I would need to analyze data sets which would be impossible to understand without computers.
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Aporras1 (talk) 23:09, 2 October 2017 (PDT)

User Page: Antonio Porras

Emma Tyrnauer's Responses

  1. I think I am most familiar with the core competency of discovery and acquisition of data. Many of the classes I have taken at LMU have exposed me to the practice of supporting my experimental data and claims with what is already in the literature. Furthermore, my non-science classes have required me to support my claims with evidence from both primary and secondary sources.
  2. I want to learn more about the core competency of quality assurance and how it is carried out. I think that this is a very practical core competency that would be beneficial to anyone who plans to take data from outside sources.

Links

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

Signature: Emmatyrnauer (talk) 20:19, 2 October 2017 (PDT)

Zachary Van Ysseldyk's Responses

  1. Yes, for this assignment, I coded in HTML even though Bootstrap did most of the formatting. We must have used a standard library because if he used no standard library, the computer would not know how to interpret our new language. I think that I understand what Paul Ford is saying when he says that coders are angry. He describes the culture of coders which often lead to "anger." For example, many coders are very defensive and opinionted about their code which may lead to an argument. Even Paul Ford writes: "Coding is a culture of blurters."
  2. I think that there are similarities and differences when it comes to Tim Berners-Lee original vision for the World Wide Web. He denotes that the web will open up a new marketplace as well as open up a whole new way of communication. I agree with his vision in both of these aspects, however I got the sense that the World Wide Web was primarily meant for research and science. Of course this is not the case, everybody uses the Web. Overall, I think that the reality of Tim Berners-Lee's World Wide Web extended far beyond his vision.
  3. My favorite database was SGD. It was the easiest and most aesthetically pleasing website to use. The data was set up in a way so that I was able to easily navigate the page. My least favorite was NCBI. I did not like how unfriendly the website was for new users. I think that SGD is navigable without prior knowledge about genetics whereas NCBI requires some knowledge on what exactly someone is looking for.
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Zvanysse (talk) 12:36, 24 September 2017 (PDT)

Corinne Wong's Responses

  1. I feel most skilled with discovery and acquisition of data. In college, and even in high school, I received a lot of exposure to various resources and ways to find data through research, which gave me an understanding of how to search for reliable data. The repeated process of looking for sources that are of good quality and are relevant to my topic, whether it be science or English, was good practice, and the skills have stuck with me.
  2. I would be interested in learning more about data visualization. I can make simple graphs and tables, but I would be interested in learning more ways to display data and help create a visual understanding of its significance. I find that being able to see data in various forms rather than just numbers really helps me grasp the importance and meaning of what the data represents.

cwong34

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments

Journal Entries:

Shared Journals:

Group Project

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Cwong34 (talk) 21:49, 2 October 2017 (PDT)

Katie Wright's Responses

Template:Kwrigh35 Shared Week 0

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Simon Wroblewski's Responses Week 4

  1. Based on these readings:
    • Did you code in a language for this assignment?
      • Yes, I coded in HTML, CSS, and wiki for this assignment.
    • Did you use a standard library?
      • No, I believe I remembered all of the syntax we used in our webpage.
    • Do you understand what Paul Ford meant about coders being “angry?”
      • Yes, I think Paul Ford meant that coders think and speak on very efficient, quick, and sometimes harsh levels. However, when coders start sharing their thoughts at this level, they start to come to complex decisions faster, because they were able to process everyones opinions in a very efficient way. This characteristic (that most coders have) allows them to be quick and efficient, but also come across as rude and angry much of the time.
  2. How similar or different do you think Tim Berners-Lee’s original vision for The World-Wide Web is from today’s web? State ways where you think today’s web is better, and today’s web is worse.
    • In my opinion, I think Tim Berners-Lee did a great job at defining the web because his definition is still applicable today. The web is still open, free, and accessible; the same way Tim Berners-Lee foresaw it which I think would make him proud. Although some aspects have not changed, others have profoundly. The complexity of the web has definitely gotten more daunting since the time of Tim Berners-Lee. This complexity that the web procured over time has allowed for numerous advantages and disadvantages to occur. Disadvantages such as a vulnerability to identity theft, (or any theft of information for that matter). Although some complexities added more things to be wary of while online, these complexities were also the reason we can use applications like slack and amazon, which are just some of the advantages.
  3. Out of the four databases you accessed for this assignment (SGD itself, NCBI Gene Database, Ensembl, UniProt), which did you like the best, and why? Which did you like the least, and why? (Refer back to the question about differences in content or presentation that you noted on your gene's web page.)
    • I definitely liked SGD the best because it provided the most information about our gene's function, process, history, and other interactions. I would have to say Ensembl was my least favorite database that we used due to its text heavy presentation style.

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

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Simonwro120 (talk) 23:57, 25 September 2017 (PDT)

Simon Wroblewski's Responses Week 5

  1. Out of the listed competencies, I would have to say I'm most skilled and familiar with "Data Visualization". I would argue it is because I grew up with two parents as doctors who describe biological systems using vivid imagery, in addition to me being a naturally visual learner (as opposed to auditory or tactile kinesthetic).
  2. I'd like to learn more about "Data Analysis" because I love picking complex systems apart so that I may achieve a more full understanding of the world around me.

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

Signature
Simonwro120 (talk) 19:34, 2 October 2017 (PDT)

Links for Week

Week 0 Assignment

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