Difference between revisions of "Class Journal Week 5"

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Class Journal Week Five

Tauras, Lena, and Miles

Database: TFClass

Database Webiste: TFClass

Hilda and Mitchell

Database: Protogen

Link to Website: [Protogen]

Link to Presentation: File:Protegen.pdf

1. Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?

The twelfth core competency would be the most familiar concept that I can relate to since as a student I've had to learn about citing data in my essays or in projects.

1. Which of these core competencies (if any) did you gain a deeper understanding of by doing this exercise? What about the exercise taught you about them?
2. Which of these core competencies (if any) do you want to know more about? Why?

HDelgadi (talk) 20:54, 3 October 2013 (PDT)

Alina, Stephen

Database: OrganelleDB
Website: [1]

Reflection (Alina)

• Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
  

I was familiar with the ethics competencies, having taken science and engineering ethics one semester, where there was a huge focus. It is a topic highly stressed in most scientific settings.

• Which of these core competencies (if any) did you gain a deeper understanding of by doing this exercise? What about the exercise taught you about them?
  

'Databases and Data Formats' and 'Discovery and Acquisition of Data' were greatly improved, as we were forced to navigate different databases and find answers to questions about them. Looking at different kinds of databases gave me a better knowledge of what kind of information storage is actually available.

• Which of these core competencies (if any) do you want to know more about? Why?
  

'Quality Assurance' seems like something I would interested in learning more about, specifically being able to recognize flaws in data sets, etc.

Ajvree (talk) 21:39, 30 September 2013 (PDT)

Reflection (Stephen)

• Prior to this class, I was already familiar with Databases and Data Formats, Discovery and Acquisition of Data, Data Analysis, Data Visualization, and Ethics, including citation of data. Most of these skills were introduced to me when I took freshman biology lab. These skills were further developed when I started doing independent research and was presenting at conferences.
• This exercise helped enforce the aforementioned competencies. In addition, I am more well attuned to Data Curation and Re-use and Cultures of Practice after this exercise. Doing research on how the research is synthesized and made available was a very different experience for me and helped introduce me to these core concepts.
• Quality Assurance and Metadata are two competencies I feel I should improve upon. Both competencies are a bit confusing to me, but I believe they would be very helpful with the independent research I am doing. At the very least, I'll be continously be dealing with biological databases for a while.

Slouie (talk) 02:51, 3 October 2013 (PDT)

Katrina Sherbina and Gabriel Leis

• Database: PrePPI
• To use the database, go to the following link: PrePPI

Gabriel Leis: Response to Reflect Questions

Katrina Sherbina: Response to Reflect Questions

Lena Hunt

1.) Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?

• I think I was fairly familiar with 1 (Databases and Data Formats) because I have used a few databases in other classes and understood how to search them, 11 (Data Visualization) because my cell function class used data visualization a lot to show how proteins work, and 12 (Ethics) because, as a college student, we are constantly reminded to cite our sources and not to steal information.

2.)Which of these core competencies (if any) did you gain a deeper understanding of by doing this exercise? What about the exercise taught you about them?

• I am not sure that I have gained a significantly greater understanding of any of these. The lecture materials helped, but databases are still pretty mysterious. I maybe understand 2 (Discovery and Acquisition of Data) better because of all the various databases I looked at in the Uniprot exercise.

3.)Which of these core competencies (if any) do you want to know more about? Why?

• I would like to know more about 4 (Data Conversion and Interoperability) because I think it is important when working with data to be able to use that data in various format. Of course, I am sure all the items in the list are useful to know more about as well.

Lena (talk) 17:37, 26 September 2013 (PDT)

Lauren Magee & Dillon Williams

• Database: GeneDB

Lauren Magee: Reflection Questions

1. Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
   • I was pretty familiar with all of these competencies before taking this class, because I was involved with a freshman research lab dedicated to building up phage databases. In the lab, we sequenced the genome of a phage that had been isolated, by one of our peers, from a soil sample on campus. We then inserted this information into the phage database and related it to others that may have already been found and sequenced.
2. Which of these core competencies (if any) did you gain a deeper understanding of by doing this exercise? What about the exercise taught you about them?
   • I thought more about the “Ethics” competency during this exercise, because I had never thought to look at who contributes to these databases and who modifies them. Databases always seem to be so public that I assume no one owns the right to them, but from answering the questions above, I realized all that goes into the management of the database.
3. Which of these core competencies (if any) do you want to know more about? Why?
   • I would love to learn more about “Data Visualization”, because I am very drawn to the creative arts. I noticed the way each database expresses their data, sets the tone for my personal understanding of what they are offering to the reader. If the visuals are fun, clear, and concise, I can pick out information with ease. If not, however, I become easily frustrated with the database and move onto another that might be organized more effisciently.

Laurmagee (talk) 23:45, 26 September 2013 (PDT)

Kevin Meilak

Database: Spliceosome Database

Database Website: Spliceosome Database

Kevin Meilak: Response to Reflect Questions

1. I was familiar with Discovery and Acquisition of Data, Cultures of Practice, Data Preservation, Data Analysis, and Ethics, including citation of data. I became familiar with these aspects through research papers for classes which required familiarity with the relevant data for the field (typically biology, but also liberal arts such as theology and philosophy), and by doing research through the Summer Undergraduate Research Program (SURP) this past summer at LMU.
2. By doing this exercise, I now feel that I have a better understanding of Databases and Data Formats. Finding information about and acquiring information from a database I had never interacted before and whose contents were (and remain) foreign to me required that I understand data in different formats (in this case a spreadsheet as opposed to text or graphical depiction). Furthermore, more practice interacting with a database allowed me to grow more comfortable interacting with databases.
3. I would like to know more about metadata because I have had little if any experience with it despite it being a powerful analytic tool.

Kmeilak (talk) 18:17, 29 September 2013 (PDT)

Kevin McGee, Viktoria Kuehn

Database: Ensembl

Viktoria Kuehn

1. Which of these core competencies (if any) were you familiar with before taking this class? How did you become familiar with them?
   • I was most familiar with numbers 11 and 12. I am a very visual learner so I appreciate the use of various ways of displaying data so that is why I am familiar with using data visualization through my biology courses. I have taken a bioethics philosophy course where we talked a lot about intellectual property, which is why I am familiar with 12.
2. Which of these core competencies (if any) did you gain a deeper understanding of by doing this exercise? What about the exercise taught you about them?
   • Through this project I have learned the importance of Data Conversion and Interoperability because it is so much easier to work with large amounts of data if they are easier to categorize and to incorporate in various databases. I have also learned about the importance of data curation, and how much constant upkeep is necessary to run a database with up to date information.
3. Which of these core competencies (if any) do you want to know more about? Why?
   • I would like to know more about Quality Assurance because it seems like a useful skill to have; to be able to tell when data has been tampered with.

Vkuehn (talk) 19:25, 2 October 2013 (PDT) Database Website: http://uswest.ensembl.org/index.html

Kevin McGee Responses

1. I was familiar with discovery and acquisition of data before this assignment. I, like the rest of the world, use google and many other types of databases (like facebook) to look up information every day.
2. I learned about curation and reuse of data. Ensembl has a system of pipelines that allow it to automatically curate data from other sources.
3. I would like to learn more about Data preservation, analysis and visualization. All three of these competencies seem essential to me when looking at how to interpret scientific data.

Kevinmcgee (talk) 19:32, 2 October 2013 (PDT)

Mitchell Petredis

1. I was familiar with Data Management and Organization, Cultures of Practice, and Data Preservation core competencies prior to taking this class via my various jobs at Information Technology Services (ITS), where the primary objective was to utilize software such as DeepFreeze to prevent excessive files from accumulating on publicly available computer hard drives and to install core updates to those computers when needed or on a schedule
2. I gained a better appreciation of the importance of Quality Assurance and Data Curation by doing this exercise by realizing that potentially many people utilize these databases constantly for research purposes; being able to provide the latest, verified information on a regular basis is vital to the integrity of the scientific community.
3. I'd like to learn more about Data Analysis so that I can fully understand the information behind all the results of a query and how to use them properly.

Mpetredi (talk) 15:57, 2 October 2013 (PDT)Mitchell Petredis