BIOL398-03/S13:Class Journal Week 5

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*Which of the three databases did you like the most? Why?
*Which of the three databases did you like the most? Why?
**I liked the SGD database by far.  Searching for genes and pathways was rather simple.  The information about each gene was organized in an easy-to-follow format.  Having a list of references was also nice if further research is needed in the future.  The thing I liked most was the schematic of the pathway.  It was very easy to follow and the labels were nice.  The other databases used a mixture of symbols and words.  SGD limited the symbols and used mostly words so a legend was not needed to decipher what exactly was being illustrated.
**I liked the SGD database by far.  Searching for genes and pathways was rather simple.  The information about each gene was organized in an easy-to-follow format.  Having a list of references was also nice if further research is needed in the future.  The thing I liked most was the schematic of the pathway.  It was very easy to follow and the labels were nice.  The other databases used a mixture of symbols and words.  SGD limited the symbols and used mostly words so a legend was not needed to decipher what exactly was being illustrated.
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*Which of the three databases did you like the least? Why?
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**I didn't like the Reactome database.  Both of the databases that involved filtering species were difficult to use, especially this one.  It was extremely hard to find what I was looking for.  I'm not even entirely sure I found the right thing.  I also didn't like that a number of pathways were all on the same page meaning you have to zoom in on specific spots and then zoom back out to see what was going on.  The large legend required to look at the pathway means there are too many symbols.  I didn't like all the various symbols because it was hard to follow what was going on in the pathway.  Also, some of the shapes on the legend looked differently in the actual pathway which was frustrating.
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*'''[[User:Matthew E. Jurek|Matthew E. Jurek]] 21:58, 14 February 2013 (EST)''':

Revision as of 22:58, 14 February 2013

  • The purpose of this assignment was to learn how to navigate these three biological databases for future reference.
  • I liked the SGD database the most because it was the easiest to use for me and stated information directly.
  • I disliked the Reactome database the most because it was VERY hard to navigate and find the reactions I was looking for. I was actually unable to find the reaction, only a part of it.

Kevin Matthew McKay 15:00, 14 February 2013 (EST)

Contents

Laura Terada Week 5 Journal

Laura Terada

Questions

  1. What was the purpose of this assignment?
    • The purpose of this assignment was to familiarize ourselves with the different databases available in regards to genes and their pathways. Secondly, this assignment allowed us to better understand the pathway we have been discussing in class.
  2. Which of the three databases did you like the most? Why?
    • I liked the second database, SGD, because I found it to be the easiest to navigate through. I liked how the pathway diagrams showed the input and outputs in comparison to KEGG and Reactome that used symbols/legends. There were also different levels of detail, which is another aspect that I liked. Lastly, the summary section of each gene page was helpful.
  3. Which of the three databases did you like the least? Why?
    • My least favorite database was Reactome because its pathways were difficult to go through. It was difficult to search for pathways/reactions with specific enzymes.

Laura Terada 15:03, 14 February 2013 (EST)

Paul Magnano

User: Paul Magnano

  • 1.What was the purpose of this assignment? I believe that the purpose of this assignment is to help us becoe familiar with scientific databases, specifically ones that are relevant to this class. By learning how to navigate these databases, we can get a better understanding of the various gene exprssion pathways we re learning about in class, as well as get additional information that isnt specifically covered in class lectures or the scientific papers we are reading.
  • 2.Which of the three databases did you like the most? Why?
  • 3.Which of the three databases did you like the least? Why?

Paul Magnano 20:58, 14 February 2013 (EST)

James P. McDonald Week 5 Journal

James P. McDonald

  1. What was the purpose of this assignment?
    • The purpose of this assignment was to practice using databases to look up pathways in different organisms. We got to look specifically at the pathway we have been discussing in class and see different representations of it from different databases. We also got to familiarize ourselves with the databases that I'm guessing we will be using in the future in this class.
  2. Which of the three databases did you like the most? Why?
    • I liked the SGD database the most. It was the easiest to use and I liked that you could look up an enzyme directly by searching for it directly, unlike the other databases. I like how the pathways on this site were listed conveniently and it was not hard to find the correct pathway I was looking for. Also the diagrams of the pathways were the most straightforward and easy to use. The diagrams showed explicitly what you were looking at, including full names of the amino acids and enzymes.
  3. Which of the three databases did you like the least? Why?
    • I liked the Reactome database the least. It was difficult to navigate and it took me a little time to narrow my search down to the yeast species I wanted. Also, the diagrams were hard to navigate and there were no enzymes labeled.

James P. McDonald 21:11, 14 February 2013 (EST)

Matthew E. Jurek Week 5

Matthew E. Jurek

  • What was the purpose of this assignment?
    • This assignment allowed students to become familiar with various databases. The databases were used to look at mechanisms and pathways discussed in class throughout the previous weeks. Each database presented similar information, however it all appeared differently. Each database offered unique features.
  • Which of the three databases did you like the most? Why?
    • I liked the SGD database by far. Searching for genes and pathways was rather simple. The information about each gene was organized in an easy-to-follow format. Having a list of references was also nice if further research is needed in the future. The thing I liked most was the schematic of the pathway. It was very easy to follow and the labels were nice. The other databases used a mixture of symbols and words. SGD limited the symbols and used mostly words so a legend was not needed to decipher what exactly was being illustrated.
  • Which of the three databases did you like the least? Why?
    • I didn't like the Reactome database. Both of the databases that involved filtering species were difficult to use, especially this one. It was extremely hard to find what I was looking for. I'm not even entirely sure I found the right thing. I also didn't like that a number of pathways were all on the same page meaning you have to zoom in on specific spots and then zoom back out to see what was going on. The large legend required to look at the pathway means there are too many symbols. I didn't like all the various symbols because it was hard to follow what was going on in the pathway. Also, some of the shapes on the legend looked differently in the actual pathway which was frustrating.
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