BIOL398-03/S13:Class Journal Week 5

• BIOL398-03/S13:Week 5

• 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)

• user:Kevin Matthew McKay

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 become 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 expression pathways we are 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? I liked the SGD website the best because it was easy to navigate and find the pathway I was looking for. If i had to find other pathways in the future this website would be the easiest to use.
• 3.Which of the three databases did you like the least? Why? I did not like the reactome website at all, it barely loaded on the three different computers that I tried to use it on, and when the website did work, i couldnt find a complete pathway for the reactions we discussed in class. To my it seemed like the least useful of the 3 websites. When I did find a reaction pathway that we discussed in class, the image of the pathway would not load. I would hate to blame this on the website but considering that every other website worked (SGD, KEGG as well as reddit, facebook,netflix, etc.) I dont really see what else was causing my technical issues.

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.

• Matthew E. Jurek 21:58, 14 February 2013 (EST):

Ashley Rhoades Shared Journal Week 5

Ashley Rhoades

1. The purpose of this assignment was to get comfortable using these databases so that we may use them to obtain information about our modeling. Each database is different and can provide different information so it is good to be comfortable with more than one.
2. I liked the SGD database most because it was easiest to use. I had the easiest time finding what I was looking for on the SDG and it was very straightforward and explicit.
3. The Reactome database was my least favorite. This is partially because I could not load the page, but even when I did I had trouble finding what I was looking for. When I did find the pathway it was part of a larger map and I couldn't get as a specific of an image as the other databases.

Ashley Rhoades 23:18, 14 February 2013 (EST)

Salman Ahmad Week 5 Journal

Salman Ahmad

1. What was the purpose of this assignment?
   • The purpose of this assignment was to learn how to use online databases. Different databases have different ways to show the same information. It is important to be able to look at the many ways the same pathway can be shown so we can understand it better.
2. Which of the three databases did you like the most? Why?
   • The SGD database was my favorite to use. It was definitely the easiest to use and it was helpful for it to already be narrowed down to a specific organism. The information was very easy to find by just using the search bar provided on their website. The information was shown clearly and it was easy for me to understand the information provided.
3. Which of the three databases did you like the least? Why?
   • The database I liked the least was the Reactome database. First of all, it took much longer to load the database than any of the others. Once it was loaded, I had a hard time finding any of the information at all that I was looking for. As of right now, after much trying, I have still been unable to find anything useful or related on the Reactome databse.

Salman Ahmad 23:27, 14 February 2013 (EST)

Anthony J. Wavrin Week 5 Journal

Anthony J. Wavrin

1. What was the purpose of this assignment?
   • I believe the purpose of this assignment was to familiarize ourselves with these three databases. When we are working on our projects, this type of information may be needed and having multiple sources in which you can obtain this information is crucial. Additionally, these websites will undoubtedly be used again in the future.
2. Which of the three databases did you like the most? Why?
   • I liked the Saccharomyces genome database the best because it was very clean to use. It also had good general information with a summary but, there were a lot of citations and additional information available. Also, the layout was very clean and finding information was easy.
3. Which of the three databases did you like the least? Why?
   • The database I liked the least was Reactome. Reactome was a running very slow, perhaps due to a server issue, but it took several minutes to load each page. Additonally, it was very hard to navigate and get to the pathway I was looking for. Lastly, when I did get to the pathway I was searching for, it was almost impossible to read. The layout of the pathway was very unconventional and unconnected making it very difficult to utilize it.

Anthony J. Wavrin 00:47, 15 February 2013 (EST)

Elizabeth Polidan Week 5 Journal

Elizabeth Polidan

1. What was the purpose of this assignment?
   • The purpose of this assignment was to get us familiar with the use of these three databases. They are useful tools, but complex, so practice is important. It also gave us a different angle from which to view the elements of the nitrogen metabolism pathway. This gives us a deeper understanding.
2. Which of the three databases did you like the most? Why?
   • I liked the SGD the best, mostly because it was the cleanest. There was basic information on the main page with lots of links to additional information. It made it less confusing and overwhelming than the others.
3. Which of the three databases did you like the least? Why?
   • Reactome was horrible. I have NO idea whether what I managed to find was the correct page. It is very confusing to use, and the display was so terse that information was not clear.

Elizabeth Polidan 01:23, 15 February 2013 (EST)

Kasey E. O'Connor Week 5 Journal

User:Kasey E. O'Connor

Questions

1. What was the purpose of this assignment?
   • The purpose of this assignment was to become familiar with the sites that could prove useful in future projects and assignments. It also gave us a better understanding of all the enzymes we have been talking about in class.
2. Which of the three databases did you like the most? Why?
   • I liked SGD best. It was the easiest to navigate, especially because all of the enzymes were only from the yeast cells, so there was no need to refine the search. Also, the summary paragraph at the bottom of each of the enzymes page was very helpful in answering the questions.
3. Which of the three databases did you like the least? Why?
   • I did not like Reactome at all. It was very confusing to try and find the correct pathway, especially without any of the enzymes that I would recognize being labeled.

Kasey E. O'Connor 01:35, 15 February 2013 (EST)

Helena M. Olivieri Week 5 Journal

User:Helena M. Olivieri

What was the purpose of this assignment?

• The purpose of this assignment was to introduce us to various databases and how they relate to the current project that we are exploring.

Which of the three databases did you like the most? Why?

• SGD seemed to be the most clear cut and easy to navigate.

Which of the three databases did you like the least? Why?

• Reactome, in comparison to SGD, was confusing to navigate through... then again I'm still figuring out how to navigate this wiki.. I managed to stupidly edit the 'assignment page' thinking that it was my user page... awkward... I think I was able to 'undo' my changes though... sorry... Anyway, I think I'm probably slightly stupid on how to navigate websites and databases, and I'm not quite sure I'm entirely clear on how to recognize the enzymes on Reactome and relate them to the enzymes we are studying in class.

Helena M. Olivieri 02:41, 15 February 2013 (EST)