Class Journal Week 4

Miles Malefyt

1. What was the most beneficial aspect of working collaboratively on this assignment?

The most beneficial part of working on the assignment with someone else is that If I make a mistake there is always someone there to point out that mistake

1. What was the most challenging aspect of working collaboratively on this assignment?

The hardest part is to find times when both of us are available

1. Would it have been easier to do this work by hand/pencil? Why or why not?

For a very short sequence of genes I think it would be easier to use a pensil and paper but with very long sequences, the computer would be the preferred choice

1. What strategies did you use to check the correctness of your work?

I went over the code and attempted to pinpoint the places that didn't work when I input the code into the computer. Expasy was also helpful to find the conjugated pairs

Dillon Williams

1. The most beneficial part of working in a group was the ability to bounce ideas off of each other, which allowed for a more efficient process. Also, if one person in the group didn't understand how to do a certain process, the others could help.
2. The most challenging aspect was working with a medium that was unfamiliar based on a lack of previous experience with command line.
3. For this (somewhat) small portion of DNA, I think that a pencil and paper likely would have been more efficient. However, if there was a larger chunk of DNA to transcribe, the computer method would be much more ergonomic.
4. The results that I got when entering code allowed me a way to kind of self check my work as I went. If the program wasn't spitting out the information that I was expecting, I knew that I was inputting the code wrong and should take the necessary steps to change what needed to be changed.

-Dwilliams (talk) 23:26, 19 September 2013 (PDT)

Tauras

1. The most beneficial part of working with someone else was being able to bounce ideas of each other and it increased efficiency as two people could be trying new ideas at once.
2. The most challenging aspect was that it was the blind collaborating with the blind. Neither of us knew what we were doing and this made it incredibly difficult to figure out how to more forward and everything had to be explained multiple times. There was little meeting of the minds on concepts early on.
3. Yes, a manual method would have been easier for a DNA region this size. However, it would be much easier to do a larger chromosome fragment through the software, especially given a generalize coding line to start with.
4. I checked my work against gut common sense, what doing a sample by hand produced, and using ExPASy.

Taur.vil (talk) 22:27, 19 September 2013 (PDT)

Alina Vreeland

1. What was the most beneficial aspect of working collaboratively on this assignment?

Having someone to bounce ideas off of was extremely helpful, since we could work through it together and have a better chance of getting the correct answer. it also saved some time, since multiple people would be working towards the same answers.

1. What was the most challenging aspect of working collaboratively on this assignment?

Finding time to meet and actually work on the assignment together was the hardest part.

1. Would it have been easier to do this work by hand/pencil? Why or why not?

It probably would have been easier, just because your brain processes the commands you want without actually having to tell the commands before being able to come up with a product.

1. What strategies did you use to check the correctness of your work?

Entering the code we came up with into the system was a good way to see if it actually worked and got the results that we expected. We also referred to our crib sheet to see if we used the commands properly.

Ajvree (talk) 12:36, 17 September 2013 (PDT)

Hilda Delgadillo

1. What was the most beneficial aspect of working collaboratively on this assignment?

The sharing of ideas and constant reflection of the commands that were administered and the recognition of the coding was very helpful. I was able to become more aware of what I was communicating to putty with the help of my peers.

1. What was the most challenging aspect of working collaboratively on this assignment?

My group and I fed off of each others' ideas which was very rewarding, so the only real challenge I can think of was our schedule compatibility which made it difficult to meet at a more earlier time.

1. Would it have been easier to do this work by hand/pencil? Why or why not?

I think it would have been easier to do this work by hand because it is much simpler to write out what we actually have in mind, but when it comes to giving the computer a command to perform your task, that's when it gets tricky. However, in the long run, once I become more comfortable with all the commands, this process will be much quicker than doing everything by hand.

1. What strategies did you use to check the correctness of your work?

We decided to hand-write the terminator sequence in order to visualize our work. Furthermore, ExPASy was used in order to check my work in terms of checking to see if the translation was correct.

HDelgadi (talk) 19:20, 18 September 2013 (PDT)

Lauren Magee

1. I think the most beneficial aspect of working collaboratively on this assignment is having another brain to tap into. Sometimes its hard to remember all of the different commands used in putty, so it's nice to have someone else who might be able to investigate with me, or if I am lucky, remember the command themselves. It's also nice to return the favor and help out one of your peers, because when you teach the material back to someone else, it is better instilled within yourself as well.
2. The most challenging aspect is finding time to meet with those who you are paired up with. Everyone has such busy and inflexible schedule, so it is hard to find common ground.
3. It would not have been easier to do this work on paper, I know from first hand experience. It is very time consuming to translate the DNA and note the specific areas of interest, such as the ribosome binding site.
4. I checked my hand written translation by entering the original sequence into ExPUSy and selecting the appropriate translate buttons. It was also helpful to check my work against the results of the putty translation that we programed. However, I thought it was also helpful to check my programming against my previously translated sequence, to make sure my commands were correct.

Laurmagee (talk) 01:33, 19 September 2013 (PDT)

Lena Hunt

1. What was the most beneficial aspect of working collaboratively on this assignment?
   • It was nice to have a partner to bounce ideas with. I think I am less likely to get frustrated and give up when there is someone else who can suggest new things to try.
2. What was the most challenging aspect of working collaboratively on this assignment?
   • Definitely scheduling. I have almost non-stop classes Wednesday and Thursday, and finding time to work with someone else is really difficult.
3. Would it have been easier to do this work by hand/pencil? Why or why not?
   • Yeah, I think it would have. We did this in class and it took way less time. Although, if we were working on a longer strand, and doing it by hand, it would be very time-consuming. I think that once I get used to the commands, it will seem easier by computer, but at the moment, I have more practice with pen and paper.
4. What strategies did you use to check the correctness of your work?
   • The coding strand we found initially was very small, and didn't seem likely to be the right answer. We used ExPasey to compare how long the strand should be, and used that as a reference to change our code.

Lena (talk) 12:06, 19 September 2013 (PDT)

Kevin McGee

1. The most beneficial part of working with a partner was that we were able to fill each other in in areas that the other did not understand. I am a bio major while my partner is a computer science major, so it was very beneficial for both of us.
2. Scheduling time to work was probably the most challenging part.
3. I think it would have been harder to do on pencil. Once you figure out the command line, problem solving becomes much easier.
4. Understanding what you are trying to accomplish helps the most, although we also used the Command Line crib sheet to check our commands. ExPASy could also help check final answers.

Kevinmcgee (talk) 14:19, 19 September 2013 (PDT)

Kevin Meilak

• The most beneficial aspect of working collaboratively on this assignment was having another person to bounce ideas off of and give a unique perspective to the challenges of coding.
• The most challenging aspect of working collaboratively on this assignment was finding time where we could both meet to work on it.
• Yes, doing this by hand would be much easier because it is difficult to learn how to tell the computer what to do, whereas we all have a lot of practice using pencils and paper.
• Simply trying out the code was most helpful. If it gave the result you wanted, then it was correct, and if not it needed to be changed.

Kmeilak (talk) 20:14, 19 September 2013 (PDT)

Gabriel Leis

1. The most beneficial part of collaborating with a partner was access to a broader, combined knowledge of the command line interface.
2. The most challenging aspect of working together was deciding a plan of action for completing the assignment. An assignment like this weeks was particularly difficult because multiple paths could lead to the same solution.
3. The command line interface provides instant feedback which I think is preferable to a hand/pencil assignment.
4. The ExPasy tool would have been a great tool to check my work if I were able to create a command that provided a proper mRNA sequence.

Gleis (talk) 21:21, 19 September 2013 (PDT)

Stephen Louie

1. The most beneficial aspect of collaboration is having someone else who can fill in gaps of information you may have missed.
2. The most challenging aspect of working together was if there was a coding issue that neither person was familiar with.
3. It would have been more assuring to do this on pencil since I am more familiar with this method. As time goes on, I'll get used to using the command line.
4. Having a partner observe and edit your code while you typed it out was helpful. Sometimes when you're the author, it's easy to skip over typos or mistakes that can cause an error in the code.

Slouie (talk) 22:13, 19 September 2013 (PDT)

Mitchell Petredis

1. The most beneficial part about working collaboratively on this assignment was that it allowed us to share ideas with each other as to how to write or fix the commands per individual part of the sequence. We were able to proofread each other's work to check for accuracy and faults.
2. The most challenging aspect of working collaboratively on this assignment was being able to meet with each other. Me and my partner had conflicting schedules that prevented us from meeting in person more than once; however, chatting via Gmail messages resolved that issue.
3. Longer gene sequences like this are generally harder for me to do by hand since I have a tendency to get lost after writing so many codons.
4. I used ExPAsy to check and compare the location of the start and stop codons between the given sequence and my sequence. ExPAsy also helped me check the proteins of my sequence as well.

Mpetredi (talk) 22:35, 19 September 2013 (PDT)Mitchell Petredis

Katrina Sherbina

1. The most beneficial aspect of working collaboratively on this project was finding out how well I could explain my reasoning for putting together piped sequence of text to complete the exercises. In discussing the code, I was inspired by some of the ideas my collaborators suggested that ended up making the code more efficient.
2. One of the most challenging aspects of working collaboratively on this project was finding a good time for all of the group members to meet and work together on the different exercises.
3. This would not have been easier to do by hand on paper because the genetic sequence this week was longer than any other we had previously worked on. In comparison to working with this sequence by hand, I think it is much easier to instruct the computer to find what you need to find for a sequence of this length.
4. My group members and I used ExPasy to check the translation of the mRNA sequence.

Ksherbina (talk) 23:49, 19 September 2013 (PDT)

Viktoria Kuehn

1. I found the most beneficial thing about working together the fact that we could exchange ideas and figure out why certain things worked while others didn't rather than just guessing until it worked. I also thought it was helpful because it allowed us to explain things to each other, which helps you solidify something you already knew.
2. The most challenging part of doing this assignment was figuring out a time when we could meet up together.
3. I would have rather done this by hand. I think that that way it is easier to visually separate out the certain parts which makes it more clear to see the different markers. However, I understand why this is useful to learn on the command line, because in longer sequences it would be more difficult to do by hand.
4. I compared my work to the work of my partner and made sure we had similar outcomes when trying it both ways if we had different answers.

Vkuehn (talk) 22:39, 23 September 2013 (PDT)