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| He is pretty hot |
Hi guys welcome back to a more standard blog post. To start off we will take a look at the meme of the week: Salt Bae. Salt Bae has taken the internet by storm, as Nusret Gökçe uploaded a video of himself carving a steak and sprinkling salt onto the meat. The video from Instagram blew up within 2 days, and currently Salt Bae is definitely the meme of 2017 for now.
Now in terms of my research, I have only barely begun. I have collected the Lac1 PDB files and trimmed them into usable sequences. However, I am having trouble finding the PDB files of Galactose, Fructose and other proteins to compare the analysis off of. Dr. Ozkan does have a database for obtaining such sequences, but neither of us can work the terrible interface for now. My boy Paul should be able to help me with that. Finding these sequences are a little bit tougher than I anticipated, but my trials should be rather robust and efficient. Of course I haven't gotten into the meat of the research yet.
The measures I can take to ensure success in my methods is reliant upon my efficiency communicating with Dr. Ozkan and her graduate students and the computer's errors. In the past, there have been days where I have been unable to complete certain tasks due to a lack of communication between the lab team and myself. I will have to be on top of my game to ensure that my analysis proceeds in a timely manner. Hopefully I will have the samples ready for trial before I leave school. Ideally, they should be complete on February 6th. After that point, I must learn how to run the trials and the DFI analysis, which will probably take up about half of my first week on site. Then running the trials and performing the analysis should conservatively take two to three weeks. Which means I will be finished with my trials before March begins.
If I ever fall behind on time, I can always limit the number of samples I decide to analyze. At the minimum I will do 2 new mutated samples, but the point of the analysis is to understand the dynamics changes within the protein. One sample is more than enough. But for validity checks and different changes more samples are necessary. I plan to pull off 4-6 samples for now, but I can cut back if I need to.
I am not able to run the trials remotely at this point in time because I need mentorship to learn about running the DFI trials. Luckily I have received advice on how to prepare my samples, and that is what I am to do for now.
Ashwath, I feel like your articulation of obstacles and how you'll overcome them is rather vague. I'd like to understand how your "boy Paul" is going to help you figure out how to work with the interface that both you and your professor is struggling with. Also, why are you guys struggling?
ReplyDeleteMoreover, it seems like your way to compensate in your schedule is doing fewer samples, but it seems to me that doing fewer samples with disrupt the integrity and strength of your research. Is there any other way that we can mitigate any scheduling errors?
Yo 'Shwath!
ReplyDeleteI was wondering what that meme was... Well, now I know, so thanks for that!
I concur with your point about communicating with your research team. As a fellow intern at the OG PSF 3rd Floor, I know how important it is to communicate with other interns and mentors because our projects are really specific and often times crazy things can happen in the lab, and your stuff falls down the priority list. So, you and me both need to be assertive and ensure we are making good progress on our projects.
I would've liked more information about this Paul character and what the specific computational issues you were encountering. I like that you have checkpoints in your research, where you can choose to analyze various numbers of samples -- that flexibility will be really helpful.
My question for you is: what do these "samples" look like? Are they series of letters (like A, G, U, C) or what? What kind of files are they?
Excited to see where your project takes you -- it's pretty cool stuff!
Lil' Yash
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What's good Ashwath?
ReplyDeleteAlso, thanks for the meme explanation, things make a lot more sense now.
As for your research project, I have a few questions. What does trimming the PDB files mean? And how much of your actual project is that? Also, will Paul somehow fix this interface or is he the only one who knows how to properly access it? Also, who is Paul? Anywho, as long as you can properly get all the necessary information out of that "terrible interface", I think you will be good to go.
Furthermore, I totally agree with Mrs. Haag that you cannot just account for lost time by reducing sample sizes. Is there potential for you to do the same number of trials but with a little more time spent each day? I feel like you've come too far now to just reduce trials for time's sake.
Also, you say that you cannot do remote trials at this point, but once you learn the DFI trials, will you be able to do your research from home? If so, would this allow you to gain back some time and potentially still do the same number of samples? I would try to find a way to keep the same number of samples even if you fall a bit behind.
Other than that, I hope you find this Paul and that he is the one you are looking for. Glad to see you're planning ahead, and, as always, feel free to ask any questions you have!\
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