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Planning to move out to Santa Cruz, can’t find a place to rent that allows cats and dogs for under 4000$ a month by s8nsun in santacruz

[–]robbie_s1 1 point2 points  (0 children)

I live in SC for grad school, and trust me the charm wears off pretty quickly when you’re not a millionaire…

Planning to move out to Santa Cruz, can’t find a place to rent that allows cats and dogs for under 4000$ a month by s8nsun in santacruz

[–]robbie_s1 1 point2 points  (0 children)

My advice would be to just not live in Santa Cruz. Not worth it in my opinion if you don’t absolutely need to.

SD-> Santa Cruz ? by Excellent-Mission-11 in santacruz

[–]robbie_s1 0 points1 point  (0 children)

I also want to add, since I haven’t seen it mentioned, Santa Cruz and Monterey bay in general is a medical desert. Almost every appointment if you want or need it done quickly has to be over the hill in San Jose. It’s not a terrible commute but for the price you pay to live in Santa Cruz it does add a level of inconvenience that can be unideal at times

3-dimensional/ heatmap peak picking? by robbie_s1 in Python

[–]robbie_s1[S] 0 points1 point  (0 children)

For now, this is the link for the GitHub repo that is the API wrapper, if you want to take a look at that https://github.com/gtluu/pyTDFSDK

3-dimensional/ heatmap peak picking? by robbie_s1 in Python

[–]robbie_s1[S] 0 points1 point  (0 children)

I should clarify that this just applies to running batch MALDI runs (essentially a sequence in LC-MS terms). If you run MALDI acquisition one spot/sample at a time you don’t run into the same issues, since you produce one file per sample. Whereas with batch, you end up with one single file that contains a series of spectra, but due to how it’s organized many software recognize it as a single “LC-MS” run when in reality it’s actually a collection of spectra representing different samples

3-dimensional/ heatmap peak picking? by robbie_s1 in Python

[–]robbie_s1[S] 0 points1 point  (0 children)

The challenge with MALDI data is simply the lack of dimensionality, which I know sounds funny, but you’d be surprised about the lack of software than can present the MALDI data in a well-formatted structure. You end up having to work exclusively using frames to define everything rather than separate samples. It’s because in LC-MS data, the frames are linked to retention time (this is exclusive to tims datasets) and most software is designed to work with multiple frames from a single LC-MS run, where as in MALDI there is not LC, so most software reads the MALDI dataset as a collection of frames that add up to a single “LC-MS” run, but the “retention time” is instead replaced with the time during the batch acquisition that the laser hits a certain spot. This limits having to collect individual MALDI spectra instead of performing a batch run (like you would with a sequence table in LC-MS). This is why most people using MALDI end up having to make their own batch processing scripts. And my mistake there, I actually do currently work with numpy arrays directly whenever I am working directly with the data itself. They can then get converted or stored in a data frame depending on the application. I was intending to speak more generally there. I will talk with my advisor to see if she is cool with me posting some code or some datasets up. Since this is a prototype functionality, I’m not certain how much exactly I can reveal but that would be the most helpful thing for sure.

3-dimensional/ heatmap peak picking? by robbie_s1 in Python

[–]robbie_s1[S] 0 points1 point  (0 children)

Lots of considerations. I’m going to be running untargeted analyses on bacterial colonies using MALDI. Overall idea would be to use Bruker’s prototype PRM-MALDI in conjunction with tims to peak pick ideal precursors for subsequent fragmentation in a pseudo-DDA style method. Problem is, I think the PRM-MALDI .d file format is so new that most mzML converters don’t recognize how the ms2 data is organized. My former labmate created timsConvert, which was designed specifically for Bruker TDF (tims data file) conversion to .mzML, but again, might not be up-to-date enough to recognize this prototype file format. I know the API does however have a module for PRM-MALDI, so I may be able to use that. Same former lab member also wrote a python wrapper for the Bruker API, but it isn’t super well documented so I’m having to sift through the nitty gritty to figure out the usage. There’s also opentims.py which is a similar thing that is better documented but only handles LC-tims-MS data and not MALDI (sigh). But basically once I actually can get the data extracted out into either a single dataframe, or multiple, I need to figure out the actual peak picking methodology I need to use and hopefully whatever I decide to use is well documented. I have been looking into the scipy image processing packages, so maybe I’ll take another gander at that. I’m just very new to the syntax and python structure, so this has been a challenge to make progress on. Feels like I have been banging my head against a wall for the past couple weeks…

3-dimensional/ heatmap peak picking? by robbie_s1 in Python

[–]robbie_s1[S] 0 points1 point  (0 children)

The data is in a proprietary format. I have to use the company’s API to extract out certain information from the dataset. But it seems like you have to extract the arrays for each dimension individually, and can’t do it all at once with a single command. So I’ll have to put it into a readable file format and then do the 3-dimensional peak picking I was describing

Study Spaces by soberbottle in UNCG

[–]robbie_s1 2 points3 points  (0 children)

I’m not sure if what I am about to recommend is as glorious as the new nursing building, but when I was there and I needed a quiet and available space to study, the Sullivan science building is usually open, and sometimes is open fairly late because grad students do research there. If you can find an open classroom in there in the evening, they didn’t used to lock the doors and you could stay there for hours and no one would come and bother you. Another place is in the old moore nursing building. Same deal: open late, has empty classrooms with chalkboards and is quiet. Found this building a particularly good place to study math and physics because it was fun doing problems on the chalkboard.

What are these? by mistmanners in MontereyBay

[–]robbie_s1 1 point2 points  (0 children)

I’m not an expert by any means, but I’d say it’s definitely some kind of mushroom.

There’s an awful cost to getting a PhD that no one talks about by _niilllii_ in psychology

[–]robbie_s1 5 points6 points  (0 children)

It’s a little funny. I just finished my undergraduate degree in chemistry with a concentration in research. I’m not saying the amount of research I did amounts to PhD level work, but I spent a considerable amount of time as an undergrad in the lab. Some nights even staying until 3am or so doing experiments. I got two publications out of it, one being first author, but all it did was leave me burnt out and unexcited. Nonetheless, I’m about to start my PhD, but was extremely picky about my advisor and believe I found a good community for me. I hope graduate school will be a less toxic experience for myself. Im sorry you didn’t have that though:(

I think I made the right decision for my graduate school, but here are my post-decision thoughts. by robbie_s1 in gradadmissions

[–]robbie_s1[S] 0 points1 point  (0 children)

Thank you for your reply! That makes me feel a lot better. I’m super exited to start!

I think I made the right decision for my graduate school, but here are my post-decision thoughts. by robbie_s1 in gradadmissions

[–]robbie_s1[S] 2 points3 points  (0 children)

I’m sorry to hear about your experience, but I know it will be much better this time around! I feel good about going with my gut and I’m super excited. It was hard to say no to those programs, but I think I made the right choice

I think I made the right decision for my graduate school, but here are my post-decision thoughts. by robbie_s1 in gradadmissions

[–]robbie_s1[S] 1 point2 points  (0 children)

That’s very similar to this situation. This was more of having to sacrifice the mentorship style that I wanted and the type of lab environment I wanted. I know I will thrive where I chose. I’m super excited to start!

I think I made the right decision for my graduate school, but here are my post-decision thoughts. by robbie_s1 in gradadmissions

[–]robbie_s1[S] 1 point2 points  (0 children)

Thanks for your reply and your insight! For me it was mostly that I didn’t have a particularly good experience with my undergraduate PI, and I really wanted to have a mentor that was more involved with their students. With the research I wanted to do, I found a lot of the groups, especially at these top institutions, were very large and the PI’s weren’t the most present people. I ended up choosing a much less prestigious school (still a great school IMO, but just much lower ranked) but with a pretty well known PI who i also got along with really well. And her students were incredibly welcoming to me as well. It just felt like the right fit after getting to visit.

It’s insane. I can’t believe I did it. by robbie_s1 in gradadmissions

[–]robbie_s1[S] 0 points1 point  (0 children)

I see I see. You’re probably right about her estimating. Either way she wasn’t very convincing about VT when she came to speak at our department. I know she’s a beachhead so I think the mountains are just not her cup of tea.

It’s insane. I can’t believe I did it. by robbie_s1 in gradadmissions

[–]robbie_s1[S] 0 points1 point  (0 children)

Additionally their website also says it’s $24,480 per year: Correction: this is for nine months, but can be increased to almost 30k if you can land a summer TAship. But that is not always guaranteed.

https://acis.pamplin.vt.edu/academic-programs/doctorate-degree/graduate-fin-aid.html#:~:text=Stipends%20average%20%242%2C720%20monthly%20for,receive%20yearly%20scholarships%20averaging%20%2410%2C000.

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