sanguinemare

March 29, 2017

Struggles of a grad student – Part 1

Filed under: "Me" updates,Grad school,Research — sanguinemare @ 1:49 pm

Today was the epitome of Murphy’s law for a grad student – the classic case of needing to order supplies for a key experiment, and the lab not having it… and then not being able to order it due to a series of unfortunate events: the supply center which I’d sent the order in to yesterday is apparently closing and not accepting any more orders –> the other person we place orders from has an auto-reply e-mail saying they are out having surgery and not to place orders until they’re back tomorrow unless it’s an emergency, then contact person b –> person b also has an automated e-mail reply saying they are out of the office today and won’t be responding e-mails until tomorrow –> another supply center that I found out about from the one that’s closing ALSO has an auto-reply e-mail saying they are out of town right now and will only intermittently check e-mail.  *Sigh*  At least that means I should be able to place an order first thing tomorrow, but it also means that’s another day’s delay before I can start the assays.  At least there’s a few other steps (aka days’ worth of work) that I have the resources for beforehand.

Generally this sort of thing can be avoided if 1) there is good communication in the lab (and/or a good lab manager and/or a good system in place so you can easily check the lab inventory), and 2) you plan ahead.  Both are good practices to have so you don’t need to delay your work just to wait on things to arrive.

Sometimes, however, it is not really avoidable, such as in this case, where the study only recently finished, I only just figured out how many samples I had total, and then found out that there’s a 384-well plate machine on the 2nd floor that we are allowed to use that would make my life a LOT simpler (less reagents used per sample and a lot less plates to run: 12 vs. 46)… but the catch is that we’d have to buy the plates ourselves.  So I decided to try to go for that, and that’s how this happened.  Also decided to order some different primers to try based on the literature, and those need to be custom-made and take time, so yeah.  Timing is so tight right now because I have a committee meeting set for the end of April, and the extractions and processing itself will likely take 2-3 weeks of full day schedules, plus analysis time and putting together a presentation (while writing 2 papers and my thesis).  Additionally, I just found out from the lab I was supposed to get my samples from today that because they aren’t getting in the new freezer until tomorrow, I won’t be able to access my samples until Friday afternoon after they’ve re-put everything back where it needs to be.  These are the little day-to-day things that people don’t really think of being part of research, but are snags that will affect how quickly things can be done.

Anyway!  At least the couple days’ reprieve from retrieving and processing samples means I have time to look over the short students’ Letter to the Editor I wrote with a couple students on a side project that just got accepted with minor revisions, as well as to re-draft my 2nd paper, which my PI and I just decided we should expand to a full manuscript yesterday (as vs. the Brief Report we were originally thinking of submitting it as – there are different lengths and purposes of publications, which I might get into in a future post if anyone’s interested).  So yeah, that’s life at the moment!  No rest for the grad student – at least not one who’s trying to graduate in a couple months.

Catch you guys later!

March 24, 2017

Just sent in my revision for my first paper! (And why that is a big deal)

Filed under: "Me" updates,Grad school,Research — sanguinemare @ 4:12 pm

HELLO all you lovely people (aka the 1 person who may actually see that I have finally posted after months of hiatus)!  I’m so sorry for dropping off the face of the planet, but well, PhD life is somewhat of a struggle and between that and battling long bouts of depression, it’s been difficult to drag myself up to write something substantial like this.  (I have also come to realize that I think almost all graduate students go through a mini existential crisis/period of depression before it’s over, unless they are extremely lucky and really love their work, mentor, and are extremely fortunate in their ability to generate and analyze data, but that is a story for a different day… if I ever get around to it, haha).

… and now that I actually revisited my last post, I realize I have somewhat reiterated myself, so I guess not much has changed over the last… 7 months?  Haha whoops.  Oh well.  Also apologies in advance for the somewhat incoherence of thought on this post as my brain is currently rather fried.

Anyway!

So I literally just clicked “submit” on my revision for my first paper.  This is a big deal for multiple reasons:

  1. It’s a graduation requirement. Of course, this is my first priority right now, so it gets to be first on this list 😛  As a graduate student, at least in the biomedical sciences, we are usually required to have at least one paper published under our name before we are allowed to graduate.  This is because, as I’ve mentioned in my last post, publications are essentially the “currency” of academia, and programs want to help their students show that they are competent and competitive in the scientific world, which will help with their upcoming job search.  The slightly less altruistic reason is that it also reflects well on the department/program/school/institution if they can show that a significant portion of their graduate student population are publishing good papers in peer-reviewed journals (important statistics for funding purposes).

    The publication requirements will vary based on said department/program, school (i.e. school of health professions vs. school of bioengineering) and institution, but my particular one requires at least 2 papers published before graduation, with at least one being a first author paper (*note: review papers – which are essentially summaries of a particular topic based on research that has already been published – do not count towards this second stipulation).  The paper that I have just turned in is my first, first-author paper, and thus is super important to get accepted since I am trying to graduate in May/June, and it has so far seemed to take an average of 2 months for responses from journals, which means timing is really tight right now. Speaking of which…

  2. Revision = higher chance of acceptance (?). Considering this is my first experience with submitting a manuscript, I’m not entirely sure how accurate this statement is, but from what I gather, a revision decision is usually a positive sign for a manuscript to get accepted into a journal for publication, especially if the revisions are minor.

    To give a little walk-through of this whole process thus far, I first started the analysis for writing up this paper a little over a year ago, ~Feb 2016.  The first complete draft was written by June, and after many (many) revisions, we finally submitted this article to a journal in August.  We waited for a long two months, during which one of my co-authors casually mentioned that perhaps it was actually a good sign we hadn’t heard in so long because she had also submitted to the same journal a couple weeks later and had already gotten a rejection letter.  She was right in a way, because in October, we got our paper back with reviewer notes, which is better than an outright rejection since it means that the editors thought it was at least interesting enough to send out to reviewers.  However, the journal ultimately rejected it after the review, though they did give us an option to do an internal transfer to another of the journals in their group.  We took that option and I did revisions based off of the reviewers’ comments.  We then resubmitted it to the new journal this January (there was a brief hiatus on this work as I was out of the town/the country for a little over a month between Nov-Dec).  After waiting another 2 harrowing months, we finally got the decision letter last week, which basically said they thought it was interesting, but reviewers had concerns which made it unacceptable at the present moment. Hopefully that means it will be acceptable after the changes…?  So I made the changes, and sent it in today. (Though a slightly concerning note at the bottom of the letter said that any decision after the revision was final, which induced a minor paranoia as I went to click the submit button earlier today. Heh).  Here’s to hoping it gets accepted!  Which brings us to the last point…

  3. (If accepted =) it’s a milestone as a scientist/researcher.  I kind of alluded to this above, but basically, having a first-author paper in a peer-reviewed journal helps to establish your worth to the scientific community.  The first author is the one who has generally been involved in all the aspects of the study, including conception/design of the study, conduction of the experiments, analysis, reading of the background literature, and writing the manuscript. Thus, in a way, a first first-author paper establishes the level of work others can expect from the author in the future, and is thus like a debut of sorts into the scientific world.

So yeah. In a nutshell, that’s why I’m actually quite happy with myself/life for once, and will likely take this weekend to celebrate (some of us in MSTP are going to Six Flags for a day!) before the massive freak-out session starting next week about how I only

Thanks for reading and see you on the other side (after my defense)!

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