A graphical representation of my frustration

(by genomicrepairman) Sep 17 2015

I'm working on making figures for a paper that I walked into and have done some work to wrap up the study. I'm currently going batty digging through old files to find the raw files that were used to create graphs that apparently only exist in powerpoint files. These things are spread out to the four corners of the earth and its getting really annoying. Some of the files are in prism, some are in excel, some are in jmp, its getting crazy. If I make a figure I keep the raw data in excel but tend to make the polished figure in prism so its sitting there waiting to go into a publication.

Do you guys have a standard for graphs and how you want to see them?

2 responses so far

A Discourse on Electronic Lab Notebooks

(by genomicrepairman) Sep 11 2015

Is anyone using an ELN system for their lab. I've been looking at a few, Evernote in particular, to help me keep my multiple projects organized? Didn't know if you found a helpful system or what difficulties you had in implementing this?

7 responses so far

With all the hubbub about postdoc pay...

(by genomicrepairman) Jul 10 2015

I think I might need that $8k to purchase a license for Ingenuity Pathway Analysis. Goddamn that stuff is not cheap.

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(by genomicrepairman) Jul 01 2015

For the summer I have been fortunate to be assigned (read: saddled) with a high school intern. It turns out this kid kicks ass and has been nothing less than a pleasure, making reevaluate my dim view of summer interns. My goal from day one was to make them fairly autonomous but giving them a real project for which they have helped to collect data on. And they've done a great job helping me finish up the last few figures for a paper we are trying to push out the door soon. And its a win win for them to as they are wanting to use the work they did in the lab towards gaining an International Baccalaureate diploma.

I've been really impressed at their desire and ability to grasp not just the procedural stuff but also the conceptual aspects of what we do. This intern has been fun and really rejuvenating, I'll be sad to see them go. But we might work out some type of research arrangement in the fall.

2 responses so far

The equality of pain

(by genomicrepairman) Jun 27 2015

No one has the right answer! Everyone's proposals to fix the NIH funding situation boils down to give money to folks like "me" and fuck everyone else. So I have to agree with Odyssey's premise, maybe the current system is as good as we get. Maybe, the current system just cannot function properly when it is heavily taxed by an expanded investigator pool and a not enough resources to support them.

A shift to a HHMI style process is quite ludicrous as HHMI could never exist in a vacuum without the NIH and as Drugmonkey posits, the scalability of this is laughable at best. And once again you create a very insular version of science that looks more like a circlejerk amongst friends that limits the playing field even farther.

Is the answer that there is no answer and that we but here to play the game, trying to adapt and survive each day, while trying to make incremental beneficial changes to the system? Fuck it I don't know, but I know its not Germain's plan. To me there is a macabre but reassuring thought that all of us, the good, the bad, the riff raff, and (to some extent) the BSDs are all being crushed under the same terrible wheel. It could be that is the justice of the system, when the times are tough, to some extent we all bleed together.

6 responses so far

Post Ph.D. transition to Postdoc

(by genomicrepairman) Jun 15 2015

So now that I'm ensconced in my new position as a postdoc, I felt it was time to talk about the post Ph.D. Transition. The last few months of my Ph.D. program felt like a wild ride. It also felt so far removed from the rest of my experiences in grad school.

1. Thesis Writing: I wrote the thesibeast in about a month and a half of full time writing, followed by a round of making edits with the boss before submitting to my committee. What really helped was developing a solid outline and sticking to a writing schedule. Otherwise I would have fallen apart. I also learn that while I work best in the lab in the morning, my most productive writing occurred between 8pm and 2am. Nights were spent writing, just getting thoughts to paper and leaving placeholders, no worries about editing. Mornings and the rest of the day were better spent doing routine editing or working on figures.

One other huge benefit during the thesis writing was enlisting a really good editor who dissected it line by line pointing out issue. It is humbling to have some just ripped though your stuff and have so much red ink on it that it looks like a prison knife fight took place over my thesis. But it was good, it made me realize where I need to clean up my writing and how to make me a better writer and communicator of ideas.

2. The Defense: I'd like to say that I spent a lot of time honing a well-crafted and beautiful presentation, but I didn't. I spent 30 minutes putting it together and my boss spent 5 minutes reviewing it with me the day before my public seminar. There were no practice presentations, no run throughs with trusted friends and lab mates, none of that shit! I had already given a similar evolving talk on multiple postdoc interviews (more of this later) so it wasn't much work or effort to give the talk.

The public seminar went really well and then came the room. This had been filling me with fear and dread. Not because I thought it was going to go like 12 rounds in the ring with Mike Tyson, but because I never really knew anything about the whole closed door meeting. My boss was tied up before the seminar so I couldn't ask them what was standard operating procedure for this so I went to another professor. Their question to me was how did you enjoy your qualifying exam, it would be like that. I nodded my head and feigned pleasure at their response saying that the qualifying exam was a pleasant experience. This dear reader, was a bald face lie. My experience with the qualifying exam was tantamount to sandpapering the asshole of an alligator in a telephone booth and the exam was chaired by the professor who I had sought advice from. This same person came to apologize to me the week following my exam about how rough they went on me. I'd like to say I remember a lot of the details from this event but I guess we tend to repress the most painful of memories.

But my time in the room with the committee post-public seminar was brief (~45 minutes), the committee had minimal edits to my thesis (most of these came from my boss). Most of the discussion centered around clarifying things that I had written about and then talking about future directions of the project, even though I wouldn't be there to do them. I amended portions of my thesis that caused any confusion to be much more explicit so whoever (read no one) picked it up to read it would have an easier time understanding it.

It took all told about a week and a half to finish all of the edits and get it into final format to be submitted to the graduate school. And because it had a good chunk of preliminary data I had to go through channels to embargo its publication on Digital Commons for at least one year to give us time to publish the data.

3. What's next: Okay, so you are about to get or just got a Ph.D., what the fuck are you going to do for that? That's a very personal question that we all have to answer our own self. For me I knew I wanted to do a postdoc in order to expand my knowledge base and skill sets. About 5 months prior to my defense I sent out enquiry packets to prospective labs for postdoctoral positions. This was timed as the main publication of my thesis was set to come out a month later. My first interview occurred a week before the publication went live, so everything was happening really fast and was a bit exciting and nerve wracking.

I feel that part of my success at getting postdoc interviews was crafting a nice application packet that included a personalized cover letter, cv, and copy of my in press manuscript. The email was also personalized and literally every person I sent it to, I got a response from whether it be an invitation for an interview or a sorry I'm out of money. Even the folks who didn't have space or money told me to check back later or suggested someone else to contact.

Interviews...I had all kinds of interviews...less than 24 hours on site, three days there, skype interviews, phone interviews, you name it, I did it. Dinner with the PI, dinner with the grad students, nice PIs, standoffish PIs that try to elicit a response from you, it was like Patty Hearst in the bank video...all a blur. But I was there. My suggestions for interviews are to make sure you have enough cap space on your credit cards as some places made me pick up my accommodations and then I would get reimbursed or other places would pay. Everyone I met I always asked them the same few questions: what makes their lab different from any other lab, what frustrates you about their lab, and if you could change one thing about your lab what would it be. Its interesting to see the spectrum of answers that come from techs, students, postdocs, and even the PI. It also provides insight if everyone says the same thing is a problem then it probably is a real problem.

If you want to chat more about the postdoc interview process and how and why I selected the lab that I did, shoot me and message or email and we can chat in a more private manner.

3.  Ramblin' Man...This is the really tough part, when do you put the pipets down, pack your shit, and hug your friends. For me the decision was easy. I got my main paper out and one co authorship out. Other future stories that I was developing were proceeding with some progress and could be capably handled by other members of the lab that I had trained. I decided jump shit approximately one month after my defense so that I could start my postdoc. This was due in part to the fact that my previous lab was going through a period of funding troubles, so one less mouth to feed at the table, means you can feed the rest of the mouths for that much longer. The good news is a grant came through for the lab, spurned by some of my work and contributions.

I think the main reason that I bugged out quickly after the defense was that we had a glut of papers that still needed to get out. Those papers would take close to at least one year before anything else of mine may come out. So to quote the Allman Brothers "When its time for leavin', I hope you understand, that I was born a ramblin' man."

4. FNG. I'm still the FNG and the stench has yet to wear off. Making the long move and starting the postdoc was exciting but brought with it a whole new set of frustrations: orientations, trainings, byzantine rules of supplies and procurement, etc. The lab is good and I'm making good data (which I'm happy about) but not at the pace that I want (which I'm not happy about). But overall things are looking up and my new master, at least for the time being, seems to be pleased with me. I'm adjusting to the differing mentoring styles and how this PI likes to conduct individual progress and laboratory meetings compared to my old PI.

The folks in the lab are great about teaching me new techniques and in return I'm showing them things from my bag of tricks, so its been great. I'm still less than four months in the lab but I feel like I have yet to be able to turn it up to 11.

So in conclusion, the transition has been interesting and is still ongoing. I'll post more as time allows. Feel free to leave feed back about your own journeys and transitions from post graduate school. Maybe this will help someone out or at least bore them into fitful sleep if the Ambien has yet to kick in.

2 responses so far

Happy Festivus 2014 edition

(by genomicrepairman) Dec 23 2014

Break out the Festivus Pole its time for the annual Airing of Grievances and Feats of Strength.

"Festivus for the rest of us!"

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The Hunt for Red October....er...postdocs--is over!

(by genomicrepairman) Dec 23 2014

I found a great lab with good folks, great ideas, and stable funding.  I'll be starting there soon and sent out my unfortunate Dear John letter's to the labs that I didn't choose.  I felt bad about all but one of them, the outlier was a major douche and a bit of nasty bastard to even his own people. Science is hard enough, I don't want to have to worry about someone's mood swings.

3 responses so far

Thesis Writing Tips...I need them

(by genomicrepairman) Nov 17 2014

I'm in the throws of writing my Ph.D. thesis right now and could use any tips.  I mean anything, crazy ass endnote tricks, how to deal with the boredom, etc.


I already got pissed off at my laptop for being slow and maxed the hell out of the RAM, so now its running like a methhead from the cops.

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The Hunt for Red October...err postdocs (Pro-Tip Edition)

(by genomicrepairman) Oct 27 2014

Just some thoughts as I'm rolling through interviews:

1.  Don't wear jeans and wrinkled t-shirt on the day of your interview. (Not me, someone else interviewing in the lab next door).

2.  If you are presenting from your laptop, please bring VGA and DVI adaptors (Like I do).  Invariably they don't have the one you need.

3.  If you are presenting from your laptop, clean up your laptop (Don't leave talks from prior interviews on the desktop or anything compromising for that matter).

4.  If someone asks you where you are interviewing, just be frank and tell them.  If you don't you just come off as a slippery eel.

5.  Clear some space on your credit cards if you are doing multiple interviews back to back.  Some places make you buy your own plane tickets, hotel rooms, transportation, etc and then reimburse you (this is dependent upon the institution and its purchasing regulations).  This begins to add up really fast.

6.  I always ask everyone in the lab what's one thing they wish they could change about the lab.  This question usually is a kind way of asking them what they think is something negative about the lab and leads them to answer candidly.  I also pose the same question to the PI but I rather ask it as what are your current and future challenges you face with the lab.  This usually elicits a pretty good response and you get an insight into what PI is battling with in the lab and finds important.

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