Archive for: March, 2011

Pimp My Lab

Mar 27 2011 Published by under Lab

So recently Dr. Becca had a post up about suggestions for her own very new brand spanking laboratory.  Now I may be a lowly grad student but in a former life I was a technician who participated in the design phase of a new lab building, it was a process that took almost two years (just for design) and I left before they ever broke ground.  However touring the site years later I see the ramifications of our input.  Sometimes you have to know when to tell the consultants to fuck off when they say well so and so designed this feature.  That's great but the shit doesn't work for us here.  But you also have to know to listen to them to pick up new features you hadn't thought of and prevent potential missteps.  So like Xzibit from MTV's Pimp My Ride, GR is going to pimp your lab.  Here are some tips:

-Power: Baby its all about the electrons, they got em, you need em.  And like Coldstone Creamery its not a like it or love it situation, you gotta have it.  You want as much power routed to your lab as possible.  How many times did we want to get new fancy swinging dick equipment that couldn't at this particular spot in the lab because of power issues.  Think lab placement, don't put all your heat blocks, table top centrifuges, and thermocyclers in one area or you will have breakers popping like a motherfucker.  Spread that shit out son.  Also check every plug to make sure if its active.  If its not, ride physical plant's ass like Zorro till you get what you want.

-Internetz: You gotta power the Google Machine to do your PubMed searching.  I don't give two shits what anyone claims, university wireless internet is like cheap hotel wireless internet, 60% of what it should be.  Plus some of the nodes die and university tech can be slow as shit to replace them.  Make them run ethernet cable.  Everywhere.  Hard connections are where its at.  And they may balk at this but push your point.  And it really is expensive.  Numerous universities hire outside tech companies to run CAT5 cable (demand CAT6 by the way) and charge a shitload to do it.  I know, I used to do it to pay tuition.  Its not that hard and they can drop it in from the ceiling anywhere in the lab you demand.  Also make them activate every single port you have, its much harder after the fact to get a port activated because someone has the wrong number or it got plugged into the wrong jack in the closet.  Make sure they have the appropriate outlets for freezers and centrifuges so you can place them where you want.  If they don't, demand it.  You have to live in this space for a long damn time, why not make it comfortable and convenient?

-Water: Some of your experiments may be sensitive to water quality.  House dH2O are notoriously shitty if they supply a large building and I wouldn't even wash my balls with the shit.  Get a resistance meter and check it out.  18 microOhm, now we're talking.

-Cabinets: If you don't need the doors on them, rip them off!  They only get in the way.  If you do need the doors, get glass fronts so you can see what lurks behind the doors.

-Labels: Label the shit out of everything so that your noob grad student doesn't have to bother you to find the damn lab tape.

-Data: You better have something to back up your data to.  I suggest purchasing a desktop to run as a backup server or use university server storage if available.  I still suggest doing individual backups using Time Machine if you have a Mac and keeping offsite for important data.

-Hoods: Check the airflow regularly, especially if you are working with hazardous chemicals.  You'd be surprise how often they do maintenance on the hood motors and accidentally throw them in reverse or just run them at half speed.  If you don't have any apparatus to test the laminar flow, ask a smoker to hop in there and light up.  Hell a guy I worked with used to take smoke breaks in an unused hood when he couldn't break away from his chromatography columns.

-Space for animal work: Most IACUC's require a dedicated space in your lab for animal work if you are doing it.  Bear that in mind when laying out your little science factory workspace.

-Chairs: We like comfy chairs too, especially when we are hunched over the bench doing tedious work.

-Balances: If you are using an analytical balance, you need a sturdy surface that isn't going to screw with your readings.  Put a balance down and lean on the counter and see if the reading changes, if it does, move it ASAP.

-Food in the lab: WTF is this, we don't eat in the lab, you do fucking science in the lab.  You want to go eat in the lab go work in the fucken Chiken McNuggetz factory.  Go eat in the break room or set a small table outside the lab so people can leave their water or coffee.

-Temperature: Is it so hot in the lab that your agar plates are melting or so cold in cell culture that you have space heaters going?  Sadly temperature is the hardest fix of all because the HVAC systems are usually maintained by outside companies like Johnson Controls, etc.  If its too cold, you can tape up some cardboard to block the vent.  Just don't let EHS catch you doing it.

-Music: A centrally placed radio or iPod dock would be quite nice for your minions.  You can let the inmates determine what music is playing in the asylum or set up a rotation.  Music soothes the soul and the disgruntled trainee.

-Freezers: Try to place these in convenient areas.  Having worked next to a -20°C for a year the white noise created by the damn thing almost drove me insane.  Try to keep mechanical noise at a minimum in the lab if you can.  Its hard to hear yourself think when its loud as fuck in the lab.

6 responses so far

Help a blogger out

Mar 24 2011 Published by under LinkLove

So Krystal D'Costa is a super rad anthropologist and unfortunately a Mets fan, but we'll let that crap slide.  Anyways she is trying to get a panel together for New York Internet Week and she needs your help.  Her panel, "The Evolution of Communication will trace the social ripples of communicative technologies through history (and prehistory if time allows) investigating what exactly is new about new media."

Click here and go vote for her.  Now get off your asses and get the vote, consider it preparation for 2012.  And folks, I heard a rumor that if she gets her panel she'll send a dozen warm fresh baked cookies to anyone that voted for her.  Sorry I wasn't supposed to let the cat out of the bag.

No responses yet

Creepy Vendor

Mar 23 2011 Published by under Vendor

So once in a while we have this scuzzy fucking vendor rep that will show up and troll the halls from time to time.  This guy is a creepy mcfunster who has this leering gaze that makes all the females in the building tense up and freak out.  Hell every time a guy in our lab sees this moosebag, you can tell his asshole is probably involuntarily clenching in discomfort and he scurries off to get away before the vendor sees him.  Thanks a fucking lot.  I'm tied to the bench doing some shit so that means I've got to stand there while Shasta FuckinMcNasty chats me up.

What makes matters worse is he is picking his nose as he is coming down the hallway and I can see it.  He rounds the corner to my bench and I turn to look at him just as he adjusts his dick in his pants.  So gross, I'm about to puke.  But the worst part is, while he is trying to shoot the shit with me and get me to buy his stuff for which I have no additional need, the dude is digging in his ass.  I mean this motherfucker was going to China.  I hope he had a permit because homeboy was digging deep and hard, it was so bad he was standing on his tipey toes trying to find some buried treasure.

Thank goodness I had gloves on and didn't have to shake his hand.  And if you guys want to kick in some money for therapy that cool, its gonna be expensive to get this visual out of my head.

12 responses so far

I wonder if you can weld this onto my wedding ring...

Mar 20 2011 Published by under Uncategorized

So I can count colonies and never worry about using you...

I will now invoke some PLS:  Dude. Fuck. Sigh.

One response so far

Pubwhat?

Mar 16 2011 Published by under Publishing, PubMed

I was talking to a grad student about publications and access to articles a while back and thought that I should write a little primer on it for other noobs to read. So I think somewhere somehow sometime someone listed the stat that NIH funded projects generate nearly 80,000 articles per year. And since the government is coughing up the money for us to do the work, in the spirit of transparency, these articles and the results and conclusions contained in them should be made available to the public.

And since Joe and Josephine Six Pack can’t really afford access to medical journals, researchers, whose research is funded by the NIH, are required to post articles in the PubMedCentral (PMC) library within 12 months of publication. The requirement is limited to peer-reviewed articles, and doesn’t include book chapters or conference proceedings, etc. I believe these requirements kicked in for anyone receiving direct funding from the NIH starting FY 2008, so don’t go grieving some PI about stuff they published back in ’68. Why are we doing this?
-Well first off, you are letting your investors, the taxpayers, see what we are up to.
-Next you are putting your science out there and hopefully making a name for yourself.
-Pumping up your citation stats
-Prepping yourself for future Open Access regulations that are starting to take root in other agencies such as the NSF.
-So Nana who lives in East Jesunuckistan can see your latest article when she fires up her Prodigy account on her 14.4 kb/s dial up account.

And for you noobs, PubMedCentral ≠ PubMed. PubMed holds citations for more than just journal articles dating back to around post-WWII, it also includes links to PMC in it. Also PMCID is not the same as PMID, but if you have one and need to get to the other, here is the converter. And sometimes you will have to wait since articles don’t always get a PMCID number right away and you are just stuck with the temporary NIHMSID.

So how do you make sure your stuff ends up in PMC? Great question, there are generally four typical routes that this happens.

1. Publish in a journal that deposits all final published articles in PMC that don’t require any action on the author’s part. This is the easiest option of all and here is a list of journals that will do it for you.
2. Make arrangements to have publisher deposit final published article into PMC.
3. You deposit the peer-reviewed manuscript via the NIH Manuscript Submission (NIHMS) process. This differs from the previous two options in that those options use the journal’s final article and this option publishes the article in the manuscript format, so it’s not as pretty.
4. Some publishers will kick start the submission process in NIHMS but you have to finish it. They’ll dump the article in the hopper but you have to give it the thumbs up.
A lesser-known option is that you can pay me to do it for you. Yeah it will cost you a little more, but when your article’s PDF pops up on PMC with actual liquor stains on it, you’ll feel mighty proud.

7 responses so far

Casting your net...

Mar 14 2011 Published by under Grad School, PubMed

So I think one of the smartest things that I did as a grad student was to create an NCBI account so that I could schedule in saved weekly searches of the PubMed database.  That way I don't miss the pertinent literature or have to go lurking for it, it comes straight to me.  For instance, lets say you study Rump Shakin, why not follow the big whig Rump Shaka of your field, that way you can see that groovy person's new papers to determine if they are pushing the field more towards the Humpty Dance or are they skewing towards Poppin & Lockin.  There are endless possibilities of searches to set up and can come to you, daily, weekly, monthly, etc, but here are some that I recommend:

-Big Whigs in the field

-Competitors (always good to know what they are putting out there)

-Your gene or protein

-Your field/subfield (I do a broad and narrow search)

-Collaborators (its sometimes nice to keep tabs on what these scalliwags are up to, when they aren't taking for damn ever to get back to you)

Hope this helps, I use this as a way to comb the literature without literally having to comb it, I just open up my inbox and the beautiful bounty of the aggregated pubs glows like the briefcase in Pulp Fiction.  I'm sure many PI's do this but I have known more than a few grad students and postdocs that had no idea of this and were manually searching every week or two for topics.

I'm lazy and if "If Mohammed will not go to the mountain, the mountain must come to Mohammed," then I let the PubMed citations come to me.

13 responses so far

Reflections for the week...

Mar 13 2011 Published by under Uncategorized

-BoHonkeyPimpStick Francis Collins will be discussing his vision for NCATS on Wednesday via a webinar. (h/t: Writedit)

-Watching a kid crash a $2000 RC jet airplane at the park was hilarious and the kid had no idea what was going on as I shouted out "Goose..." as it smacked into the ground and caught flames.

-Daylight Savings Time is not conducive to nursing a serious hangover.

-CPP has a great post up on why you should always have multiple grants in the hopper.

-Go see Rue Mapp holding the Outdoor Afro court in the Gueste Blogge.

-March Madness is upon us and you can join the bracket pool by getting in touch with me (see here).

-Beer makes you feel like you can take on the world.  Whiskey makes you feel like you can take on the world and the rest of the fucking universe.

4 responses so far

Publication Strategy...If I can't beat 'em, I'll wait 'em out...

Mar 08 2011 Published by under Uncategorized

So I was chatting with someone about the Journal of Biological Chemistry, a solid journal whose IF suffers from the diverse amount of biochemical work, but still remains one of the top cited journals. So way way back in the day when future Nobel Prize winner Arthur Kornberg was trying to publish his discovery of E. coli DNA polymerase I, he chose to publish his work at JBC.

Based upon previous work on glycogen polymerization by glycogen phosphorylase by the Cori's, Kornberg assumed that Pol I just polymerized the nucleic acids but didn't give much thought to DNA also serving as a template for polymerization.  Upon recognition that the addition of all four of the dNTPs were necessary, he recognized that the DNA he added to the E. coli lysates served as both the primer and the template.

Kornberg wrote up his work into two separate reports and submitted both manuscripts to JBC in the fall of 1957.  The reviewers, to kindly put it as my mom would say, took poor Artie out back behind the woodshed.  Some of the scathing criticisms of the rejected paper included:

"It is very doubtful that the authors are entitled to speak of the enzymatic synthesis of DNA"

"Polymerase is a poor name."

"The authors had to show genetic activity in the synthetic substrate to qualify it as DNA."  (This had never been required before).

Rather than shop his papers to other manuscripts, Kornberg waited until John Edsall took the helm as Editor in Chief of JBC before resubmitting the papers which were eventually accepted and published in 1958.

So patience is a virtue after all.

If you are a bit of a science history nerd, you can find some correspondence between Edsall and Kornberg about the manuscripts here.

7 responses so far

The Science of Bracketology

Mar 07 2011 Published by under Uncategorized

So, I'm thinking of putting together an NCAA bracket competition if folks want to join in. The prize will be something like an Amazon or iTunes gift card for the winner, but really we all know its about the bragging and shit talking. So if you want in on the fun, click on the about page and drop me an email or a tweet.

2 responses so far

Blessed are the departed...

Mar 01 2011 Published by under Uncategorized

This was my crazy Twitter rant from the other day. Thought it was funny enough to turn into a post...

Blessed are the departed,
for they are no longer graduate students.
Dare not let thy heart be consumed with darkness,
for on the seventh day, they shall arise agin as postdocs.
They shall endure much suffering and persecution.
The faculty search committee shall judge both the not so quick and the brain dead.
But the faithful shall be rewarded with tenure track,
and seated at the right hand of the department chair.
They shall liveth and reigneth as the PI.

Until then thou art commanded to honor thy PI,
but love thy lab manager.

The word of Collins.
Thanks be to Varmus.

The 10 Commandments
-Thou shalt not mansplain
-Thou shalt not fake data, least thee be reported on writedit's blog.
-Thou shalt not covet thy neighbor's ESI status.
-Thou shalt not molest the eyes of the audience with the most vengeful powerpoint color scheme.
-Thou shalt not use up the buffer without reordering.
-Thou shalt not pirate software, lest thy need it for a grant proposal due tomorrow. But thou should feel bad if thy do.
-Thou shalt not be the 3rd reviewer.
-Thou shalt not covet false idols such as #K3rn or #N00n4n.
-Thou shalt not apply for an R21 when thou should be applying for an R01 instead.
-Thou shalt not forget to troll Scientopia.

8 responses so far