Archive for: February, 2011

Got Data???

Feb 28 2011 Published by under Data

Actually you've probably got too much and you probably don't have the time to sift through it, let alone store it in an organized fashion for perpetuity.  Data management is (at least for some of us) becoming almost as cumbersome as getting the damn stuff to begin with.  It would be great if we had a bioinformatician chained next to us at the bench so they could be analyzing and processing the data as we are creating it in real time.  And a few labs even do, but they are the serious outliers.  At best some of us are crunching our own numbers but the rest of us poor saps are having to hand off our data to others for this task and wait in queue.

Next where are we storing these vast quantities of digital data?  Are your universities and institutions setting up and running secure servers so that you data is at least protected and accessible to you let alone the public?  Do you have a mini-server or a more complicated RAID5 setup humming away in the corner of your lab?  Or are you the poor bastard whose data is only on the hard drive of your desktop that is infrequently if ever backed up?

I think a huge problem that is on the horizon, especially with doing research that is data intensive is:

-Where are we storing it?  Should we be dumping it all into government repositories like some folks stash their microarray data in GEO or Gene Expression Atlas.

-Should we be using a standardized format for data that we store?  Excel, ASCII, comma versus tab separated values?  Ugh!

-Do we do our own bioinformatics or just farm it out?  Before the rate limiting factor of some my research was doing the experiments.  Now its data processing and analysis.  A recent survey in Science showed that only 24% of respondents had the capability to do in-lab data analysis. 34% were using collaborators and 23% felt that they did not have the necessary skills to analyze their own data.

-Do we store published data on university servers which are more stable and kept current than those that exist in many lab currently?  And who the hell is going to pay for this?  80% of those surveyed said they did not have sufficient funding for data curation and 50% of the labs were keeping data archives on computers in their lab.  And as Dorothea has previously brought up, there is a general lack of research IT.

-What are our policies for data requests?  Should there be a standardized policy put forth by the NIH, universities or just leave it up to the individual lab?  Less than half of the labs that asked for data got it, with the other half only getting requests for published data fulfilled "sometimes."

We've got to tame this tiger before it gets too out of hand.

10 responses so far

The best lab prank ever...

Feb 21 2011 Published by under Grad School, Pranks

So I was talking to a friend of mine about how we used to play lab pranks back in the day when I used to be known as Canz, and I used to be a bit of a motherfucker back then.  The best prank we ever played together was on a technician from another lab named Carl.  This prank was epic and honestly we probably should have been fired for what happened to Carl and the darkroom.  But first, why play a prank on Carl?  Glad you asked, Carl was a bit of a prankster himself and would set up timers all over the place to go off in a coordinated sequential manner.  And I mean he hid them everywhere, I shit you not I had to get a ladder to get up into our 15 foot vaulted ceiling to get one down.  He would also rewire your computer setup, good luck printing shit.  After getting pranked by Carl, the departmental jokester, a couple of times it was time he paid the piper.

So let's get to the organizing of the prank.  We knew that day that Frank was going to have to go into the dark room to process expose and develop a western blot.  This was going to be the site of the prank.  So we went around to all the other labs and warned them to stay the hell away from the dark room.  I went to a store that rhymed with Smadio Smack and purchased five 130 db personal safety alarms, the ones that have the pull pins to activate, and grabbed some fishing line from my apartment before returning to work.

We wired the alarms in place, I'll get to the details of this later and turned off the lights.  And then we just waited, along with everyone else on the floor who knew what was about to happen.  I grabbed one of those wooden triangle blocks that you use to hold doors open and traversed the hallway as Carl was walking to the dark room.  As soon as he went into the revolving door, I took off like a fucking gazelle for the door and jammed the wedge in so the door couldn't open.

Poor Carl, as he stepped out of the revolving door, his foot kicked the first trip wire, pulling the pin out of what is ostensibly an alarm that a college coed would carry on their person at night walking home from the library.  Well in the small confined spaces of the darkroom, pulling the pin activated a 130 db alarm that is almost as loud as a plane taking off.  The only way to shut off the alarm is to put the pin back into the alarm, not easy in the dark, especially when the light switch is all the way across the room.

I imagine Carl tried to make his way across the room to the light switch but he activated the four alarms which made the room deafening.  By the time he got the lights on and saw all the pins, Carl was left with the choice of taking his hands from his ears to put the pins back in leaving him vulnerable to the alarm or just run back out of the darkroom.  Carl chose the running option.  Unfortunately the little door jam was still in place, Carl about ripped the revolving door off his frame trying to get out, while I'm trying to get the fucking door jam out to let him out.

At this point, I go in with some ear plugs and put all the pins back in and come back out of the darkroom to find Carl laying on the ground holding his ears and tears running down his face.  Luckily Carl suffered no permanent hearing damage, but his hearing was shot for the rest of the day.

Best prank the lab.

19 responses so far

Grab a pen and paper, or your keyboard...

Feb 15 2011 Published by under Blogging, CongressCritter, LinkLove, NIH Budget

Hat tip to Dr. Isis, for her post on the letter from FASEB asking for scientists to contact their congressional representatives to oppose the proposed $1.2 billion dollar budget cut to the NIH budget in HR1.  Paylines are already tight, and between the potential 5% cut in the budget proposed in HR1 and the ever increasing cost of doing science, this would put many people out of work.  I've already broken out pen and paper and am writing a handwritten letter to my congressman.

This is go time people and if you ever complain about people not getting into the fight to advocate for science, this is your chance to make a difference.  Pass this on to a colleague or better yet bring it up in your lab or faculty meeting and have folks in your lab or department write letters to their representatives.  Tell them what you do, how it will make a difference, how it will make the human condition a much better one.  Also tell them the detrimental effects to you and those personally around you if this funding cut goes through.  People laid off, studies left undone, patients left untreated.  Make them see that this would be more than cutting a line item on a budget, this is about cutting the careers of many who have worked so hard to see that our lives are improved.  Please take the time to communicate the importance of science funding with your congressional representative.  I fear that if we do not advocate for science, and quite strongly for this manner, this will be the first of many cuts to come our way in the future.

Also check out PiT, GertyZ, Thomas Joseph, and JuniorProf take on HR1.

See the contents of the letter below:

"Dear Colleague,

For months the new House leadership has been promising to cut billions in federal funding in fiscal year (FY) 2011. Later this week the House will try to make the rhetoric a reality by voting on HR 1, a "continuing resolution" (CR) that would cut NIH funding by $1.6 billion (5.2%) BELOW the current level - reducing the budget for medical research to $29.4 billion!

We must rally everyone - researchers, trainees, lab personnel - in the scientific community to protest these draconian cuts. Please go to [this link] for instructions on how to call your Representative's Washington, DC office today! Urge him/her to oppose the cuts to NIH and vote against HR 1. Once you've made the call, let us know how it went by sending a short email to the address provided in the call instructions and forward the alert link to your colleagues. We must explain to our Representatives how cuts to NIH will have a devastating impact on their constituents!


William T. Talman, MD
FASEB President"

9 responses so far

Science Blogger or Science Communicator...

Feb 15 2011 Published by under Blogging, LinkLove

Who fucking cares?

So last week I put out a post about some great student bloggers that I though folks might like to read if they haven't already picked up on them.  One of the bloggers I featured was Joe from Its Okay To Be Smart.  Now Joe seems like a lovely chap but he makes the disclaimer that he is a science communicator not a blogger.  Well he recently clarified his standpoint on this and I guess he doesn't want to be painted into a corner by just communicating through a blog.

"I have run across  a lot of very talented Heroes of Science (my name for them, anyway) out there on the internet, and many of them are just amazing. Of course, the medium of choice for disseminating science “a la interwebz” is the blog. Hence so many people calling themselves “science bloggers”. I don’t like that.

To me, the word “blog” really implies the diary formats of Geocities or LiveJournal, actual “Web Logs”. What are you really setting out to accomplish? Just log some intelligent thoughts in reverse chronological order? For most of you, I am willing to bet that you want to communicate science, and writing it on the internet just happens to be your weapon of choice.

Look at it this way: A carpenter is much more than a “hammer swinger”, and a chef is certainly beyond “onion chopper and pan flipper”. If you are a science communicator on the internet, a blog is just a tool. The real mission of a chef is a meal, and your real mission is more than a blog post. I hope."

This is just semantics and dude, here is the cold splash of water.  No one gives a fuck what you call yourself.  People who read you don't give a damn what you call yourself, they read you because they find you interesting.  If you want to wear thigh high boots and call yourself Doctor PussyMagnet like BrooksPhD, do whatever suits your fancy.

So my official response to science communicator versus science blogger debate is:


Thank you and good day.

Oh and you are not going to change my opinion that Tumblr is the biggest piece of shit platform to ever be designed since fucking Xanga.

11 responses so far

Everybody deserves a second (third) chance?

Feb 14 2011 Published by under Uncategorized

Maybe.  Below is the proposed petition that has been making its way through the intertubes and might have even landed in the inbox of your Google machine.  What is being suggested is to not do away with the A2, which the NIH has just shitcanned.  So if your original grant submission (A0) gets set on fire and beaten with a stick by reviewers you only have the A1 revision left in which to secure funding with that exact proposal.  If your A1 goes about as well as your A0, then you have to create a new proposal.  Exactly how new this is remains to be seen.  Can you just change one aim, shift your model system, or does this require a radical change in your proposal.  Which might not be such a bad idea depending upon how bad you did in the review process.

A reason for bringing back the A2 that is tossed out there in this petition is that, elimination of the A2 is inherently unfair and will be detrimental to new investigators.  Their thought process is that as a new PI are at a severe disadvantage because they don't have a developed research program that could make a "substantial" change in their aims/focus while they are dealing with limited people and funds.  I guess they don't want you burning up your playbook just trying to get your first major award or that maybe you dont' have a big enough playbook.

On the first point, this is all based off the old data where we had the system that included the A2 revision, which some say is being removed to eliminate serial resubmitters or to eliminate the systematic approach of making researchers wait through first or second review before being funded on the A2.  This is a gray area and I understand concerns on both sides of the A2, but I think we have to sit tight and see what happens.  If it can break the pattern of reviewers shelving a fundable proposal until its "their" time, then that would be great.  Besides, if removal of the A2 is a giant flop, who's to say they won't reinstitute it.

On the second point, you gotta have a decent playbook.  If you aren't creative enough to be able to sell your science on different fronts to different ICs, then you are in serious doodoo as the first President Bush used to say.

To see more on this debate, check out BlueLabCoats for the pro-side and CPP for the con side.  The scientific blogosphere awaits an a response from the venerated Drugmonkey.  As for me, I'm not a PI, I'm going to shut the fuck up and sit on the fence and see how this goes.

Dear Colleagues,

I am writing to solicit your help in changing  a new NIH policy that I believe will have an enormous negative impact on our field. As most of you know, a recently adopted rule states that if a grant proposal is not funded on the first submission, only one revision can be submitted with the same specific aims. If that revision is not funded, the proposal must be "substantially" changed. As far as I understand, the rule was adopted to discourage "serial resubmitters". While such a policy could make sense in an era of reasonable paylines, with the projected budgets rumored to be funding at the 7th percentile in some sections, this could have a dramatic and I would argue devastating effect on the research efforts in this country. Consider the following:

The rule will have a disproportionately negative impact on young investigators with early stage and therefore less diverse programs, or more senior investigators who also have more narrowly focused programs. How can a young investigator, for example,  who is just starting "substantially" change their aims when they have to focus their efforts on a very limited number of projects undertaken with limited funds and staff. These people are often hired by senior faculty on the basis of their first projects and to be told they must change on the basis of applications that might fail despite being ranked

better than 90% of grants submitted, seems patently absurd. And worse, it is likely to be profoundly discouraging and destructive.

All of us who have sat on study section know that we cannot distinguish a 15th percentile grant from a 5th percentile grant. It is simply beyond the resolution of the process. Therefore, this new rule will have the consequence of redirecting the science of many of our very best scientists on the basis of what will essentially be an arbitrary criterion.

The meaning of "substantially changed" has not been clearly defined.  Program Officers themselves are not sure what this term means and are not being given adequate guidance. I have heard things from "51% different",  change the tissue or cell type you are working on, any aim included in either the first application or revision cannot be included, etc. We need clear and unequivocal guidance on this point, and I would argue we need it immediately as "new" applications are being prepared by a large number of investigators at this time.

The alternative that I advocate would be to go back to a system where at least 2 revisions of the same application would be allowed. While we will still obviously lose some superb applications if the pay line stays where it is, I think this would provide a much fairer assessment of the research proposals received by the NIH.

My intention is to let the feelings of a large number of scientists on this

subject be known. If you are willing to sign an email that will be sent to

both Francis Collins and Tony Scarpa (Director of Center for Scientific

Review) that raises these points, please let me know by simply responding to this email and (if possible)  forwarding it to 10 people who you know (not on the current recipient list) that might also want to sign. If I can accumulate a large enough number of signatures (100-500, say) I will draft a letter and send it first to all who have expressed interest in signing to get feedback.

I must say, I am not generally prone to such activism but I think things have just gotten to the tipping point.

I look forward to your responses.

With kind regards,

One response so far

Guest Posting and Guest Blogging

Feb 14 2011 Published by under Blogging, LinkLove

Okay folks, first up I am guest posting over at Scientific American today, stop by and check out "What Guido Fanconi taught us about chemotherapy."

Next up, Scientopia has set up a Guest Blogge to showcase some non-network bloggers.  The first couple of posts have been great so make sure to stop by and read them.  The schedule is posted below and I wanted to especially thrust some accolades at Mark, Comrade Physioprof, and Dr. Isis for bringing this to fruition.  Thanks guys, you hard work is appreciated.

February 13-26
Zygoma and Frautech

February 27-March 12
Thony C from The Renaissance Mathematicus and bloggers from Disability Studies, Temple U.

March 13-26
Rue from Outdoor Afro

March 27-April 9
KJ Haxton from Endless Possibilities v3.0 and Patrice Brassard and Émilie Pérusse-Lachance from Le Physiologiste

May 8-21
Scientist Mother

One response so far

The Laboratory Decathlon

Feb 12 2011 Published by under Uncategorized

Okay folks, you have ten events showcase your scientific skills and solidify yourself as #1 Lab Ninja with mad skills.

Event #1: Sequencing Gels
I don't want to see air bubbles or leaky gels, when you come to the sequencing gel event you better come strong. And as a test of interpretation we'll go old school Sanger sequencing of a known template.

Event #2: Weaning Mice & Genotyping
Accuracy is a must, that better not a dude in the ladies cage and are you really sure its a heterozygote. Points will be deducted for overaggressive tail snips

Event #3: Nuclear Extracts
Contestants will be given the same number of cells and asked to generate nuclear extracts. Don't even think about picking up that kit, I want to see you prepping buffers and sweating over a dounce homogenizer. Scoring will be based upon concentration and total protein yield. Also I'll be checking your extracts for quality, there will be no degradation in my house Holmes!

Event #4: Metaphase Spreads & Chromosomal Analysis
That's right, this shit just got intense. If Painter could do it, so can you. I want to see good mitotic indices, and better know if those cells are 2N, 3N, or 4N. Is that a radial? You better know.

Event #5: The Dreaded PCR Event
You will be given template DNA and a set of primers. Optimization of the reaction is up to you. Style points will be given.

Event #6: Hot hands
A tube of 32P labelled probe falls to the floor, whatcha gonna do? Spill containment will be judged by EH&S employees. Harshly. Good luck.

Event #7: The Tip Shoot.
Bring your favorite pipetor whatever it may be, we are shooting off 1000 μL tips. The event will be broken down into two objectives: Distance and an Accuracy shoot (gotta make it in the tip bucket). John Daly's and sharpshooters are welcome.

Event #8: Tip Box Pack and Stack
Since you used up all of my tips in the last event, time to repack the tip boxes and get them stacked up for autoclaving. Fast hands are a must.

Event #9: The Amazing PI Race
This sprint is used to simulate the dash of the trainee to the PI's office when they have hot data. Make sure the stretch properly, no whining over a strained hammy.

Event #10: Get This Piece Of Shit To Work
Nuff said.

18 responses so far

Don't ever....

Feb 11 2011 Published by under Get Me Outta Here, Grad School

make 3-D structure of your protein dance to the beats of Outkast's Hey Ya while in PDB Viewer, its intoxicating. Structural analysis has never been so fun.

Have a great weekend everybody.

11 responses so far


Feb 10 2011 Published by under Uncategorized

If you could set one annoying piece of equipment in your lab on fire, what would it be?
I've got a fucking ChemiDoc that's living on borrowed time!

13 responses so far

Who you should be reading: Grad Student Version

Feb 09 2011 Published by under Blogging, LinkLove

So from time to time I like to find new blogs to read and post links to them. This time around I'm doing med/grad students, so here are 4 bloggers and 1 science communicator (WTF?) for you all to take a look at.

Its Okay To Be Smart
Joe is a science communicator, not a blogger? Whatever, the guy has got something to say and its usually pretty good. Check him out if you want to read more about pop science culture, as well as science and society. He also has a Tumblr site but I don't understand how the fuck that system works so I refuse to link to it.

Ret Mutant is a developmental biologist who is just cutting their teeth in grad school (working their way through the rotation system). Really high quality research blogging posts here people.

Disease Prone
Have you been jonesing for another microbiology blog, well here's another Joe. This Aussie microbiology grad student muses on all things bug-related.

I Can't Ask My Doctor That
Ever had some really freaky naughty questions that you were to embarrassed to ask your doctor? Great, then asked this med student and trained sex educator. This blogger covers everything from A (Anal) to V (Virginity).

Samia is a biology grad student who is hilarious and is currently working her way through rotations. Stop by and say hello.

8 responses so far

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