Archive for the 'Uncategorized' category

The Trouble with Service.

Sep 14 2012 Published by under Uncategorized

A couple of weeks ago I wrote, in high spirits, about finding an NIH Funding Opportunity Announcement that matched perfectly with something I’ve thinking about doing. It was an R21 grant, which is a small 2 year award for novel, exploratory research. The little bit of funding would have covered someone on my team to try and do something new and fun with one of the tools we have at our disposal, and see if we could broaden its impact and predictive power. If it worked then we could apply for a larger R01 type grant and fund expansive and scalar development of this tool. If it didn’t work, then no-harm, no-foul.

I called my dear friend and co-Scientopian, Dr. Becca, because I know she has been funded by this exact FOA and she encouraged me to apply, and even very generously shared her successful application with me so I could get a handle on the constraints such a small award carries (you only get 6 pages to explain how you’ll take over the world).

I met with the professor who would be joint-PI on the grant with me (adding the clinical & professional clout we’d need to get on the NIH radar). She was super supportive and had some great ideas on how to focus down the project to make it very straightforward and predictive. She was aware of some other work in the general field and offered to make some phone-calls to check out the possible “competition”.

This was a little over three weeks ago. The grant is due, in its completed form in our Office of Research Administration (the institute submits the grant for you) in 27 days time. I had 7 or 8 weeks bookmarked to work on this bloody thing and I haven’t even jotted a note or drafted a budget.

I guess I still have time to rattle something out; 27 days isn’t bad really, but there have been made on my time new and un-refusable demands that is making focusing on this personal project almost impossible. I run a core service unit – we are “contracted” (if you will) by faculty to perform their biomedical databasing and computing needs for their research (what a horribly clumsy sentence!). One of these projects has arisen and it is for a MONSTER of a project. It involves working on another grant ($4million/yr), due at approximately the same time my paltry little R21 ($120k/yr), and alas I’m having trouble multi-tasking with this.

I am not sure if I should just call my Program officer and tell her that we’ll apply for the R21 next Spring when “things calm down”.  I guess one of the hardest parts of this “new” job is learning how to balance my time to fulfill contractual obligations with the prospective demands on my career development.

I’d appreciate input, especially from faculty readers. Am I being a wimp? Should I be doing both, or is prioritizing the big a more useful and productive measure?

2 responses so far

There is Life After the Bench

Aug 30 2012 Published by under Uncategorized

I take career development very seriously, and spend a fair bit of time on and offline talking to postdocs who are looking for help in moving their careers in new directions. I was one of them once (and may be again one day, who knows?), and I was incredibly fortunate to have a great mentor help me transition away from the bench when my lab career sputtered and died.

I am kind of a LinkedIn evangelist and also attend networking meetings with a couple of local groups, some science focused, others not so much. At one of these last year I met a local postdoc and we got to chatting. We've gone for beers a couple of times and I've done my best to offer ad hoc advice when it's been asked for; nothing formal, just offering experience and perspective. I wasn't convinced that hir mentor was taking hir career development seriously, and worried it was dead-end tech position that was being held to postdoc standards: you spend all day doing scut work, but are still expected to produce real data and papers and so forth...I firmly voiced my concerns once and left it that. This person seemed happy just puttering along, until recently.

I received an email from hir about how hir position was gradually being undermined from within the lab and how hir relationship with hir mentor had gone from indifferent to bad (as I expected when hir productivity was necessarily so low). There was a great position at local hospital being advertised, but zhe wondered if the job was beyond hir reach because of being stuck as a postdoc/tech for so long and not getting as much clinical experience as might have benefited hir.

Although I didn't know anyone in this department at the hospital I went on LinkedIn and saw someone only once removed my network who worked there. And in addition I was directly linked with a former colleague who knew this individual personally. I was able to facilitate an introduction and then an informal meeting between my postdoc friend and the person recruiting at the hospital. The meeting went well and my chum was encouraged to apply for the position. We spent quite a bit of time on hir resume and cover letter - after all, no one outside the lab gives a damn how good your western blots are, they care about your experience in delivering output on time and under budget, for example.

Fact: Most postdocs do not appreciate all the "soft" (non-bench) skills they possess that should be nurtured at the same time as patch-clamp technique JUST IN CASE you need your Career "Plan B".
Fact: Most mentors do not appreciate all the "soft" (non-bench) skills that should be nurtured at the same time as patch-clamp technique JUST IN CASE their postdoc needs Career "Plan B".

Anyway, to cut a long story short, I got an email this morning and this is what it said:

"I just got offered the job! I would like to thank you for all of your help. I don't think I could have done this without you."

This makes it all worth while. There is Life After the Bench.

9 responses so far

Postive Discrimination

Aug 24 2012 Published by under Uncategorized

From the BBC News site:

"Two people are dead, including a gunman, and up to eight others are wounded in a shootout near New York's Empire State Building, officials say. The gunman was reportedly killed by police, and officials said eight others were wounded in the rush-hour incident in the heart of Manhattan....Some of those hit by bullets may have been accidentally hit by police, New York Mayor Michael Bloomberg said in a news conference. But he said their injuries were not life-threatening and they were expected to make a full recovery...One woman, Aliyah Imam, told TV station Fox 5 News that the gunman was "shooting indiscriminately at people"."

The gunman was shooting indiscriminately at people? And so were the fucking police by all accounts! This happens far too often - Officer Smith, in the heat of the moment, whips out his police issue Glock and starts shooting off rounds *towards* the perceived threat. When one learns to shoot and takes carry permit classes one is taught that everything that happens to your bullet, from the moment it leaves the barrel to the moment it impacts the "Bad Guy", is YOUR responsibility. And without constant training (and possibly even then) you WILL fire wildly under pressure, you will not be in your Weaver stance, you will not think "front site". You WILL grab the trigger and keep grabbing it until you're out of ammo. And all those bullets are your responsibility.

I wonder how much practice time, and live fire time and shooter-drill time those cops had. And I wonder if any of them will be held responsible for their bullets? Actually, no I don't.

8 responses so far

New & Early Stage Investigator

Aug 22 2012 Published by under Uncategorized

It is a much remarked fact that the age to first award of substantial independent funding from the National Institutes of Health (NIH) has been steadily increasing, such that "new investigators" are now, on average, in their early 40s before they get their first major research award (typically an R01). To this end the NIH put into place some new rules to help weight the review process in favor of meritorious new investigators. This lead to much hand wringing and foul crying because it meant that very established and experienced scientists could claim NI status just for not having had an R01.

For example, one might be a Research Associate Professor within the lab of a Greybeard or Bluehair and be made PI on a "new" grant, even though the work was to be done within the lab of the aforementioned senior faculty member. (As usual, I defer to the expert commentary of M'Learn'd Colleagues Drugmonkey & PhysioProf for more cogent discussion of these issues.)

To help out the poor unwashed masses of junior scientists a bit more, the NIH then brought in the Early Stage Investigator policy, which weights in favour of scientists who are less than 10 years from the completion of their terminal degree (PhD or MD).

here lies the rub, my friends, I am just a year out from that ESI cut off. It will be ten years next August that I graduated from my Alma Mater with my PhD (although, like most scientists I count the date of my successful defence and the great moment when my PhD advisor (a man who looked strikingly like Bill Murray) left the conference room where my committee had debated my performace and said, "Congratulations Dr. Brooks" with an enormous grin on his face. I admit, I burst into tears and gave him a hug).

So, given that the clock is well and truly ticking here, my current plan is to apply for an R21 this fall, and an R01 next year. Both should fall under the NI and ESI categories, because even if the R21 is funded it is not counted as a major award for determining NI status.There are two deadlines I can aim for with the R01 in 2013 to maintain the ESI status: February 5th and June 5th. Can I submit in February and then significantly re-write and submit as a new grant in June? Then if (when?) the February submission ricochets out without review, I have a bit of time to take any comments and tweak a new submission for June?

Now, I've worked on many, many, many grants over the last four years since I left the lab. I've contributed to old and new format R, U and P mechanism awards. But - I've never actually had to write a "whole" grant myself. and it needs to be a palpable hit to count if I'm to get my (assumed) resubmission in in time.

I won't be writing alone - I have a very good team of experts I work with and we'll craft this together, but the ideas, and the bulk of the work will be mine. They'll contribute some technical portions and language but that's all. It's going to be a busy few months I think...I'm debating cancelling our Christmas vacation to the UK...

9 responses so far


Aug 20 2012 Published by under Uncategorized

You know what's really, really, really annoying?

Finding a grant application announcement that PERFECTLY fits some directions your group is moving and getting all excited and calling collaborators to ask their opinions and the small print and realizing you've missed the fucking deadline.




You know what's really, really, really AWESOME?

Finding a grant application announcement that PERFECTLY fits some directions your group is moving and getting all excited and calling collaborators to ask their opinions and the small print and realizing you've missed the fucking deadline...and then one of your collaborators emails you to point out that in your sleep-deprived zombie state you misread the deadline information and there is still 2 months to go!

And then your Vice Chancellor (my boss) says, "Of course you should apply! You should be PI, not co-PI. You need this. Do this and I can get you on the tenure track."

4 responses so far

No spare time

Aug 15 2012 Published by under Uncategorized

I was going to write about the broohaha over at Freethought Blogs and Thunderf00t accessing an email listerserve he was removed from. But then I thought, what an odious little toad he is, but I don't have time. Plus, he's an odious little toad and it's not worth it.

So I thought I'd write about a post PZ Myers has at Pharyngula on a Boing Boing article by Maggie Koerth Baker about fundamentalist Christians decrying mathematics (set theory - great article and worth reading). I like PZ Myers & blog and I am kind of a firebrand atheist myself, but I thought his analogy to mushrooms missed a fundamental point in the argument about fundamentalist Christians and their blinkered beliefs. But...I don't have time

I had and have a bunch of things that I want to write about, some serious (see above), some infuriating (see more above), some less serious and some even fun. Some about careers, some about networking and the value of a professional network. Some about events I've been to along these lines.

None of which I have the time or energy to do. I think the lack of sleep is making me into a zombie. I love being a father and husband, but I wish I had more time.

8 responses so far

New tech, new woes

Jul 25 2012 Published by under Uncategorized

This is a rant.

We had money left in our budget at the end of the financial year so it was a great chance for us to upgrade our computers. I ordered a new Macbook Pro running OS 10.7.4 and left for my vacation (hence radio silence here recently).

I got back from vacation last week and walked into a the maelstrom that had to be waiting for my return. You can't be the boss and be away for two+ weeks without a world of shit and a million tiny things happening in your absence. So, my new MBP sat in the corner of my office and I had to ignore it while I caught up on business, and budgets, and rogue staff, and Ramadan, and so forth. I did, however, take the opportunity to make sure all my current computer files were nice and clean and organised, and backed-up properly to my external hard drive...ready for the exciting moment when I would find time to play with my new computer.

That day was Friday 20th July!

Today is the 25th and the motherfucker is still giving the fucking gyp.

1. My perfectly functional 27" external monitor wont work on the new MPB because it seems not to like the perfectly functional DVI-mini-port adapter that I had been using. So...2 days of testing, tweaking, plugging, unplugging, calling Helpdesk and having the "Mac Guy" come to my office twice, and now a new adapter ordered.

2. Adobe hate me. This is obvious. I "had" the full CS4 suite - Photoshop, Illustrator, Dream Weaver and Acrobat Pro (v9) on my old computer and it seemed the easiest thing in the world to deactivate on that and simply install and reactivate the licences on the new MBP. Except that the new MBP doesn't have a fucking optical drive. So, 3 hours on the interchat with a variety of mouthbreathing reps at Adobe to find out that I can't transfer the licence even via software download because the new MBP run on Flash and Adobe hates Flash. Or something. By this point we'd switched to the telephone and when he finally confessed that nothing we tried would have worked anyway I utterly lost my shit and hung up on him. So I'm stuck with fucking Adobe Reader and trusting MS Word not to remove the "Save as PDF" function. Here's hoping I don't need to, oh, I don't know, WRITE A FUCKING GRANT or BUILD A WEBPAGE sometime soon.

3. New MBP comes with hard disk encryption. This is awesome! This is a security requirement for our work and saves a bunch of headaches and stress about some impending federal rules coming down the pipeline. Now we're compliant, yay! Except...I seem to be stuck with a double encryption that means I can't back my fucking hard drive up anymore. OS 10.7.4 can't seem to decrypt the file encryption that the "old" Mac had employed (so called Legacy FileVault). So because I moved all my files over without decrypting them first, if I want to use the new hard disk encryption I will have double decrypted files. Which is slow as fuck. And also means that the Time Machine back-up has thrown some kind of epic brainfart and I don't seem to have  A FUCKING BACKUP OF ALL MY FILES....except for the perfectly functional, really still useful "old" Mac sitting right next to me on my desk.

To fix all this shite and get a simple, back-up and encrypted set of files and drives I am going to have to delete my user account on the new MBP, re-furb the fucking thing back to zero and then buy a new external drive and try all over again  because this Olympic fuck-knuckle of encrypto-fail has borked my external drive so I can't use it on my "old" Mac. So there's another $200 gone.

But, I hear you cry, why not just back up to a remote disk somewhere and use that? Because the new fucking Macbook doesn't have an Ethernet port so I'm using our wireless service which is just feeble enough in my office to make anything over about 20Mb download a massive fail-prone pain in my fucking arse.

I should have spent the $2000 on the fucking ponies and gone to Vegas instead.

This is the end of the rant.

10 responses so far

Yes Virginia, there is non-NIH money

Jun 19 2012 Published by under Uncategorized

I think the majority of my (US-based) scientist friends, and perhaps even you, Dear Reader, work in biomedical sciences of some sort or another. From early in our training we learn of the mystical edifice that is The National Institutes of Health. The NIH, as we endearingly know it, is the major funder of most *biomedical* science in the US, and its coveted R01 research award is key to success, promotion and tenure. M'Learn'd Colleagues  PhysioProf and DrugMonkey are well funded and write with authority on the complexities of applying for, receiving and renewing NIH research dollars.

In addition, M'Learn'd Colleagues Gerty-Z and Dr. Becca, among others, have recently written of their experiences in beginning to negotiate these treacherous waters.

It is worthy and vital to note that the NIH funds *biomedical research*. This is broadly applied, but vital. If you're working on other basic processes in the Life Sciences you are more likely to apply to the NIH's red-headed stepchild The National Science Foundation (NSF). The NSF has a broader remit (and a much smaller budget), and funds non-biomedical research. M'Learn'd Colleagues Prof-Like Substance and Odyssey both enjoy the fruits of the NSF money-tree, and can be relied on for wisdom and council with regards the mores of the NSF application.

[Note added in proof - for brevity I'm not going into any of the detail about NIH vs. NSF and this "biomedical science" malarkey. It's complex, and can be read about elsewhere. See Prof-Like for e.g.]

But what of those of us that work on the applied fringes of biomedical research? As a biomedical informaticist I have two options - Option A) Piggy-back on other folks grants to seek the salary coverage afforded by providing core databasing services, or B) Apply for my own funding to cover the development of novel systems and providing databasing services. This latter is much harder for reasons I will explain in another post, and is also, alas, not really an option for me. I am not allowed to apply for my own funding as a Principle Investigator (PI). This was part of the contract offered to me when I accepted the position. It has pros and cons and, again, that's fodder for another post. (FWIW, and for those who understand such jargon, I am allowed to Co-I as long as my FTE is under 10%/project. I am a Co-I on a NIH-funded DB/PC/RCT R01 right now. Which is nice.)

So, most of the grant writing I do (and I do a lot) falls under Option A - convincing our faculty they should use a CFR21pt11, HIPAA, FISMA, HITECH & FIPS140-2 compliant and validated database for their data warehousing. And when you frame it like that it's actually fairly easy to convince them it's a good idea. Funding agencies like to see you've thought your shit out and covered your ass on any weak spots, and professional database protection and software design is a fairly common weak spot. We have the added advantage that as a core facility at the University, we are non-profit (as it were) so I can charge much less than my for-profit competitors for these services. I need only salary coverage - no mark-ups and no hidden fees.

In addition, because most of what we provide is *clinical* databasing we don't always have to rely on the NIH & NSF for funding. There is a world of other funding opportunities out there for those of us away from the lab bench. Most recently the Centers for Medicare & Medicaid Services (CMS) have been actively seeking proposals to help it spend a large wadge of cash. These "Innovation Awards" are competitive awards to fund cost-saving measures across a range of CMS-funded services. (Medicare & Medicaid are, essentially, the health insurance for people without health insurance. Confused yet?)

Given the awful problems my home town faces in health and racial disparities we have a large population that can be reached via CMS-funded projects so we were well placed to apply. My group was on two of three CMS-Health Care Innovation Award grant applications that went out in January, and of these three two were funded! Only one of the ones we're named on has been funded, but there is some hope that a second round of announcements will be going out later in the year, so maybe we'll get hit twice. The money arrives in October and covers 10-15% (pre-funding trim) of the salaries of myself and three of my staff. Which is nice.

In addition, the 'technology' that will result from our work will be broadly applicable across a range of health care interests so there's a great incentive to build something truly scalable here.

So, there we go. We  got another grant funded, and we've got our names on three more we expect to hear from soon - one NIH R01, another CMS grant (under a different "mechanism") and one funded by yet another non-NIH/NSF player - The National Institute of Justice (NIJ). Who knew there was so much investment in our scientific and research infrastructure huh?

6 responses so far

You shall douche no moar!

Jun 16 2012 Published by under Uncategorized


I am a huge fucking fan of invective. Invective snaps are instinctive and contain power. But Power needs to be used carefully or else it becomes tyranny. A child fucking swearing for fucks sake is a tyrant and a poorly educated idiot. That can be fixed.

The other side of the coin is a finely crafted retort. That takes years of practice; one shows the empty minded, invective slinging youth the error of hir ways by teaching hir to cut a motherfucker with words. You stupid, inbred, slackjawed pigfucker. There's also inventive collections, as any dickcheese nibbling badgerwankcup knows. I enjoy the latter creative expression, but can employ the former, more thoughtfully when needed.

My favourite opening line to a movie is from "Shawn of the Dead", but a lot of my freedom to enjoy that came from being English where that word seems to carry less weight as an anti-woman specific. Well, I live in the States and you fucking Yanks have different mores, so fuck it. None of that here then.

Douchebag though. Fuck me, there's a neutral swear with gravitas. But...alas Mrs. BrooksPhD disagrees. No moar douchebags in this house.


"that guy is a fucking douchebag."

"I wish you wouldn't say that. I hate that word."

"but it's a valid non-gendered expression of what a total cu.."

"Dont you fucking dare say that word"

"OK,in modern connotation it's a gender neutral expression of..."

"Fuck. that. Fuckthat. It's a fucking disgusting expression and it makes you look like a fucking pig asshole. Dont fucking say it."

"...ok darling."

I will not be a douchebag and use that term again. In front of my wife.

iPad post - internal keyboard is a douchebag invention. Edit for spelling & grammar soon.

7 responses so far

Is there a chef in the house?

Jun 16 2012 Published by under Uncategorized

My wife cooks a great breakfast. Eggs, bacon. Brilliant. Waffles? Hell yeah. We even have a waffle "maker" she's used.

Steak dinner? with brussels sprouts. And cous-cous?

Well. As one scientist to another, anyone can run a western blot, but can you pour your own gel?

I think I understand why my grad students got annoyed at me...shit. The fucken kitchen is on fire again...

One response so far

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