Phenomenal science powers!

So you toil for 4+ years in graduate school, 4+ years as a post-doc, land your first academic gig. Now you get to do all this awesome science, right? Well, sorta…

Oy! 10,000 years in the cave of graduate school will give you SUCH a crook in the neck!

Oy! 10,000 years in the cave of graduate school will give you SUCH a crook in the neck!

Proposal gambit – Betting the ranch

Last spring I posted about a proposal I’d put in where I’d published the key piece of preliminary data in F1000 Research, a journal that offers post-publication peer review.

The idea was that I could get my paper published (it’s available here) and accessible to reviewers prior to submission of my grant. It could then be peer-reviewed and I could address the revisions after that. This strategy was driven by the lag time between proposal submission and review for NIH, which is about 4 months. Also, it used to be possible to include papers that hadn’t been formally accepted by a journal as an appendix to NIH grants. This hasn’t been possible for some time now. But I figured this might be a pretty good way to get preliminary data out to the grant reviewers in a published form with quick turnaround. Or at least that you could utilize that lag time to also function as review time for your paper.

I was able to get my paper submitted to F100 Research and obtained a DOI and URL that I could include as a citation in my grant. Details here.

The review for the grant was completed in early June of this year and the results were not what I had hoped- the grant wasn’t even scored, despite being totally awesome (of course, right?). But for this post I’ll focus on the parts that are pertinent to the “gambit”- the use of post-publication peer review as preliminary data.

The results here were mostly unencouraging RE post-publication peer review being used this way, which was disappointing. But let me briefly describe the timeline, which is important to understand a large caveat about the results.

I received first-round reviews from two reviewers in a blindingly fast 10 and 16 days after initial submission. Both were encouraging, but had some substantial (and substantially helpful) requests. You can read them here and here. It took me longer than it could have to address these completely – though I did some new analysis and added additional explanation to several important points. I then resubmitted on around May 12th or so. However, due to some kind of issue the revised version wasn’t made available by F1000 Research until May 29th. Given that the NIH review panel met in the first week of June it is likely that the reviewers didn’t see the revised (and much improved version). The reviewers then got back final comments in early June (again- blindingly fast). You can read those here and here. The paper was accepted/approved/indexed in mid-June.

The grant had comments from three reviewers and each had something to say about the paper as preliminary data.

The first reviewer had the most negative comments.

It is not appropriate to point reviewers to a paper in order to save space in the proposal.

Alone this comment is pretty odd and makes me think that the reviewer was annoyed by the approach. So I can’t refer to a paper as preliminary data? On the face of it this is absolutely ridiculous. Science, and the accumulation of scientific knowledge just doesn’t work in a way that allows you to include all your preliminary data completely (as well as your research approach and everything else) in the space of 12 page grant. However, their further comments (which directly follow this one) shed some light on their thinking.

The PILGram approach should have been described in sufficient detail in the proposal to allow us to adequately assess it. The space currently used to lecture us on generative models could have been better used to actually provide details about the methods being developed.

So reading between the (somewhat grumpy) lines I think they mean to say that I should have done a better job of presenting some important details in the text itself. But my guess is that the first reviewer was not thrilled by the prospect of using a post-publication peer reviewed paper as preliminary data for the grant. Not thrilled.

  • Reviewer 1: Thumbs down.

Second reviewer’s comment.

The investigators revised the proposal according to prior reviews and included further details about the method in the form of a recently ‘published’ paper (the quotes are due to the fact that the paper was submitted to a journal that accepts and posts submissions even after peer review – F1000 Research). The public reviewers’ comments on the paper itself raise several concerns with the method proposed and whether it actually works sufficiently well.

This comment, unfortunately, is likely due to the timeline I presented above. I think they saw the first version of the paper, read the paper comments, and figured that there were holes in the whole approach. If my revisions had been available it seems like there still would have been issues, unless I had already gotten the final approval for the paper.

  • Reviewer 2: Thumbs down- although maybe not with the annoyed thrusting motions that the first reviewer was presumably making.

Finally, the third reviewer (contrary to scientific lore) was the most gentle.

A recent publication is suggested by the PI as a source of details, but there aren‟t many in that manuscript either.

I’m a little puzzled about this since the paper is pretty comprehensive. But maybe this is an effect of reading the first version, not the final version. So I would call this neutral on the approach.

  • Reviewer 3: No decision.


The takeaway from this gambit is mixed.

I think if it had been executed better (by me) I could have gotten the final approval through by the time the grant reviewers were looking at it and then a lot of the hesitation and negative feelings would have gone away. Of course, this would be dependent on having paper reviewers that were as quick as those that I got- which certainly isn’t a sure thing.

I think that the views of biologists on preprints, post-publication review, and other ‘alternative’ publishing options are changing. Hopefully more biologist will start using these methods- because, frankly, in a lot of cases they make a lot more sense than the traditional closed-access, non-transparent peer review processes.

However, the field can be slow to change. I will probably try this, or something like this, again. Honestly, what do I have to lose exactly? Overall, this was a positive experience and one where I believe I was able to make a contribution to science. I just hope my next grant is a better substrate for this kind of experiment.

Other posts on this process:



Proposal gambit – Update 1

Last week I posted about my strategy for a proposal I’m just submitting. Pretty simple really, just using a publication in a post-publication peer review journal (F1000 Research) as the crucial piece of my preliminary data in my grant. Here’s an update on the process.

So, if you’re going to predicate an R01 submission on having a citation to a paper with a crucial set of preliminary data in it… don’t leave it until the last minute. I submitted my paper to F1000 Research on Thursday (one week prior to the submission date for my grant). They responded very quickly – next day, with requests for some minor changes and to send the figures separately (I had included them in the document). No problems, but then the weekend came up and I ended up getting everything back to them on Sunday evening. Fine. Monday came and went and I didn’t have a link. Also on Monday I was surprised because I was erroneously told that I had to have the absolute final version of my grant to our grants and contracts office that day. With no citation. I scrambled to make myself an arXiv account so that I could get it out that way (a good thing in any case). But turns out it was incorrect and I could still make minor modifications after that.

So yesterday (Tuesday) I pinged F1000 Research, politely and with acknowledgment that this was a short turnaround time, and mentioned that I wanted to put the citation in the grant. They replied on Wednesday morning apologizing for the delay (nice, but there was no delay- I was really trying to push things fast) and saying that the formatted version should be ready in a couple of days and GIVING ME A DOI for the paper! Perfect. That’s what I really needed to include in the grant.

So today the updated grant was actually submitted- a whole day early, probably a first. Now it’s just a matter of settling in until June when it will be reviewed. Of course, I still need to get my paper reviewed, but I think that won’t be a huge problem.

Overall this process is going swimmingly. And I’ve been really pleased with my interactions with F1000 Research so far.

Proposal gambit

I am currently (this minute… well, not THIS minute, but just a minute ago, and in a minute) in the throes of revising a resubmission of a previously submitted R01 proposal to NIH. This proposal generally covers novel methods to build protein-sequence-based classifiers for problematic functional classes- that is, groups of proteins that have a shared function but either are very divergent in their sequence (meaning that they can’t be associated by traditional sequence similarity approaches) or have a lot of similar sequences with divergent functions (and the function that’s interesting can’t be easily disambiguated).

I got good feedback from reviewers on the previous version (though I did not get discussed- for those who aren’t familiar with the process, to get a score- and thus a chance at funding- your grant has to be in the top 50% of the grants that the review panel reads, then it moves on to actual discussion in the panel and scoring). Their main complaint was that I had not described the novel method I was proposing in sufficient detail, and so they were intrigued but couldn’t assess if this would really work or not. The format of NIH R01-level grants (12 pages for the research part) means that to provide details of methods you really need to have published your preliminary results. Also- if it’s published it really lends weight to the fact that you can do it and get it through peer review (or pay your way into a publication in an fly-by-night journal).

So anyway. I’ve put this resubmission off since last year and I’m not getting any younger and I don’t have a publication to reference on the method in the proposal yet. So here’s my gambit. I’ve been working on the paper that will provide preliminary data and it was really nearly finished it just needed a good push to get it finalized, which came in the form of this grant. My plan is to finish up the last couple of details on the paper and submit it to F1000 Research because it offers online publication immediately with subsequent peer review. I’ve been intrigued by this emerging model recently and wanted to try it anyway. But this allows me to reference the online version very soon after I upload it (maybe tomorrow) and include it as a bona fide citation for my grant. The idea is that by the time it’s reviewed (3 months hence) it will have passed peer review and will be an actual citation.

But it’s a gambit. It’s possible that the paper will still be under review or will have received harsh reviews by the time the reviewers look at it. It’s also possible that since I won’t have a traditional journal citation in text for the proposal- I’ll need to supply a URL to my online version- that the reviewers will just frown on this whole idea and it might even piss them off making them think I’m trying to get away with something (which I totally am, though it’s not unethical or against the rules in any way that I can see). However, I’m pretty sure that this is a lot more common on the CS side (preprint servers, and the like) so I’m betting on that flying.

Anyway, I’ll have an update in 3+ months on how this worked out for me. I actually have high hopes for this proposal- which does scare me a little. But I’m totally used to dealing with rejection, as I’ve mentioned before on numerous occasions. Wish me luck!

A Fine Trip Spoiled

I had a dream the other night that inspired this comic. My dream was about waiting for a connecting flight. I decided to take it easy and do something fun, then realized that my flight was leaving soon and I was nowhere near the gate. Then I got on a train and realized I was going the wrong direction. Anyway, I woke up to the realization that I’d relaxed and done fun stuff most of the weekend (I did work some in the evenings) and that I had an unfinished grant that was still due this week. As it turned out I finished up my grant quite nicely despite the slacking off- or maybe even because of the slacking off. But it gave me the inspiration for this comic.

You see, writing and submitting a grant proposal is a lot like planning for a vacation that you’ll probably never get to take. The work you’re proposing should be fun and interesting (otherwise, why are you trying to get money to do it, right?) but your chances are pretty slim that you’ll ever get to do it- at least in the form that you propose it. I’ve started to think of the grant process as a long game (see this post from one DrugMonkey)- one where the act of writing a single grant is mainly just positioning for the next grant you’ll write down the line. Writing grants give you opportunity to come up with ideas, to consolidate your thoughts, and think through the science that you want to do and how you want to do it. The process can push you to publish your work so that you can cite it as preliminary data. And it can forge long-lasting collaborations that go beyond failed proposals (though funded proposals certainly help to cement these relationships in a much more sure way).

I think “A Fine Trip Spoiled” may be the title of my autobiography when I get rich and famous.


Have laptop, will travel

One of the great things about being a purely computational researcher is that, nowadays, my office is pretty much wherever I want it to be. I’ve got my laptop, WiFi is omnipresent, and I have noise-canceling headphones for the serious business. There are lots of reasons that I have to be at my office – meetings and increased ability to focus being primary. However, it’s not the case that you have to be purely computational to get a lot out of working in non-traditional locales. Writing is the place where we all (as researchers) can do this. Writing manuscripts and grants being the biggest time sucks. Some of you will have the ability to be flexible in your actual work time, others this might pertain mostly to the ‘extra’ work you do writing grants and papers.

So here is my random collection of thoughts on this topic.

Why take your work outside the standard work environment?

  1. Flexibility and efficient use of time. If you have your laptop with you you can fit in writing wherever you are (see list below). This allows you to use your time well instead of standing around checking Facebook on your phone. Not all writing work is  suited for the short bits of time (probably no less than about 20-30 minutes at a time) but if you plan what to work on you can get a lot done this way. If you don’t have your laptop a surprising amount of work can get done with just a pen and paper.
  2. Freedom from distraction. OK, a coffee shop can be a pretty distracting place, that’s a given. But sometimes being in your office can be pretty distracting too. People stop by to chat for a minute, phones ring, drawers need organizing, etc. If you can ignore the distractions outside your office (wherever you’re choosing to work) then this can be a productive way to go. Also, try working somewhere WITHOUT WiFi (it can be done)- and cut out the social media chatter.
  3. Creative stimulation. Changing your work environment drastically can give you a shot of creative energy. It can be refreshing wot work outside at a park, or while enjoying a glass of your favorite beverage at a cafe or bar.

What to work on?

  1. Grants
  2. Manuscripts
  3. Reviewing papers/grants
  4. Catching up on answering emails
  5. Reading papers- no laptop required
  6. Planning and outlining- also no laptop required, use a pen and notebook

Where can you do this?

  1. Coffee shop. Everyone pretty much knows about this one. Can be distracting, but find a quiet corner and bring headphones. Also, try not to drink 15 double espressos while you’re there (not that I would have ANY experience with that)
  2. The Mad Scientist enjoying a beer after a long day meeting and about to do some grant writing at a McMenamin's pub in Portland

    The Mad Scientist enjoying a beer after a long day meeting and about to do some grant writing at a McMenamin’s pub in Portland

    Bar/pub. These can be awesome places to work- probably not on a Friday or Saturday night, but other times. Many have WiFi and they have BEER! Also, try not to drink 8 beers while you’re there. Alcohol is actually a consideration since it can affect your motivation pretty severely. Ordering ONE beer and some food works OK for me, but certainly use your best judgement- and they will always have alternate non-alcoholic beverage options.

  3. Public library. This is really just a no-brainer. No cost (though many libraries have coffee shops attached and allow you to bring covered cups in), free WiFi, lots of sitting areas, quiet atmosphere, surrounded by the smell of knowledge.
  4. Park. Working outside is sometimes really nice in nice weather. If you’re lucky enough to have workable weather (not too hot, not too cold, not too windy or rainy) then find a table in the shade and settle in. I’ve never found this particularly effective myself, though the idea is wonderful, but I’m sure it could work for others.
  5. Doctor/dentist office, DMV, etc. This option is one I use quite a bit, but it only works for things that you can do a little bit on before being interrupted. I find that making todo lists and outlines work well here. Also reading background material can also work well.
  6. Car. Not while you’re driving! I mean if you’re sitting and waiting for something or someone this can be a good time too.
  7. Public transportation. When I was in Seattle I rode the commuter train in from Everett to work several times a week. A great place to work. An hour of uninterrupted time while beautiful countryside rolls by. Buses can work too, though not always for actual writing since often they bump and move too much for a laptop. Subways/metros also work well. Of course, this is pretty dependent on the density of people. It’s really hard to do anything productive when you have an elbow in your face and about 6 inches of standing room.
  8. *that's me in the seat behind Rex, by the way.

    *that’s me in the seat behind Rex, by the way.

    Airplane/airport. So much wasted time in airports- which are great places to work if you find the right spots. Airplanes can be a bit problematic in terms of an actual laptop (I find I can do it if I type like a T-rex) but I bring papers to read and a notebook to do planning and write ideas. In airports try to find places where there aren’t many people- away from your departing gate if you have time. More chance of getting a power outlet and fewer distractions. If you’re really in need of an outlet try looking in places where other people aren’t going to be sitting (hallways and walkways) and sit on the floor- it can be done.

  9. Hotel. Also in the traveling realm. Hotels can be excellent places to write. Free from a lot of the distractions and obligations of home and office. If you have extra time after a day at a conference or between sessions or before you catch your plane- use it. Many hotels are set up with desks, comfy chairs, outlets, coffee makers, and WiFi. When I travel to the east coast and my return flight is early I will frequently work through the night. Not for everyone, but I’m a night owl and I find it easier to do this (sometimes) than to sleep for a few hours then drag myself out of bed at 5 AM (3 AM my time) to get to the airport. Also, no danger of oversleeping – unless of course you accidentally crash. So if you do this make sure to arrange a wake up call and set an alarm for backup.
  10. Other locations. Be on the lookout for other opportunities. I have worked on a grant while pouring wine for a wine tasting at a friend’s house (not a wine-tasting party, mind you- this was a professional activity, so quite a bit of down time). That was pretty epic really but it still didn’t get my grant funded.



Academic Rejection Training

Following on my previous post about methods to deal with the inevitable, frequent, and necessary instances of academic rejection you’ll face in your career I drew this comic to provide some helpful advice on ways to train for proposal writing. Since the review process generally takes months (well, the delay from the time of submission to the time that you find out is months- not the actual review itself) it’s good to work yourself up to this level slowly. You don’t want to sprain anything in the long haul getting to the proposal rejection stage.


Dealing with Academic Rejection

Funny, it feels like I’ve written about exactly this topic before…

I got rejected today, academically speaking*. Again. I was actually pretty surprised at how

"Not Discussed", again

“Not Discussed”, again

nonplussed I was about the whole thing. I’ve gotten mostly immune to the being rejected- at least for grant proposals and paper submissions. It certainly could be a function of my current mid-career, fairly stable status as a scientist. That tends to lend you a lot of buffer to deal with the frequent, inevitable, and variably-sized rejections that come as part of the job. However, I’ve also got a few ideas about advice to deal with rejection (some of which I’ve shared previously).

Upon rejection:

  1. Take a deep, full breath: No, it won’t help materially- but it’ll help you feel better about things. Also look at beautiful flowers, treat yourself to a donut, listen to a favorite song, give yourself something positive. Take a break and give yourself a little distance.
  2. Put things in perspective: Run down Maslow’s hierarchy of needs. How you doing on there? I’ll bet you’ve got the bottom layers of the pyramid totally covered. You’re all over that. And it’s unlikely that this one rejection will cause you to slip on this pyramid thing.
  3. Recognize your privilege: In a global (and likely local) perspective you are extremely privileged just to be at this level of the game. You are a researcher/academic/student and get to do interesting, fun, rewarding, and challenging stuff every day. And somebody pays you to do that.
  4. Remember: science is ALL about failure. If you’re not failing, you’re not doing it right. Learn from your failures and rejections. Yes, reviewers didn’t get you. But that means that you need to do a better job of grabbing their attention and convincing them the next time.
  5. Recognize the reality: You are dealing with peer review, which is arbitrary and capricious. Given the abysmal levels of research funding and the numbers of papers being submitted to journals it is the case that many good proposals get rejected. The system works, but only poorly and only sometimes. And when everyone is scraping for money it gets worse.
  6. Evaluate: How do YOU feel about the proposal/submission: forget what the reviewers said, forget the rejection and try to put yourself in the role of reviewer.
    This is YOU on the steps of the NIH in 6 months! Winning!

    This is YOU on the steps of the NIH in 6 months! Winning!

    Would YOU be impressed? Would YOU fund you? If the answer is ‘no’ or ‘maybe’ then you need to reevaluate and figure out how to make it into something that you WOULD or decide if it’s something you should let go.

  7. Make plans: Take what you know and plan the next step. What needs to be done and what’s a reasonable timeline to accomplish this. This step can be really helpful in terms of helping you feel better about the rejection. Instead of wallowing in the rejection you’re taking ACTION. And that can’t be a bad thing. It may be helpful to have a writing/training montage to go along with this since that makes things more fun and go much faster. Let me suggest as the theme to Rocky as a start.

I’m not saying you (or I) can do all of these in a short time. This process can take time- and sometimes distance. And, yes, I do realize that some of this advice is a little in the vein of the famous Stuart Smalley. But, gosh darn it, you ARE smart enough.


*For those interested, I submitted an R01 proposal to the NIH last February. It was reviewed at the NIH study section on Monday and Tuesday. The results of this review were updated in the NIH submission/tracking system, eRA commons, just this morning. I won’t know why the proposal was ‘not discussed’ for probably a week or so, when they post the summary of reviewers’ written comments. But for now I know that it was not discussed at the section and thus will not be funded.

At this point I’ve submitted something like 8 R01-level proposals as a PI or co-PI. I’ve been ‘Not Discussed’ on 7 of those. On the eight I got a score, but it was pretty much the lowest score you can get. Given that NIH pay lines are something around 10% I figure that one of the next 2 proposals I submit will be funded. Right? But I’ve been successful with internal funding, collaborations, and working on large center projects that have come to the lab- so I really can’t complain.

Goodbye to two good friends

(Note: this post isn’t nearly as sad as it might seem from the title or the introduction below)

Yesterday I lost two close friends. We had been friends for five years, though our relationships had extended a tumultuous 10 or so months before that. Given that we still have unfinished business I expect our friendships to straggle on a little longer. But really, it’s over. My friends have helped me grow in a number of important ways- become more mature, deal with different personalities, forced me to communicate more clearly and to take criticism in a constructive light. The friendships both challenged me in different ways and supported me through a fragile time in my life. I will miss both of these friends for some different reasons- and some of the same reasons.

Like many friendships they have ended because of what other people thought about them. A small number of people had comments on our friendship- some of the comments, upon reflection, were probably well-placed, others certainly were not. But that outside influence is what really broke us apart. I hope that we can become friends again in the future- but we both will have changed so much in the intervening time that we may well be unrecognizable to each other. Still it would be nice to continue this friendship.

Bye Bye

Farewell Systems Biology of Enteropathogens and Systems Virology Centers – you will be missed but not forgotten.

Here are a few mementos of our time together….

  1. Ansong C, Schrimpe-Rutledge AC, MitchellH, Chauhan S,Jones MB, Kim Y-M, McAteerK, Deatherage B, Dubois JL, Brewer HM, Frank BC, McDermottJE, Metz TO, Peterson SN, Motin VL, Adkins JN. A multi-omic systems approach to elucidating Yersinia virulence mechanisms.Molecular Biosystems 2012. In press.
  2. McDermott JE, Corley C, Rasmussen AL, Diamond DL, Katze MG, Waters KM: Using network analysis to identify therapeutic targets from global proteomics dataBMC systems biology 2012, 6:28.
  3. Yoon H, Ansong C, McDermott JE, Gritsenko M, Smith RD, Heffron F, Adkins JN: Systems analysis of multiple regulator perturbations allows discovery of virulence factors in SalmonellaBMC systems biology 2011, 5:100.
  4. Niemann GS, Brown RN, Gustin JK, Stufkens A, Shaikh-Kidwai AS, Li J, McDermott JE, Brewer HM, Schepmoes A, Smith RD et alDiscovery of novel secreted virulence factors from Salmonella enterica serovar Typhimurium by proteomic analysis of culture supernatantsInfect Immun 2011, 79(1):33-43.
  5. McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F: Technologies and approaches to elucidate and model the virulence program of salmonellaFront Microbiol 2011, 2:121.
  6. McDermott JE, Shankaran H, Eisfeld AJ, Belisle SE, Neumann G, Li C, McWeeney SK, Sabourin CL, Kawaoka Y, Katze MG et alConserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systemsBMC systems biology 2011, 5(1):190.
  7. McDermott JE, Corrigan A, Peterson E, Oehmen C, Niemann G, Cambronne ED, Sharp D, Adkins JN, Samudrala R, Heffron F: Computational prediction of type III and IV secreted effectors in gram-negative bacteriaInfect Immun 2011, 79(1):23-32.
  8. McDermott JE, Archuleta M, Thrall BD, Adkins JN, Waters KM: Controlling the response: predictive modeling of a highly central, pathogen-targeted core response module in macrophage activationPLoS ONE 2011, 6(2):e14673.
  9. Aderem A, Adkins JN, Ansong C, Galagan J, Kaiser S, Korth MJ, Law GL, McDermott JG, Proll SC, Rosenberger C et alA systems biology approach to infectious disease research: innovating the pathogen-host research paradigmMBio 2011, 2(1):e00325-00310.
  10. Buchko GW, Niemann G, Baker ES, Belov ME, Heffron F, Adkins JN, McDermott JE (2011). A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteinsMolecular Biosystems. 6(12):2448-58.
  11. Lawrence PK, Kittichotirat W, Bumgarner RE, McDermott JE, Herndon DR, Knowles DP, Srikumaran S: Genome sequences of Mannheimia haemolytica serotype A2: ovine and bovine isolatesJ Bacteriol 2010, 192(4):1167-1168
  12. Yoon H, McDermott JE, Porwollik S, McClelland M, Heffron F: Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar TyphimuriumPLoS Pathog 2009, 5(2):e1000306.
  13. *Taylor RC, Singhal M, Weller J, Khoshnevis S, Shi L, McDermott J: A network inference workflow applied to virulence-related processes in Salmonella typhimuriumAnnals of the New York Academy of Sciences 2009, 1158:143-158.
  14. *Shi L, Chowdhury SM, Smallwood HS, Yoon H, Mottaz-Brewer HM, Norbeck AD, McDermott JE, Clauss TRW, Heffron F, Smith RD, and Adkins JN. Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Salmonella Infection. Infection and Immunity 2009, 77(8):3227-33.
  15. *Shi L, Ansong C, Smallwood H, Rommereim L, McDermott JE, Brewer HM, Norbeck AD, Taylor RC, Gustin JK, Heffron F, Smith RD, Adkins JN. Proteome of Salmonella Enterica Serotype Typhimurium Grown in a Low Mg/pH Medium. J Proteomics Bioinform. 2009; 2:388-397.
  16. *Samudrala R, Heffron F, McDermott JE: Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systemsPLoS Pathog 2009, 5(4):e1000375.
  17. *McDermott JE, Taylor RC, Yoon H, Heffron F: Bottlenecks and hubs in inferred networks are important for virulence in Salmonella typhimuriumJ Comput Biol 2009, 16(2):169-180.
  18. *Ansong C, Yoon H, Norbeck AD, Gustin JK, McDermott JE, Mottaz HM, Rue J, Adkins JN, Heffron F, Smith RD: Proteomics Analysis of the Causative Agent of Typhoid FeverJ Proteome Res 2008.

*these were really from slightly before our time- but I’ll count them there anyway

A 12 step program for writing grant proposals

Recent experience talking here (interested, non-Science types, there’s a short explanation to give context at the end).

  1. Boundless, unfounded optimism: Yes! You’ve just had the greatest idea EVER! Sure it’s lacking a few details, but the reviewers are gonna love it! The whole idea is there, it just needs a little writing and you’ll be done. This time, for sure you’ll be able to knock it out quick and without much effort since it’s such a great idea. Just great.
  2. Period of procrastination: Since it’ll be so easy you don’t have to worry about it right now. Sit back and relax since you’ve still got loooooooooads of time before this baby is due. Maybe talk with some people about how you’ll need to start working on it sometime, and about how great it is, but that you’re not worried about it now because it’s not due anytime soon.
  3. Panic: HOLY SH*T! What day is it? How did that happen?! Can it be that the due date is actually that close? It’s impossible- better check the calendar and the call a few more times. Gulp.
  4. Outline stage: What were those great ideas you had early on? Oh yeah- put those down on paper. Wow. Somehow they seemed a lot grander in your head. They look a little thin on paper actually. Are you sure that’s all? Maybe you forgot that one cool part.
  5. Cut-and-paste: Take text from wherever you can, manuscripts, other proposals, your grocery lists, and put it down in the sections that kinda make sense. It makes you feel a lot better to have something on paper and you can fill it in later, right?
  6. Sculpting: Now take all that great raw material you have and make it look like Michaelangelo’s David. Hmmmm…. that’s not quite right- it looks more like Frankenstein’s monster’s ugly cousin. Well, keep sculpting- the more sculpting the better. Put hours into that transition between Aims 2 and 3. It’s super important that you phrase it perfectly so you can rip it all apart in step 8.
  7. Imposter’s syndrome: “What am I even doing here?” You’ve got the simplest idea coupled with the most contrived, Rube Golbergian implementation. Nothing really fits together into a coherent picture. And it has no point. You wouldn’t even believe this crap if you were the reviewer.
  8. Demolition derby:  A flash of inspiration and you see how all the pieces fit together. Unfortunately it requires ripping everything apart and rearranging your aims, renumbering your figures, and stitching it all back together to make it look like you meant it to go that way the whole time. Oh, and you’ve got a little under 24 hours to accomplish this.
  9. Amazing period of focus and productivity: Where did that come from and why has it been hiding for so long?! You just knocked out 5 pages of text in 3 hours and it looks great. It would have been REALLY nice to be at this point a wee bit earlier in the process.
  10. Rose colored glasses: Yes. It’s finished and it’s perfectly wonderful! There could be some blemishes, or some outright holes. It doesn’t matter now ’cause you can’t do a damn thing about it. Too late. So it’s all wonderful and the best idea ever!
  11. Last minute scramble: Generally it involves either figure or citation formatting- formatting of some sort. And it’s absolutely incomprehensible why it’s screwing up now. Why won’t EndNote work the way it was designed to? You’ve got 2 hours before your grant administrator has a friggin’ stroke and you can’t get X to work correctly (where ‘X’ is some formerly inconsequential software feature that just wants attention- but you can’t ignore it at this point)
  12. Now where did that focus and productivity go? It’s off. Submitted safely at the funding agency. A warm sense of accomplishment in your belly. The drive to do more still rattling around in your bones. OK- now that you found that amazing kernel of productivity that you didn’t remember existed it should be easy to get all that stuff done that you put off during your proposal process. If only you weren’t so tired. And apathetic. *Sigh*

Here’s a little background for those of you not so “fortunate” to be tied to the whims and whimsey of academic funding (and, importantly, are still reading this). Academic researchers (and those in national labs, like me) have to, for the most part, fund the research they do by applying for grants from funding agencies. These are governmental agencies like the National Institutes of Health (NIH), National Science Foundation (NSF), the Department of Energy (DOE), and others, or non-governmental funding agencies (private philanthropic funds, the Gates Foundation, etc.) and they issue ‘calls’ for proposals that specify the kinds of research they’re looking for. There are deadlines associated with these calls and some recur on a regular basis but others are single-shot. After you submit your proposal the agency will review it for merit using criteria generally outlined in the call. NIH does this with an established peer review process. If you are so lucky to be funded then you get to do what you propose- and live for a little longer in the academic research game. Yay!