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.


Journaling a Computational Biology Project: Part 3

Day 4 (link to previous post)

It figures that the week I decide to return to using the cluster (the PIC, in case you’re interested) is the week that they have to shut it down for construction. So ran no more permutations today- that’ll have to wait until next week.

Didn’t really do any other work on the paper or project today either- busy doing other things. So not much to report today actually. I did talk a bit about the results with my post-doc on our semi-weekly MSFAB (Mad Scientist Friday Afternoon Beer). We both agreed that the permutation test was a good idea and possibly the only way to get an estimate of real false discovery rates. Along these lines, as I reported yesterday the first round of permutations returned with some fairly significant results. These actually exceeded the Bonferroni corrected p values I was getting, which is supposed to tell you essentially the same thing. So it seems in this case that Bonferroni, generally a conservative multiple hypothesis correction, was not conservative enough. Good lesson to remember.

Journaling a computational biology project: Part 2

Day 3 (link to my previous entry)

Uh-oh- roadblock. Remember how I was saying this project was dirt simple?

It's just THIS simple. This has to work- there's no WAY it could fail.

It’s just THIS simple. This has to work- there’s no WAY it could fail.

This came much faster than I thought it would. I’ve got actual data and I have to figure out if there’s a story there. Or rather, where the story is. The results from my large-scale parallel run are interesting, but I’m not sure they clearly demonstrate how this approach is better than previous approaches. Also there I had to rerun the whole thing to all the results, turns out I was only capturing about 1/5th of the results- but the end problem was the same. The results are very significant, but not head and shoulders above previous results, and don’t really demonstrate what I was hoping they would. Strongly anyway. Time for some thinkin. Never as dirt simple as I think it will be to start with.

Down, down, down, down...

Down, down, down, down…

Anyway, pushing onwards doing permutations. The question here is how likely would I be to see the scores I’m getting just by chance alone. So I permute the labels on my data and run the thing a few times with random labels. The permutation is done on the sample level- the data I’m using is from observations under condition 1 and condition 2- and I have multiple observations from each conditions. So to permute I just randomize which observations I’m saying are from condition 1 and condition 2.

I’ve done the first couple of randomized runs and they’re actually coming up with some reasonably significant results. This means that I’ll have to compare the random scores with my real scores in order to establish a false discovery rate, which I can then use as a threshold for reporting.

I’ve also started to put things into a kind of an outline for the paper. Here’s what I’ve got so far- I’ve taken the details of what I’m doing out for blogging purposes- but you get the idea:


  1. General background about the problem we’re developing our method on
  2. Description of the previous algorithm, what it offers and what is the gap that our approach will fill
  3. Specific details about the data set we’re using
  4. Summary of what our approach is and what results we’ll be presenting in the paper


  1. First apply the previous algorithm on our data (this hasn’t been done). Possibly validate on an external dataset
  2. Show how our algorithm improves results over previous
  3. Add in the extra idea we came up with that will also be a novel twist on the approach
  4. Show what kind of biological information can be derived from these new approaches. This is really open at this point since I’m not really sure what I’ll get yet. But preparing for it and thinking about it so writing it down.
  5. Validation on an external dataset (i.e. a different one from the one I’m using)- maybe. This might be difficult to impossible.

Journaling a computational biology study: Part 1

The process of how I compose a computational biology study, execute it, and write it up seems to follow a kind of set pattern, for the relatively simple projects anyway. So I thought I’d blog about this process as it happens.

I debated on several takes on this:

  1. Blogging as it’s happening with full technical details
  2. Blogging a journal that I could then release after the paper was finished and submitted
  3. Blogging as it’s happening but not talking about the technical details

The first is appealing, but probably wouldn’t go over well with my employer- and it is a simple idea that someone else could pick up and run with. I’m not paranoid, but in this case it might be too enticing for someone with the right skills. The second seems like not as much fun. So I’m opting for the third option and will be blogging about what I’m doing generally, but not giving specifics on the science, algorithms, or data I’m working with.

Background on the project

I’m not starting cold on this project. I came up with the idea last year but haven’t had time to implement it until now. It’s a dirt simple extension of an existing method that has the potential to be very interesting. I have the problem and data in hand to work on it. Last year we implemented a parallel version of a prototype of the algorithm. Now that I can actually work on it I can see a clear path to a finished project- being a submitted paper, or possibly inclusion as a part of a larger paper.

Day 1

Started out by revisiting the idea. Thinking about it and doing some PubMed searches. I just wanted to make sure that it hadn’t been done by anyone, especially the groups that developed the original algorithm. Nothing seems to be there- which is good, because as I said- it’s dirt simple.

Mid-day talked myself out of the idea in it’s original form- it can’t work as simply as I’d thought.

Relay my thoughts to my post-doc who reassured me that it was actually that simple and we could do it the way I originally envisioned. He was right. We talked about the statistics and algorithms for it for awhile.

Got my old code working again. Revised the core bits to handle the new idea. Actually ran some data through on my laptop using a very limited dataset. Looks like it works! So fun to actually be coding again and not just writing papers, grants, emails, or notes. Opened a blank Word document to do some writing. *sigh*

Decided on a tentative title (which will change) and a tentative author list. Myself, the post-doc who I talked with about it, the programmer who coded the parallel version previously, a post-doc who hasn’t worked on it yet, but probably will, and a senior domain expert. Yes, I’m doing this very early on. But as I said, there’s a clear path from here to a paper- it’s not too early.

Day 2

More testing on the prototype code to make sure that it’s behaving as I think it should. Also coded up an alternative data pre-processing step that seems to be a good idea. Comparing results from both pre-processing methods determine that they give different answers. I’ll have to iron that one out later when working with the real datasets.

Figured out the plan for the project- at least in broad strokes. Run on complete dataset, implement a random permutation strategy to estimate false discovery rate, break up dataset and show how the method works on individual parts of it (this is specific to the problem), find another dataset for validation, write it up. Yes, it’s just that simple.

Discussed an additional very interesting strategy with post-doc number 1 that will really add novelty and hopefully value to the study. Also discussed the permutation strategy in some detail. That will be really important to demonstrate that this actually works.

Spent most of the day revising the code for the parallel implementation to get the new ideas and testing it out on our cluster to see if it works. Slow progress, but finally got the entire thing to run! I did a couple of test runs using a limited dataset and only running on 2 nodes. When those worked I did the whole shebang. Finished in about an hour on 60 nodes, which is really pretty impressive given what it’s doing. Definitely a win!

Now to work on putting some words down for the Introduction section. I also like to outline the results section by generally writing about how I think it will go in a glorified outline. I’ve posted about this process previously here.



Survival of the fitness: how to do good by your health on travel

I don’t travel a lot compared to some people I work with, but I do a bit of business travel. I just returned from a quick trip to DC. If you travel this way, and you’re trying to maintain an exercise regimen of any kind you know how hard it can be.

from DUSAN PETRICIC in The Scientist

When you get to your hotel you just want to lay in bed, relax, and veg out- meetings can go all day, and the food can be, to put it VERY generously, less than healthy. It’s easy to take the vacation way out. That is, to think, “hey, this business travel is kinda like a vacation and I can just let all this health stuff slide for a bit”. Slippery slope- very slippery. It’s not just the travel time you’re talking about, it’s also the time when you get back and start dodging your workout routines and eating well because you’re out of practice. Actually, business travel can be a great opportunity (see me with the more optimism) to actually do more than you usually do- if not in the eating area at least in the fitness area. Here are some things that have helped me (and that I aspire to, I’m certainly not perfect in this area). I’m intentionally trying to avoid the advice that’s good in this area, but could pertain any time to your fitness.


  1. Bring along healthy snacks/small meals with you. This beats the heck out of buying stuff in the airport, on the airplane, from the hotel snack bar or (heaven forbid) minibar, or from a random vending machine. This wins on the nutrition front and on your wallet too. I generally pack energy bars (the Clif Zbars for kids are actually great for grownups too and about 120 calories), instant oatmeal with extras (brown sugar, dried fruit, peanut butter) since hotel rooms almost always have coffee makers- but don’t forget a spoon, crackers and tuna fish (Starkist has cute packages, but you can easily make your own), and fruit (NOT bananas, but apples, pears, etc.). All of this should make it through security OK- I’ve never had a problem (even with the PB, which is kindof a ‘paste’).
  2. Don’t give up on eating well, but realize that there are just those times. Dinners out with colleagues, free food buffets, cookies and muffins provided at the conference, alcohol and more alcohol- all those things can be tricky. Make sure that you keep a rough estimation of caloric intake in your head and try to match it (or, if you’re really good, precede it by) doing something from the exercise list below- that way things even out, more-or-less.
  3. You probably won’t eat your best, but DON’T eat your worst. This is just common sense, but it’s really easy to forget. If you’re going to eat bad don’t go whole hog- there are generally better choices and worse choices. Try to go toward the light.
  4. Use jet lag and busy meetings to your advantage. Sometimes jet lag and busy meetings (without food available) can be your friend. You may not be hungry at the times you normally are and you may be able to avoid some of the bad by simply skipping it (this can go both ways- I get hungry early in the morning on the East coast for some reason). Also, for me busy is better. I’ll simply forget that I’m hungry (at least hungry in that bored-so-I’ll-munch way).


  1. Bring your workout clothes dummy. It seems simple, but it’s probably not the thing you’re thinking of when you’re packing. Don’t forget workout shoes (I use some flat shoes that pack easily) and an mp3 player if you normally use one.
  2. Make use of the hotel gym. Most business hotels have workout rooms. Make sure you ask when you check in where it is and when it’s open. Use it but don’t be tied to your normal workout schedule since it probably won’t work on travel.
  3. Walk. If your meeting is in the city, walk. Walk to the conference (if it’s somewhere else), to dinner, or just plan to walk around during your breaks. This is the thing that’s really helped me and it’s fun too. Do some research prior to your trip to make sure you’ll be walking in safe areas or just ask at the front desk before you venture out. Walking back to the hotel, even a longish way, after dinner can be a good way to make up some calories- but ask at the restaurant about a safe path. Running works too.
  4. Get out and see the place. If you have breaks or free time go and see the sights, but walk. Use public transportation (Metro is best) to get from A to B and walk the rest. Travel like this is a great opportunity and walking is one of the best ways to actually see someplace.
  5. Use the stairs. Not just to get up to your room, but use the stairs to work out. It may be that the hotel doesn’t have a gym or that the gym isn’t the greatest. Use the stairs. Climbing 10 floors (about 5 minutes) should burn somewhere around 50 calories– and you can do it many times. It’s likely that no one will see you sweat, but this might not be the most interesting place to workout. Listen to music or podcasts to pass the time.
  6. Do a workout in your hotel room. You can blast the tunes, watch a movie, or do this completely naked (but please close the blinds, please). There are lots of different fitness regimens that you can do with no equipment at all- and they can kick your ass. Here’s a good set specifically for the hotel room stay from NerdFitness.
  7. Dress like you mean it. Planning to put on your workout clothes provides a much lower energy barrier than actually working out. So do that first. When you’re standing around in your workout clothes you’ll start to feel stupid for not working out. It actually works.
  8. Use your layover. Airports are big. Some are really big. Use that fact. If you have a layover of more than about 45 minutes start walking. Plan out your walk so that you don’t end up far away from your gate when you need to board- which would make you feel dumb, sweat, and probably hate me for my stupid ideas. Try walking the whole thing. If you have a roller bag so much the better. Dragging one of those things around will only make things better. Skip the moving walkways- instead try to beat the people standing on them (or walking on them even) to the other end. Pretend like you’re in a super hurry to catch your plane, it’s fun.