Month: May 2009

I needed a bit of a break from work earlier today so popped down to Soulard Farmers Market. According to their website, the market has been frequented by many famous people. Local visitors include Jackie Joyner-Kersee (the Olympic athlete) and John Goodman (of Big Lebowski and Roseanne fame). Three US presidents have come to the market, the most recent being Arkansas’ Bill Clinton. That doesn’t mean anything though, Clinton visited Birmingham in 1998 and described it as a “an extraordinary jewel of a city”. Hmm.

Anyway, Soulard Farmers Market dates from 1779  – just 3 years after the declaration of Independence. At that time the Illinois Campaign was in full swing back in the bad old days before Americans realised that the British have rilly, rilly nice accents . This makes it the oldest still-working farmers market in the country, if you trust the butcher on such things.

There is much less emphasis on local or regional produce than a British farmers market, with most of the fruit and vegetables coming from thousands of miles away – mainly from the West Coast. Organic or free-range produce wasn’t particularly noticeable.

The focus is more on price, the butcher told me that farmers markets are doing great business right now, and that is down to value for money. He reckoned $60 of groceries at Schnuck’s could be gotten for $10 less at the market. Certainly they were nearly giving the produce away by the end of the day.

Tthere were a few interesting new tastes to explore. The butcher had a bunch of smoked and salted pig bits, including the “snook” still replete with nasal hair. A variety of exotic meats were in the freezer. One stand was selling “crab rangoon”, a deep-fried wonton filled with crab and cream cheese. Surprisingly nice actually.

And I also managed to pick up a St. Louis Gooey Butter Cake which was very good: buttery, crumbly pastry with a very luxurious almond-y filling. Which means my tour of St. Louis specialties is nearly complete: only toasted ravioli and frozen custard to go now (I’ve decided to take a pass on the once-popular fried calves’ brain sandwiches).

What rules of thumb would you suggest to a fledging bioinformatican? Or if you could travel back in time, what would you tell your younger self?

I thought it would be fun to try and get down some of the things I’ve learnt, some are practical and some are a bit more philosophical.

Any bioinformaticians reading I’d be interested to hear your thoughts!

1) Always “nohup” your analysis runs

Basic, but easy to forget. How many times has a long-running analysis died, usually just before the end, because my laptop went on standby, or the ‘net connection went down, killing an SSH session.

Write a script that calls your program and execute it with nohup <script-name> & to run it in the background. If it sucks major CPU time then remember to renice the process, remembering that higher nice values mean lower priority.

2) Name your directories and your files carefully

It’s no fun returning to an analysis some months or even years after you did it to find a directory called ‘stuff’ filled with files like ‘out’, ‘results’ and ‘crunch’.

Name your scripts according to function, e.g. ‘parse-glimmer-output-to-genbank’. Organise your directories into logical hierarchies, and then datestamp and serial each set of results i.e. ‘amazing-genome-work-23052009-1’.

3) Put all your scripts and primary data into Subversion or equivalent source control system

This solves two problems at once: how to ensure a copy of all your useful scripts on each server you work with and your personal machine. It is also the answer to how to keep a distributed backup of all your work.

Put primary data sources in Subversion, but add your results directory to ‘.svnignore’ so you don’t store analysis which can be re-constructed easily by your scripts.

Subversion is just an example, you might prefer git or bazaar or some other fangled system. It doesn’t matter so much what you use but that you use it.

4) Write your scripts for the guy in ‘Momento’

You remember the guy that can’t remember anything older than about 5 minutes ago. That’s you.

Make your scripts parse the command-line properly and output a friendly message when you run it with no arguments. Use a consistent scheme for input and output, either using command-line flags like “–in” and “–out”, or make all your scripts use redirection. Try not to mix different schemes.

Put a README in the directory to remind you of the order you run the scripts, and any environment variables or other gotchas when running.

5) Be able to work effectively on both your laptop as well as a server

Install a desktop environment similar to your server environment (probably Linux), and enough on your laptop so you can develop stand-alone.

That way when you are at the airport or on a plane or train, in a tedious seminar you can’t get out of, or when your Internet connection has gone down you can can still get some work done. Point 3) helps  with that.

6) Split scripts by task, and allow check-points

There is nothing more annoying than a script that takes a week to run crapping out in the last few minutes due to a bug and there being no way to restart the analysis except from the beginning. Break down tasks into modules, write a separate script for each part of the analysis, and make it so you can start from any point in your analysis pipeline.

7) Beware the “ultimate system” which solves everything

An error that affects newbies and experienced bioinformaticians alike, in my experience. In your mind there is a gleaming, shiny “system” that can solve all known bioinformatics problems. It probably has an elaborate web interface, RPC bindings, a fully normalised RDBMS and probably a full Turing AI as well. This system will never exist. Don’t start building it. Resist.

Instead build something that does something useful NOW, document it, release it and move on. If the thing you built is really useful to someone else you will start getting emails. Then you can start extending it, if necessary!

Like all advice, it is easier to dish out than to take, particularly the last one!

I had a mad plan to drive to Memphis (300 miles from St. Louis) for the weekend, but sense prevailed and have decided to work instead on a report that is due next week. But before I got stuck into a writing session, I thought I better have a spot of brunch. So I swung by City Diner on S. Grand Boulevard – which is a bit of a food hotspot – for a famous St. Louis Slinger.

A Slinger, of course, is a full breakfast (in this case, two eggs over easy, hash browns and hamburger), slathered in chilli, and then topped with cheese.

Anyway, as pictures are worth 1000 words, so here’s several thousands words for you. But they probably all say “I feel a bit sick”.

I’ve just seen that WordPress has a post by email function! It takes ages to update the blogs via the admin control panel, and even longer to insert the images, so I’m hoping that this is the answer to more frequent blog updates. Let’s see if this works?

Pam, George’s multi-talented PA thought I was portraying mid-Westerners as a ‘bunch of ol’ hicks’ in my blog – which wasn’t my intention!

So, to set the record straight, St. Louis is an amazing, cosmopolitan city full of exceptionally sophisticated, erudite people!

Is that better, Pam?

I’ve had a few days now to get adjusted to living in St. Louis in the “Show-Me State” of Missouri. My guide book says this relates to Missourians having a stalwart, not-easily-impressed character. The most common explanation of this nickname is attributed to Missouri Congressman Willard Duncan Vandivier giving a speech to a navel banquet:

“I come from a state that raises corn and cotton and cockleburs and Democrats, and frothy eloquence neither convinces nor satisfies me. I am from Missouri. You have got to show me.”

This attitude strikes me as a good one for scientists and medics (and indeed all rational people) to adopt: “show me the evidence”.

All the Missourians I have met so far have been uber-friendly. They also have a very endearing accent which has a slight twang of the South, but without being full on cowboy. “There ya go!” they like to say. It’s cute!

So, what about St. Louis itself? I didn’t know much about this “gateway to the West” before I came here. It has a strategic position, sitting astride the Mississippi river and near the Missouri too.

Lewis and Clark passed this way on their historic journey to the Pacific Ocean from Pittsburgh, and finished the return journey here, much the worse for wear.

According to Wikipedia they took two buckets, some salt and a ton of dried pork. I’m not sure what the buckets were for, but I agree you’d want some decent proscuitto on a journey like that. At least a ton, I’d think.

The most visible landmark is the iconic gateway arch. This is a seriously impressive structure which looks interesting in all the St. Louis weathers (of which there are many changes each day). It looks great when glittering in the sunshine. It also provides endless photo opportunities to frame the old and new buildings around and underneath it.

Forest Park is in the centre of the city and has over 1000 acres of landscaped gardens – twice the size of New York’s Central Park. This is where St. Louisians come out to play, particularly in the summer (but there is an ice rink for winter). There are many amenities to explore including a boating lake, the Zoo, a Science Museum and an arboretum called the Jewellery Box.

Forest Park is famous as the venue for the 1904 World Fair. It is apparently not true that the ice-cream cone, the hamburger and the hotdog were introduced at the fair, as is claimed all over St. Louis, but Dr. Pepper was.

Talking of drinks, the home of Budweiser (well, the American stuff at least, the Bavarians might disagree) is at the Anheuser-Busch brewery also downtown.

Food wise – yes, I got there eventually, culinary exports include frozen custard – similar to ice cream but thicker with less air content.  “Toasted ravioli” is on every menu and apparently are deep-fried meat raviolis. The famous St. Louis pizza I have already blogged on and we must not speak of again.

Gooey butter cake I haven’t yet found but sounds like a must try. And for the benefit of my parents and anyone else wondering what my cholesterol is: I’m going to have to find a “St. Louis Slinger” before I leave.

This is basically a standard fried breakfast, you know, eggs, hash browns, hamburger. Topped with chilli. Topped with cheese. I better get some statins.

I’ve had 3 full days at the Genome Center now and it has been pretty full-on experience. I am going to do a more detailed blog on the Genome Center later on this trip, plus treat you to some pictures of their sequencing rooms and data center. But just a brief update: I’ve been having some great discussions with the many members of the team that manage the entire sequencing pipeline. Pam has been organising my diary so I meet as many people as possible whilst I’m here. So far I’ve spoken to Dan Koboldt – a keen blogger, who is in charge of SNP discovery in the medical genomics group. He has introduced me to some great new software which is going to be very helpful for our group’s work on bacterial variance detection.

I’ve also had chats with Kym who heads up the annotation pipeline for the human microbiome project, Gary, the head informatics guy who gets to play with servers all day, plus Candace and Cindy who check samples into the sequencing pipeline and manage their progress through it. I’ve also spoken to a couple of the guys who do the Cancer Genome Atlas project. Plus the Wash-U/Gambia/Birmingham Streptococcus pneumoniae project is moving along a-pace!

Coming up, tomorrow I will be watching the 454 & Solexa sample preparation take place. Next week I will be speaking to the LIMS and the AIMS (analysis) pipeline guys, plus meeting David Dooling, head of informatics and another Wash-U blogger!

I know what you are thinking – Nick hasn’t had a meal in ages and is possibly wasting away. You are very worried. Don’t be, I am still eating but just haven’t had time to blog it. For the past 2 days I’ve been throwing myself into work and fact finding at the Wash-U Genome Center and haven’t had much time to blog hard.

But don’t worry, I am well, I am still managing to find time to eat. Last night I got a pizza from Imo’s. This is a St. Louis institution, a thin, quite tough pizza dough topped with tomato. So far, so normal. But instead of mozzarella they use an ingredient called ‘Provel’ cheese. When I heard about this first time I assumed it was just an abbreviation of Provelone, but the truth is far more sinister than that. Provel cheese is a mixture of cheddar, swiss and provelone. Why not mozzarella like the rest of the universe? Apparently because this cheese “bites” more cleanly, so there’s less stringy, gooey cheese mess to contend with.

Anyway, it tastes odd, but not in a good way. I’m not sure if it is an improvement on your basic pizza when all is said and done.

I ate it though.

OK, stay tuned and I will soon tell you all about the great city of St. Louis properly and about the amazing Genome Center where I’m working.

This is a working trip (its not all eating, honestly) and I am trying to get a number of bioinformatics projects sorted out whilst I am away. As I tend to do most of my bioinformatics on remote Linux servers this proves a problem with using high latency connections or when I’m sans internet (for example on the flight over).

So I need Linux dual-boot on my laptop. However, the Lenovo T60 that I use has an annoying problem which means that all of the hard drive space is used up by the default partitioning scheme. I know that you can resize the partition afterwards, but it is a hassle, and there’s always the risk of data loss. Yes, I know I should make daily backups, but who does that?

Mark Kennedy pointed me towards a major time-saver called Wubi, a Windows installer for Ubuntu which installs a virtual partition as a file on your NTFS partition. This means you don’t have to resize your main partition, and it also sorts out the boot-loader so that you can dual-boot Linux or Windows.

OK, nothing revolutionary but it does mean you can have a functioning permanent Linux installation on your new PC in minutes rather than hours. Although you might think running a virtual partition on top of NTFS might slow things down a lot, it doesn’t seem to in reality, and of course any slowdown is mitigated by the speed-up you get from not running Windows BloatWare(tm).

Also, Ubuntu 10 9 is seriously slick and I don’t miss Windows XP at all when I’m using it. Except perhaps for the crummy Flash support.

As you know, BBQ is a big deal in the States – and mid-Westerners like to think their version is the best. The ultimate and largest barbecue festival is the American Royal, held close by in Kansas City, Missouri at the start of October with almost 500 barbecue teams competing.

George let me know the mid-Westerners just call it “ribs” here, not BBQ. There are plenty of differences between mid-Western ribs and Southern barbecue, I won’t elaborate but Wikipedia goes into some details here.

Being Memorial Day weekend, I was sure there must be some serious barbecue action going on somewhere near by to St. Louis. But having read all the free papers over morning bagels, I couldn’t see any reference to ribs anywhere. Although I did spot there is a horseradish festival in 2 weekends time.

I struck lucky when I went to get some groceries from the fantastic Straubs – I was told to head down to the Soldiers Memorial Park for Rib America.

George & Erica agreed to take me there, which was extremely charitable of them considering they spent the last 15 years in Texas, and we had a very agreeable afternoon sampling the available wares. Each barbecue team puts up a dazzling array of garish signs asserting their teams superiority and dissing the other teams’ efforts. Each of them have a clutch of trophies and a long list of distinguished achievements.

We started off by being patriotic and plumping for a full rack of ribs from the local Chicago team. These were toothsome and moist and quite subtly flavoured. The cloying barbecue sauce is optional.

Technical barbecue note: if you want to enter the rib competition at American Royale it is a requirement that the meat only comes off the bone when you have stuck your teeth into it. If it’s hanging off already then it is deemed overcooked and disqualified!

The ribs was washed down with a Bud or two – these come from St. Louis and thus taste better here than in the UK.

Other than ribs, the other main meaty ingredients that make up the barbecue triumvirate are pulled pork butt and beef brisket. So when I saw that the Howling Coyote was available offering all three, plus sides of “Wonder Bread” – like a thick Sunblest, coleslaw and spicy beans, I knew this was my destiny.  George found me a corn on the cob too which they sprinkle with a spice mix. Yum.

Erica got a delicious funnel cake, which is a bit like a doughnut batter squeezed through a nozzle into the fryer. I didn’t have room for much of that, or for any deep-fried Oreos and deep-fried Twinkies (a kind of cake).

After all that, I felt happy and contented, a little bit sick and then really pretty tired as my portal circulation dilated furiously. I somehow managed to avert total gastric shut-down by getting a coffee, but the rest of the day was a write-off.

And, if you were wondering why I haven’t done any work yet, well that starts tomorrow!