sbrewer's blog

Provizonta recovering nicely

Provizonta had to be hospitalized after its fuser seized up. But I am informed it is recovering nicely and will be up and about in just a few days and ready to print your documents in no time.

UPDATE: Provizonta should be back to work sometime on Friday April 20. We're still waiting on hardware support. :-(

The program "structure" installed in BCRC

I have recently installed the command-line version of structure which "implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers." The program is on your PATH if you open a terminal window and type "structure". To run the program, you really need the "mainparams" and "extraparams" files -- the original ones are in /usr/local/share/structure, if you need to start with something.

I have also set up the workstations to run structure in an automated way, if you have many analyses you want to run -- contact me to get directions on how to use that. Or if there are similar analyses you would like to run using the BCRC computers.


I have installed Octave via macports in the BCRC. Just start a terminal and enter "octave" at the command prompt...

There are many resources to getting started with Octave, including this brief introduction and this programming tutorial. This Reference Card handy.

There are many extensions to octave with additional functions and tools. I've installed the octave-bioinfo tools already, but others may be of interest.

Synchronizing Folders

Someone asked me recently if there was an easy way to synchronize folders between two computers. Unfortunately, the easy ways tend not to work very reliably. But here is a method that's a little more complicated, but should be extremely reliable. You'll need to do some unix things and you'll need a place on the server where you can keep all of the files.

Note: You could avoid using the server as an intermediate space, but then you'd be limited to a system that only works inside the building. Or, rather, making it so it would also work outside the building would make it a lot more complicated.

We'll assume you're going to keep a folder in your home directory on a laptop and a desktop synchronized with a folder located on a lab hard-drive on marlin. Don't try to set this up with a folder in your home directory unless you've made prior arrangements with the technical staff, unless you only want to use it for tiny things.

Read more to learn how.

Firefox 8.0

Workstations in the BCRC will be updated to Firefox 8.0 overnight. Other labs in our network will receive it over the next few days. Also included are new versions of Flashblock, Flash Player, and Shockwave.

Using the No-Script Firefox Add-on

For Technology Tuesday on Nov 22, 2011, I will offer an overview of the No-Script Firefox add-on -- an important tool for improving browser security.

One of the most serious current vectors for security issues in computing are client-side scripts (Javascript and Flash in particular). In many ways, when you let these scripts run on your computer, it's like letting a stranger sit at your computer and do whatever they want (watch your keystrokes when you type passwords, for example). It's not supposed to be like that, but all too often it turns out that they actually can. It's worth taking steps to be aware of the issue and protect yourself.

Unfortunately, browsers don't provide simple tools to manage which sites you allow to execute code on your computer. In Firefox, there is a powerful Add-on called No-Script, which lets you choose on a site-by-site basis, which to allow to execute scripts on your web-browser. I will offer a walk-through of how to install and manage the add-on to help you make informed decisions about security and web-browsing.

RSS and Feeds

The BCRC is experimentally hosting an instance of the TinyTinyRSS Feed Reader that can be used to subscribe to (and publish) RSS and Atom feeds. Most modern websites (like this one) can provide a feed (or feeds) of articles, often by author or category -- or even the comments. Most scientific journals also provide feeds that generally include the abstract. If you're suffering from information overload, a feed reader can help you organize things to stay current with a much larger number of information sources than would be possible almost any other way.

Poster Printer Payment

We've changed how we handle paying for poster printing: we can no longer accept payment via checks or cash. We can now accept UCard payments. And we can still bill people provided you will give us a speedtype number to simply the billing. Hopefully this will represent a simplification for everyone.

New Application: 4 Peaks

I have added the application 4 Peaks to the installed software in the BCRC, Intro Labs, and ISB 264, 264, and laptops. The application is a sequence trace file analysis program that can read and translate among many different formats, recognize motifs, and do many other sequence analysis tasks. It should be on all the computers on Sept 29.

Staff Manual Migrated

In response to Ann's suggestion, I've migrated the Staff Manual to this site -- you can find it in the menus to the left. Go ahead and start updating!


I've updated MacOS X and added a bunch of other updates, including Firefox 6 and Office 2011. I've left Office 2008 installed as well.

Printer Control Info

Today, I finally got everyone entered into the printer control system so that BCRC staff can control the printers again, and increase quotas for people.

In the Print Release System, click on "Manage" to check someone's print history and add quota -- please add in 100 page chunks and let's not increase anyone over ~600 total pages without having them check with me.

You can also see the overview of queued jobs for each printer and manipulate the queues as necessary.


I've ordered more paper. If we run out, we may need to borrow some from the Copy Room.


I've set up blogging for the BCRC staff. When you discover something, learn something new, or have an idea, please post about it here.