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There’s nothing like the first day of class to make you appreciate the difference between the equipment you end up using at schools and the equipment that you get to use on the job.

For the month of January, I’m teaching a night class in bioinformatics at a local community college. We’re introducing lots of web-based programs, and databases, and concentrating on the sorts of activities that biotechnology technicians are likely to use on the job. It’s fun. It’s practical. And I don’t have to suffer through any lectures about the Semantic Web.

I’m also getting reminded (although not for the first time) that it’s really helpful to have the proper equipment for doing this type of work. So, if you are ever planning to teach a bioinformatics course, anywhere, here is the sort of equipment that I think would be helpful:

  • 1. Computers with large monitors. I really feel bad for students having to try to work on laptops, especially when they don’t have mice. Doing bioinformatics work on a laptop is like trying to do achitectural drawings on an airplane tray.

    Screen real estate is important. I normally use two monitors at work, a 20″ flat panel and my 17″ laptop, and it’s not because my eyes are bad. It’s because I usually have several programs and windows open at one time. It’s hard watching students suffer with constantly moving windows around since they’re working on little bitty laptop screens.

  • 2. Mice. And, if you’re using Macs, don’t use the Mac mice. Get mice with multiple buttons. Really, that right button on the mouse comes in handy.
  • 3. The ability to install programs. Okay, I know there are good IT and security reasons for not letting students do this, but it’s hard to teach people how to install programs when they’re never allowed to install programs.

    Plus, it’s hard to remember all the programs that should be installed ahead of time and ready to go. I have a bad habit of assuming that all computers come equipped with Acrobat Reader.

  • 4. The ability to print.
  • 5. In a truly ideal world, we would also have computers, like Macs, where you could use both the nice GUI features and pop up a terminal window if we wanted to do a little bit more. Oh well, for a short-course that would probably be too much anyway.

Addendum: I forgot to add that there are a couple of additional things that make life easier for students in these classes.

1. Have some kind of text-editing program on the computers – like Text Edit (for Macs) or Notepad (for Windows). Microsoft Word is fine, too.

2. Recommend that students get some kind of web-mail account, like gmail or yahoo, so that they can e-mail themselves from the classroom.

It’s helpful for students to be able to take notes while they work and e-mail themselves the answers.


  1. #1 Janne
    January 9, 2007

    For screen estate, you really should look into having a desktop manager with a screen pager function. You know, where you have four or six “screens” you can have applications on, and flip between them (your screen effectively shows one of them at any time) with ctrl+arrow keys or similar. You then basically have one app open per screen, and let your muscle and spatial memory keep track of where everything is (something it is very, very good at).

    I use two machines on a daily basis – a desktop Windows machine and a small notebook with Linux. The Windows machine did not have a pager function for a long time, while the linux machine does. And yes, the largish, high-resolution desktop monitor felt cramped and constricting, whereas the small laptop screen does not. To my embarrassment it actually took me several months at this job before I thought to go check if perhaps someone had implemented virtual screen functionality for XP. Now that I have a screen pager, it no longer feels nearly as cramped anymore.

  2. #2 Tyler DiPietro
    January 9, 2007

    Why stop there? If this is all fantasy and you have carte-blanch for equipment, why not go all the way? If you’re gonna dream, DREAM BIG! Here are my additions:

    2X nVidia Quadro FX 5500 video cards with Scalable Link Interface (SLI): Imagine the number of 3D models and level of detail you could run simultaneously with these puppies cranked? Sure, overclocking voids your warranty, but who cares?

    30″ LCD DVI Monitors: LCD’s typically deal with lower refresh rates than their CRT counterparts, but it’s improved to the point where the increase in visual quality offsets the loss in framerate. Plus, size matters.

    AMD Barcelona Quad-Core Chips: Okay, so they’re not even out yet, but we’re dreaming! Concurrent programming tasks for sequencing, mapping and comparing DNA strands will no doubt come in handy. And imagine the speed!

    8-button optical Logitech Mice: Buttons are always important. The more specialize-able buttons you have, the better.

    OCaml compilers: No real special reason for this. They’re actually FOSS, but I just happen to like OCaml.

  3. #3 Sandra Porter
    January 10, 2007

    Dreaming is so fun! That desktop manager sounds like a great dream and practical! All the laptops at the school are PCs with some flavor of Windows, I’ll definitely look into this, thanks!

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