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Three (or more) operating systems times three (or more) versions of software with bugs unique to one or systems (that I don’t have) means too many systems for me to manage teaching.

Thank the FSM they’re not using Linux, too. (Let me see that would be Ubuntu Linux, RedHat Linux, Debian Linux, Yellow Dog Linux, Vine, Turbo, Slackware, etc.. It quickly gets to be too exponential.) Nope, sorry, three versions of Microsoft Office on three different operating systems are bad enough.

This semester, I’m teaching an on-line for the first time ever. The subject isn’t new to me. I’ve taught bioinformatics off and on in different venues for almost ten years. It is strange for me though to communicate entirely through e-mail, an occasional video, and through writing. I miss seeing the students face to face and without the ability to watch what they’re doing when they use computers, I’m slower to diagnose problems and figure out how to help.

I’ve also found a new unanticipated challenge and I wonder how other people deal with this. This challenge is dealing with all the varieties of computing platforms, versions of different software, and bugs that seem to pop in the versions that I don’t have.


Now, there are many challenges to teaching bioinformatics in any situation, largely, I think, because it involves learning how to use several new kinds of software programs, at once, and usually a new language. The students who are experienced with programming are often disdainful of the academic databases and freeware programs that we use, (and sometimes ticked off because biologists use words that they don’t understand). Even many of the biology students do not know enough biology to understand the words that are written in a database record. Many of them are not good with using software at all. They can’t switch between windows, they don’t know any keyboard commands, and they loose files that get downloaded.

I can attest that everything that Joel said about computer users, in general, is correct about students, too. To paraphrase Joel:

1. They cannot use the mouse.
2. They do not read instructions.
3. They do not remember.

Perhaps there are challenges too, because of the way that I teach the subject. I teach bioinformatics the same way that I would teach cooking, media preparation, or gene cloning. The students get lots of assignments and no tests. My view is that a big part of bioinformatics revolves around analyzing molecular data and I would like students to finish my class having acquired the ability to do this, at least to a certain extent.

This semester, we’re working on a project that I introduced in another class last fall. We analyze chromatograms that were derived over the past four years by sequencing bacteria isolated by students at JHU. The students identify the bacteria via blastn, and count the different kinds of bacteria from different biomes. Then, we identify polymorphisms in the genes that were sequenced, align sequences, make phylogenetic trees to look at the diversity of these sequences, and see where the polymorphisms map in the structure of the ribosome, and whether they map in regions that are bound by antibiotics. It’s pretty cool since we get to apply a lot of different techniques and since we’re working on a semester-long project, we have some continuity.

So what’s the challenge?

The challenge is that my students (and I) all have different kinds of computers and different versions of Excel. As I said above, I like to have the students count and graph the numbers of each bacterial genus in each biome. If we could do this with Google Docs, we would, but Google Docs doesn’t have a feature for doing pivot tables and I’ve found that pivot tables are by far the best method for this kind of work.

I thought that things would be fine even though pivot tables are little complicated. But, I realized from student’s questions that this was harder than I thought. So, I made movies to show how to do this. Still, I didn’t realize the extent of the problem until I saw the assignments and found that only one student had managed to do the graphing correctly.

This was downright depressing.

The problem turned out to be a bug in Microsoft Excel that only appears on computers with Windows. I never saw it because this problem doesn’t happen on my Mac. I thought I had the problem solved though, when I borrowed a computer with Windows XP and Office 2003, reproduced the behavior my students described, and figured out a way to work around the problem.

Then one of my students sent screen shots to show me that his computer doesn’t have a wizard and he’s using Excel 2007, on VISTA.

Crap.

I don’t have a copy of VISTA.

I don’t have a copy of Excel 2007.

Yes, I can require that students purchase certain software, but asking them to go backwards and get Windows XP for one, maybe two assignments, is not a realistic request.

So, I wonder.

Do other instructors have these problems?

Do other instructors just avoid assignments that involve commercial desktop software?

I would quit using Excel and Word, but having taught in community college where 30-50% of our students were graduates from the University of Washington, I strongly feel that college instructors have a responsibility to leave students with at least a few marketable skills. I also know for a fact that my former biotech students had a big advantage in the job market because they were really good at using Office programs really well.

But, back to my question, are these problems that other instructors have? How do you deal with the multiplicity of platforms and software versions?

Comments

  1. #1 Richard Chapman
    March 10, 2008

    Disclaimer: I’m not an instructor, educator, or even a geek. But I do see two possible solutions (only one really but I can’t help making a jab at Vista).

    1. You and all your students need to purchase Vista and any required hardware so everyone is on the same page.

    2. I see Linux as part of the solution, not part of the problem. For a reasonably experienced technician, it’s possible to easily create a personalized LiveCD. Students could install it on a partition on their hard drive or just use it as a LiveCD and save files to USB stick. The advantages are no cost, absolute consistency in all aspects of the computing environment right down to the wallpapers, all links and email addresses and any other communication protocols could be “hard wired” in. I’m just a lowly non-geek Linux user and this is what I could come up with. Someone more knowledgeable would have a lot more ideas and suggestions.

    Whatever the case, I hope you find a good solution for you and your students.

  2. #2 Sandra Porter
    March 10, 2008

    Thanks Richard,

    I’m checking with the school re VISTA.

    Is it possible to run Windows and Microsoft Excel on a LiveCD?

  3. #3 Richard Chapman
    March 10, 2008

    What about Open Office. It is not a light-weight. It’s similar enough to Office 2003 so students will have little difficulty making a change. It’s cross platform too. It’s available on the Mac as NeoOffice I believe. And it’s available for the cost of a download.

  4. #4 Chris
    March 10, 2008

    I concur with Richard. Stick to open-source, multi-platform software, and many of these issues go away. Tools like OpenOffice, R, and even many Java programs will work the same everywhere. This saves you a lot of hassle, (and potentially saves you and your students a lot of money).

  5. #5 Sandra Porter
    March 10, 2008

    I think, if students were already using Linux, Open Office would make sense. As it is, I think it’s best if I stick to platforms and software that the students already have. It’s harder for me, but easier for them.

  6. #6 Chris
    March 10, 2008

    Oh, and for what it’s worth, Open office has the equivalent of pivot tables, called data Pilots

  7. #7 Sandra Porter
    March 10, 2008

    I don’t know.

    All my students have Windows and I have a Mac. If my students were ask why they can’t use the software that they’ve purchased or that comes with their computer, I wouldn’t have any kind of rational explanation.

    Does Open Office run on Windows and Macs?

  8. #8 Sandra Porter
    March 10, 2008

    Those data pilots look way harder than pivot tables.

  9. #9 Richard Chapman
    March 11, 2008

    Does Open Office run on Windows and Macs?

    See #3

  10. #10 Richard Chapman
    March 11, 2008

    “Keith: Students do get a pretty good discount on software. It’s probably cheaper for them to buy a copy of Office than it is to get a copy of RedHat Linux.”

    Hey, if you’re considering paying for Linux I can supply you with as many PCLinuxOS CD’s as you need at $300 each. Because this is for a college, I’ll give a student discount of 50%.

    Look, Linux is free, and it is also free. You’re a learned person so I trust you understand the difference between the two. If you want to pay for Linux that’s your choice. Your choice among many free equally qualified distributions. And before you attempt to squash that with “But there are 300 bazillion distributions, who could possibly choose from all of them?” nonsense, you need only to look at the top 5 or so on Distrowatch. Or, find a Linux knowledgeable technician at your institution’s IT center to help you.

    It really seems as though you made up your mind about your solution before you even posted a ‘call for ideas’. I’ll try one more time. It looks as though you’re “stuck” with a Windows “solution”. If that’s the case then you have only two choices. Everybody uses Office 2003/Office 2007 or they use Open Office. I thought you were kidding when you said “Is it possible to run Windows and Microsoft Excel on a LiveCD?”. I see now that you weren’t. This is difficult to say, but anyone who could make such a statement should defer all issues concerning computer/student interaction to the IT people. I don’t know what your spreadsheets will entail, but to dismiss Open Office as a light-weight amateur application can be a very expensive mistake.

  11. #11 decrepitoldfool
    March 17, 2008

    To fill in for a couple of previous non-answers to your question, OpenOffice runs on Windows, Mac (but it’s called something else) and Linux. It’s faster on Linux than it is on Windows but I wouldn’t give a nickel for the difference between it and MS Office. It can output in OpenDocument Formats or in the proprietary MS Office formats – maybe not the latest one yet but that’s coming.

    I work in a College Of Business and oh-my, the depth of Microsoft’s brand recognition is amazing. I’ll say this for them; they have done one hell of a marketing job, at least until recently.

  12. #12 Winawer
    March 19, 2008

    Decrepitoldfool: OpenOffice has a build that runs on OS X; the “called something else” you’re talking about is NeoOffice, a native build of OO on OS X. They’re nearly the same thing.