Field of Science

GeneSpring not needed?

Several years ago we did quite a lot of microarray work, looking at changes in gene expression as wildtype cells developed competence and in response to various mutations and culture conditions. The analysis was greatly helped by use of GeneSpring software, which displayed the results in various intuitive and insight-increasing ways.

But the GeneSpring company charged us about $3500 ($US) per year to run their software on a single computer, so when the work was done we let the subscription lapse. Lately I've been wanting to look at some of the old microarray data, but dreading the hassle involved in getting GeneSpring set up again. We wouldn't need to pay for a subscription, as another lab in the BARN research group has it and would let us use it. But my past experience setting up our data on Genespring means that I expect hours and hours of fussing and fiddling with incompatibilities and upgrades and emailing tech support and the people in London who made the arrays, etc.

But this afternoon I realized that I don't need GeneSpring to look at the data. We have simple text files of the array data that I can open in Excel. I won't see pretty visualizations of genes and sequences and colour-coded expression ratios, but I can look up the numbers for the signal intensities of different genes under different conditions.

If I needed to look at a lot of genes, or under a lot of conditions, setting up GeneSpring would be worth the trouble. But I think I only need to check a few critical genes under a couple of conditions. The only problem will be finding the files I need, and I'm pretty sure I know where they are.


  1. If I was asked for one key piece of advice to give to people aspiring to combine computing and biology, it would be that the plain ASCII delimited text file is the most useful type of file that there is. It's easily readable by people and machines. You can import it to a spreadsheet, drop it into a database table, use it to plot simple graphs with any graphing package, read and parse it with e.g. Perl, edit it in any text editor and any number of other things.

    GeneSpring not needed? Commercial software not needed, period. The only way that companies can market software is by tying you to their proprietary file formats, unreadable by anything but their programs. There are so many thousands of freely-available packages based on the absurdedly-simple but effective notion of plain, simple text files. You'll wonder why you ever paid for software.

    Congratulations on taking a step towards freedom!

  2. Just yesterday I made a backup of our array data on Black Swan. I shall deposit the disks in your office tomorrow morning. This came about because Black Swan was down to a 100Mb of memory and was having startup troubles/couldn't burn disks/etc. There were several gigs of Otto lab array data that I backed up and then deleted - now Black Swan appears to be swimming smoothly again.


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