The Essential Software Toolbox

Let's face it: Life scientists need computers. They need word processors to write grants and manuscripts; spreadsheets and statistical software to crunch numbers; image manipulation software to put the data into publication-ready formats; and sequence analysis software to, well, analyze sequence information. The Scientist recently conducted a survey in which readers were asked what software is used in their laboratories, and to what tasks they think the software manufacturers need to pay greater attention. Of 1,493 surveys sent out to our readers, 248 responded (16.6 percent). Every respondent was automatically entered in a drawing for a Palm m100 handheld organizer; Duna Penn of the Louisiana State University Health Sciences Center in New Orleans, La., was the winner. The survey polled readers concerning ten software categories: operating system, Web browser, standard productivity applications, database applications, graphics software, image manipulation software, sequence analysis and plasmid drawing software, graphing software, bibliographic management software, and primer analysis software. A number of labs also rely on other, more specialized types of software, for analysis of microarrays and gels, and for microscopy applications, for example. These applications tend to be proprietary and come bundled with hardware, so there is less flexibility in the selection of one product over another. These categories were therefore omitted from the survey. For each question, respondents were asked to indicate all software used in the lab; thus, the sum of the fractions represented by each answer does not necessarily equal 100 percent. Not surprisingly, the lion's share of respondents use Microsoft Windows (86.3 percent) and Microsoft Office (94.8 percent), from Redmond, Wash.-based Microsoft Corp. A surprising 29.4 percent use Macintosh OS from Cupertino, Calif.-based Apple Computer Inc., indicating that this operating system is more widely used in research environments than by the general public. Other operating systems, including UNIX variants and Houston, Texas-based Compaq Computer Corp.'s OpenVMS, are being used in 13.3 percent of the labs represented. Neither Microsoft's Internet Explorer nor Mountain View Calif.-based Netscape Communications Corp.'s Netscape Navigator dominates the laboratory Web browser market; the former captured 66.1 percent to the latter's 62.5 percent. In several of the categories surveyed, one product dominated the field. San Jose, Calif.-based Adobe Systems Inc.'s Adobe Photoshop rules the image manipulation software market (76.6 percent), trailed distantly by the freeware National Institutes of Health's NIH Image application (13.3 percent; available at rsb.info.nih.gov/nih-image/). Microsoft Excel dominates the graphing software category (69.8 percent), followed by SPSS Inc. of Chicago's Sigma Plot (29.8 percent). Berkeley, Calif.-based ISI Researchsoft holds the top two positions in the bibliographic software category. The company's EndNote is used by 51.2 percent of the respondents, followed by Reference Manager (18.1 percent). In the graphics software category, Microsoft PowerPoint was the clear winner (90.3 percent), followed by Adobe Illustrator (23.0 percent), Ottawa, Ontario-based Corel Corp.'s Corel Draw (19.0 percent), Miami, Fla.-based Deneba Software's Canvas (14.1 percent), and San Francisco-based Macromedia Inc.'s Freehand (4.0 percent). Nearly 75 percent of respondents use some sort of database package in their labs. Microsoft Access received a plurality in this category (39.5 percent), followed by FileMaker Pro from Filemaker Inc. (a subsidiary of Apple Corp.) of Santa Clara, Calif. (18.5 percent); 11.7 percent use another database product, and the most widely indicated choices in this case were Oracle from Oracle Corp. of Redwood Shores, Calif., and Foster City, Calif.-based Applied Biosystems' SQL*LIMS. A little more than half of the labs surveyed have sequence analysis and primer design software packages, but no title dominated either field. The most popular sequence analysis and plasmid drawing software product was San Diego-based Accelrys Inc.'s MacVector (13.3 percent), followed closely by DNAStar Inc. of Madison, Wis.'s Lasergene (11.3 percent) and North Bethesda, Md.-based InforMax Inc.'s Vector NTI suite (10.1 percent). However, 10.9 percent selected 'Other' in this category, and of these, Christian Marck's DNA Strider, Accelrys' GCG Wisconsin package, and Biowire.com's free Jellyfish application were the most popular choices. Cascade, Colo.-based Molecular Biology Insight Inc.'s Oligo software was the most popular primer design choice (14.5 percent), followed by the PrimerSelect module of DNAStar's Lasergene (10.1 percent) and the freeware choice Amplify, written by Bill Engels at the University of Wisconsin (4.8 percent; available at www.wisc.edu/genetics/CATG/amplify/index.html). Those who selected 'Other' in this category (10.9 percent), most frequently cited DNA Strider and the GCG Wisconsin package. When asked which additional software packages they find most valuable in their work, researchers indicated a wide range of titles, as expected. The most commonly cited application was Adobe Acrobat Reader. The Acrobat file format is a de facto Internet standard for document transmission, to the extent that some funding agencies require grant submissions in this format. A number of researchers also find statistical analysis software packages invaluable in general (see profile). Memo to Software Developers... We also asked readers to describe any tasks they thought could not be solved easily with currently available software. Most of the responses could be lumped under the "image preparation" umbrella. A number of replies indicated that image manipulation programs are not sufficiently user-friendly, while others wrote that graphing applications could be improved. Additionally, a number of respondents commented on the lack of compatibility between various file formats--for example, the ability to export sequence data into a word processing program, or the ability to migrate sequence files between competing sequence analysis applications. As with all things, the results of this survey must be put into perspective. Do the survey results paint the picture of a group of users that can "get by" with the available software, but who find they need to cobble together disparate packages in order to do so? Or do they suggest that the ability to find an application to fulfill almost any need is in fact a benefit? Undoubtedly most researchers would gladly have these packages improved if they could. Nevertheless, as one respondent says, "The flexibility of the newer software products is truly amazing and helpful to our research output." Another adds, "The lab has a wide variety of software for every application. It is one of the lab's strengths." The detailed results of this survey are available at www.the-scientist.com/yr2001/jul/results_010709.html. --Jeffrey M. Perkel (jperkel@the-scientist.com)

The Essential Software Toolbox

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