In Boston last week, just a few days after Microsoft announced its BioIT Alliance initiative at the Bio-IT World Life Sciences Conference and Expo, some of the first fruits of that effort were on view at LinuxWorld on the other side of town.
Bioinformatics consulting firm the BioTeam performed a live demo of an Excel add-in it is developing that enables researchers to launch Blast queries directly from Excel and then get results back directly into the spreadsheet application. The demo accompanied a keynote address at LinuxWorld in which Bill Hilf, director of platform technology strategy at Microsoft, spoke about the software giant's interoperability initiatives.
Michael Athanas, a BioTeam founding partner, told BioInform that the Blast add-in is a "taste" of what the company is developing as it moves toward a concept he described as "the scientific desktop" the extension of scalable computing power to common productivity tools like Excel to perform scientific computing tasks.
"The target for these kinds of tools is the bench scientist," Athanas said. "It's trying to bring together the data and the applications in a more native way. The idea is to improve productivity and to make the usage barrier to many different types of applications much smaller."
The philosophy is in line with Microsoft's goal for the BioIT Alliance [BioInform 04-07-06], which is no coincidence. BioTeam is a founding member of the initiative.
BioTeam "looked at how people actually use Blast services in their day-to-day research, and in the end, they put everything into a spreadsheet."
"BioTeam is working very closely with Microsoft, but what we're doing is very complementary to what they're doing," Athanas said. "I think there's going to be a lot of exciting things happening in the next few quarters in terms of scientific computing and Microsoft."
The Blast add-in served as an effective demonstration of the potential for productivity software in scientific computing, "because it was an example that people could relate to," Athanas said. "We're not going to focus only on Blast."
In developing the add-in, Athanas said that BioTeam "looked at how people actually use Blast services in their day-to-day research, and in the end, they put everything into a spreadsheet. So instead of going to a web page, pasting in your query, then waiting and getting the results, this can make your Excel spreadsheet into a logbook, which is what people are doing anyway."
The add-in connects the Excel worksheet to a remote server via the BioTeam's iNquiry web services framework. Users select their query, database, and Blast program directly from the spreadsheet. Results from all runs are summarized on a single worksheet, while detailed results for each Blast run are available on separate worksheets.
Athanas stressed that the add-in isn't in user hands yet. The BioTeam is still fleshing out its strategy for making its scientific desktop available, though it is aiming for a release in the third quarter.
While he declined to provide specific details of what the scientific desktop will entail, Athanas said that it's an "evolution" of the idea behind the firm's iNquiry cluster and web portal, which includes a suite of common open source bioinformatics tools. "This is on the path of what iNquiry is all about," Athanas said. "INquiry is meant to bring many popular applications closer to the scientist and make them more accessible. This is, in a sense, a logical progression of that."
Bernadette Toner ([email protected])
CeuticalSoft Builds Informatics Business Around Excel
The BioTeam isn't the only life science informatics firm that sees Microsoft's Excel as a shortcut to scientists' desktops CeuticalSoft of Hillsdale, NY, has built its business around a suite of Excel add-ins for drug discovery.
The firm, launched in late 2003 [BioInform 01-05-04], has signed on five major pharmaceutical firms and five biotechs as customers so far. Chip Allee, founder and CEO of CeuticalSoft, said that adoption has been strong because "the science community is very comfortable with Excel, so it makes it easier to deploy and train and get user acceptance."
In addition, he said, "many labs are already doing everything in Excel anyway, but it tends to be disorganized and hard to maintain and there are a lot of problems with homemade stuff." CeuticalSoft also offers services to "take existing processes and streamline them and bolt them into a better framework," he said.
The firm offers five Excel-based analysis modules: Curvature, for automated curve fitting; Kinetiture for kinetic assay data analysis; Calcature, for automated plate calculations; Filature, for plate reader file conversion; and Templature, a plate layout template generator.
But Allee said that much of the company's business comes from instructing scientists about features that Excel already offers for scientific analysis. "The real problem with tools like Excel is that there's an enormous amount of capabilities and the vast majority of users have no idea how to use most of them," he said. "They maybe know 10 percent of the tool, and by making an easier presentation of existing capabilities, they get a lot more out of the tool than they knew was there."