Software builds bridges in science community

Christoph Sensen, head of the National Research Council (NRC) of Canada’s Bioinformatics Group, had a problem. He had to connect 800 scientists to more than 100 databases and about 1,000 applications to make the country’s bioinformatics project work.

Canada’s government created the NRC’s Canadian Bioinformatics Resource (CBR) in 1995 to coordinate genetics research within the country and track work being done abroad.

The council’s existing Unix platform was used to support the necessary databases, which included information regarding DNA sequencing and the status of various genome projects around the world, according to Terry Dalton, who is the information technology manager at the NRC.

The scientists in the group were spread across Canada. Each of them was using a different X Window System emulator – software the users installed themselves to access Unix applications. Sensen said he and other council members soon saw the need to streamline access to the databases and shore up security.

Early last year, the CBR installed Go-Joe software from GraphOn Corp. in Morgan Hill, Calif., to link the organization through a common browser-based desktop application.

The software, which has since been renamed Bridges, connects the CBR’s scientists to existing Unix applications and databases.

With Bridges, a user needs only a Web browser such as Netscape Navigator or Microsoft Internet Explorer to access the databases. To provide access, the software uses a small Java applet, which GraphOn says can be downloaded onto almost any Java-enabled desktop.

Bridges replaces a cumbersome process in which X servers communicated X protocols to X interfaces, which is standard for Unix systems, said Robin Ford, vice-president of technology at GraphOn. This process often caused delays because of the frequency of communication between the user’s terminal and the server, Ford said.

The CBR outsourced the software to application service provider GraphOn, so scientists wouldn’t have to install and maintain the software, Sensen said.

“User knowledge of Unix is not strong, and this service is the best way to stay connected,” he said.

The researchers must stay connected to the databases so they can continue to work on their projects, Dalton said.

The information in the databases provides background for the projects and also prevents scientists from duplicating research.

The databases are updated nightly, so information is always being added, Dalton explained.

Bioinformatics combines biological sciences with practical computer knowledge – especially with techniques for using a computer to simplify data.

For example, the mapping of human genes is such a cumbersome process that an extensive database is needed just to store parts of the genetic code information.

To make matters more complex, the inconsistency of programs used to access the applications caused the system to slow down because the X server would have to send different X protocols to different X interfaces.

“How could we share information if everyone was using a different program?” Sensen said, adding that it was also difficult for all of the users to maintain their own software.

Bridges is ideal because the scientists just have to click on a Web site address to gain access to the Unix databases, according to Dalton. The Bridges technology allows a desktop-enabled program to instantly become a Web-based program, without changing any code, Ford said.

Because the program is centralized, Sensen said, it’s easier for all the users to access it.

Before the NRC deployed Bridges, slow connections often prevented researchers from being able to access the databases, according to Dalton and Sensen. “There are hundreds of users across the country. They need something to allow them to go into the database without thinking,” Sensen said.

Dalton noted that security was also a concern because the old system had many access points, which left the system vulnerable.

Everyone had their own individual point of entry via their own computer and software, but Bridges now lets all the members of the CBR access the databases through a single address.

Sean Hemmingsen, a senior research officer at the NRC, said the Bridges system has greatly improved the network. “This gives us the functionality and connectivity that we didn’t have before,” he said.

Bridges allows users to run Unix applications from any desktop, thick or thin. The application can be transmitted over anything, from a slow dial-up modem to a high-speed LAN, said Ford.

Prices start about US$300 per user, but large organizations can get discounted rates.