This article has been changed from a previous version to provide updated information on the download rate for the software.
A New Zealand startup is betting that a blend of open source software and a familiar user interface will help it succeed in the challenging commercial bioinformatics market.
This week, Aukland-based Biomatters launched the first version of its flagship software product, Geneious 1.0. The software "uses a metaphor that is very familiar to any user, and that's the metaphor of an e-mail client," Biomatters CEO Daniel Batten told BioInform.
The freely available software integrates numerous open source analysis packages for sequence alignment tools, phylogenetic reconstruction, sequence annotation, and 3D protein structure viewing into a single package. The user-friendly interface resembles common e-mail readers like Outlook, Eudora, and Macintosh Mail and includes a list of folders on the left side of the screen for storing and organizing documents, searches, and datasets. Items that are selected are displayed in a viewer in the central panel, which also offers a number of analytical options depending on the type of data that is displayed.
Nucleotide sequences, for example, are displayed in a sequence viewer that allows users to toggle between text and sequence format, to zoom in or out, and choose a number of other viewing and analysis options. Icons at the top of the window allow users to select several sequences and quickly run multiple alignments or build a phylogenetic tree with a single click, enabling them to easily navigate through a number of analytical steps without leaving the application.
The software also offers an "agents" feature to enable real-time updating of all the information in the system. "Rather than you having to do a lot of searching for the information, you can set up agents that will automatically look for information in the background, and then just like e-mail, you shouldn't have to go to a central server to find out if something new is coming; it actually comes and finds you," Batten said.
Biomatters was founded in June 2003. Batten said that the company's goal was "integrate a lot of the top algorithms in sequence analysis, sequence alignment, and phylogenetic reconstruction, but also to do a lot of work on the human-computer interface side, because we didn't feel that anyone in the marketplace had really nailed it, and as a result the supposed revolution that was going to be happening in bioinformatics was not happening because the tools were not reaching the general molecular biologist."
The company released a beta version of the software in February, and Batten said that the download rate has so far been around 1,000 per week — about three times what it was expecting. "People are picking it up and it seems to be seeding the message that this is a tool that can make bioinformatics available to a broader audience," he said.
The "core package" underlying Geneious "will always be free to academics at all times," Batten said. The company is in the process of developing a fee-based version of the software, called Geneious Pro, that it plans to release in the third quarter of the year.
Batten said that the company has not yet determined the price range for the commercial version of the product.
Batten described Geneious as "more like an operating environment for bioinformatics than another bioinformatics product." The company is making its application programming interface available so that developers can enable their own tools to work as plug-ins with the system.
"There's a lot of really good open source technology that people don't use for two reasons. One, it's not supported, and two, the user interface is typically not good because it's been written by academics who don't have time to deal with these issues," Batten said. "But if they're using our user interface and using a commercial entity that can cope with all the support issues, we can actually utilize some of the best and yet unknown technologies in the world by overcoming these support and usability issues."
Biomatters currently employs 15 people. The firm has so far raised around NZ$2 million ($1.25 million) in grants and private funding.
— Bernadette Toner ([email protected])