PALO ALTO, Calif.--Molecular Applications Group will soon release into beta a significantly upgraded version of its flagship Look software product, which is a fixture in high-end bioinformatics labs.
The new release, set to debut in beta this summer, will probably be known as GeneMine Pro, although it has also been called Look version 3 and Big Sur. Commercial rollout will probably occur in the late fall. According to Molecular Applications, GeneMine Pro automates the process of gathering data, integrates that data with the appropriate scientific tools, and allows bioinformaticists to communicate their findings with others in the organization via hypertext. It offers several internet-technology features for sharing and retrieving data, including the ability to operate through the user's resident browser. The Unix-based product runs on Silicon Graphics workstations, but a second generation, which will appear in beta later this year and is likely go commercial during the first quarter of 1998, will be Java-based, platform-independent, and targeted to nonexpert users. Some components of that system could be available sooner because it will be modular, Molecular Applications' President and CEO Myra Williams told BioInform.
One of the most significant advances in GeneMine Pro is that it "is essentially an intelligent agent for bioinformatics," Williams explained. "It can go out and understand all the vagaries of how information is stored and do that retrieval in an automated fashion, including analysis and validation of the results. There is a major need for intelligent agents that can be customized to the user's preference," she claimed.
"Today there simply are not enough bioinformatics experts available, and companies desperately need to be able to get meaningful information from the genomics information they have internally," Williams continued. "We believe there is a very significant opportunity for us to respond to that need, and we have the product set that's going to do it. We'll move from requiring the expert to do the information-gathering and analysis to facilitating that by any scientist who has the need to use this tool."
Among the benefits of the product she cited were its ability to automate the retrieval of information about gene sequence and integrate, analyze, and cross-validate it from a number of different sources.
GeneMine Pro is being alpha-tested in the Department of Macromolecular Modeling in Bristol-Myers Squibb's Pharmaceutical Research Institute. According to Stanley Krystek, senior research investigator, who has used it since early this year, "this really is a huge change from Look, because the strategy that was taken in Look itself is really limited to structure generation from sequence information, and perhaps a little bit of literature searching. Now they've gone one step farther and you can link analyses with sequence alignments, and you can better manipulate the sequence links that you have. With bioinformatics and genome data becoming very important, those links are going to be very powerful."
"The paradigm has changed from one sequence at a time, where in the past we tried to learn things about that particular sequence and develop structural hypotheses--that's what Look was developed for," he said. "The new package really is not Look any more. What you're talking about now are companies trying to develop tools that allow you to analyze multiple sequences simultaneously, and look for the functional relationships."
"Where they're going is in handling massive amounts of data and in preprocessing the data. They clearly have a very good start in the new tool," Krystek continued. "Until this current tool they did not handle nucleotide data, so that's one big change over Look 2.0; the previous version was focused on protein structure, protein sequence information."
"We're running the new software in what we call the expert mode, where we authored many of the preferences, and that is done by allowing users to actually get at the query preferences themselves when you submit queries, so you actually get at the HTML web page and can then change the preferences," he added. "The previous version, Look 2.0, didn't have links to the other software from within the package that allowed this functionality, but since web browsers allow users to interact with the actual Web page, Molecular Applications Group didn't have to encode this in their package, they just call up whatever resident web browser you have on your PC, Unix machine, whatever, and then utilize that as your tool."
GeneMine Pro runs on workstations running IRIX 5.3 or later and requires 32 megabytes of RAM and 50 megabytes of free disk space.