INDIANAPOLIS--Dow AgroSciences, along with its parent company, Dow Chemical, announced recently that it has licensed Pangea Systems' bioinformatics software, to be used by a number of US sites.
Specifically, Dow has contracted to use Pangea's GeneWorld, GeneMill, GeneThesaurus, and Pathway Tools. GeneWorld is an automated, high-throughput analysis software package that allows researchers to access, annotate and analyze large volumes of public and proprietary data. GeneMill is project management software for DNA sequencing efforts. GeneThesaurus is a subscription service that links data from public databases of gene and protein sequences, and protein structure information. Pangea's Pathway Tools enable scientists to visualize sets of biochemical pathways and the compounds involved in them.
Sam Reddy, global R&D leader for genomics at Dow AgroSciences, told BioInform that Dow had been seeking a way to manage large amounts of data. Lsst August, Dow Chemical and Dow AgroSciences formed a committee to survey commercially available bioinformatics software packages. The selection of Pangea later that year was driven by the committee, the users, and also by a Dow collaborator, Biosource Technologies, he said.
While Reddy declined to name Pangea's competitors in the systems contest, he did discuss the reasons behind the choice, one of which was the completeness of Pangea's toolkit. He explained that Dow uses GeneMill to collect sequence information from automated data sequencers, placing that data into GeneWorld, which employs an Oracle database. "Then you can do the queries using all kinds of algorithms that the Pangea system comes with," said Reddy.
"We can quickly find out and then search not only the public databases but also our own proprietary databases. We can submit hundreds of sequences using GeneWorld," he remarked.
Another factor in Pangea's favor was its Pathway Tools module for metabolic pathway reconstructions, which Dow AgroSciences is "very, very interested in doing," enthused Reddy.
"How do we complete an understanding of a pathway when we get sequence data? How do you relate sequence data to a function to a pathway?" he asked, adding, "Pathway Tools will get us there, then we'll have a global picture of where things are going." With that, Dow AgroSciences will be able to simulate a metabolic pathway, which is its "ultimate goal," he acknowledged.
The third aspect of the decision involved the functional genomics collaboration between Dow AgroSciences and Biosource Technologies. Because Biosource had already licensed Pangea's software, it made sense for Dow AgroSciences to use the same technology to facilitate data sharing. "Pangea's software fulfilled our needs for what we are planning on doing in the genomics program across Biosource and Dow AgroSciences," said Reddy.
Dow AgroSciences has begun rolling out the software running on Sun Microsystems 5500 and 6500 workstations--"the most powerful machines that Sun can offer for doing these kinds of analyses," Reddy claimed.
The sites that will use Pangea's software include Dow AgroSciences' offices in San Diego and Indianapolis and Dow Chemical in Midland, Mich., along with Biosource's head office in Vacaville, Calif. Additional Dow Agro locations may be announced in the future, explained Reddy, adding that the Pangea software will play a "crucial role" in Dow AgroSciences' genomics program, as well as in other projects.